Exhibit 10.1

CONFIDENTIAL SETTLEMENT AGREEMENT AND MUTUAL RELEASE

This Confidential Settlement Agreement and Mutual Release (“Confidential Settlement Agreement”) is entered into as of the Effective Date by and between Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (“MPG”), Max-Planck-Innovation GmbH (“MI”) (collectively referred to herein as “Max Planck”), and Alnylam Pharmaceuticals, Inc. (“Alnylam”), on the one hand, and Whitehead Institute for Biomedical Research (“Whitehead”), Massachusetts Institute of Technology (“MIT”), and the University of Massachusetts (“UMass”), on the other hand.

This Confidential Settlement Agreement is made with respect to the lettered recitals below. The Definitions set forth in Section 1 below apply to the recitals.

A. MPG, MI, Alnylam, Whitehead, MIT, and UMass are parties to the Litigation, which involves a dispute concerning the Tuschl I Patent Family and the Tuschl II Patent Family. One of the claims asserted in the Litigation is UMass’s claim pursuant to 35 U.S.C. § 256 to have Phillip D. Zamore, Phillip A. Sharp, and David P. Bartel named as co-inventors of two issued patents in the US Tuschl II Patent Family.

B. The Parties deem it to be in their best interests and to their mutual advantage to settle their disputes on the terms and conditions set forth in this Confidential Settlement Agreement (including the exhibits attached hereto), without admitting liability, in order to achieve certainty in their business dealings and to avoid the expense of litigation. As part of their settlement of the claims in the Litigation, including UMass’s counterclaim to correct inventorship (described above), the Parties have agreed to common ownership of the US Tuschl II Patent Family on the terms and conditions set forth in this Confidential Settlement Agreement, including in the attached: Assignment Agreement, Amendment to the Alnylam License Agreement, and Exclusive License Agreement.

NOW, THEREFORE, in consideration of all of the terms and conditions of this Confidential Settlement Agreement, the Parties agree as follows:

1. Definitions . The following words and phrases shall have the meanings set forth below solely for purposes of this Confidential Settlement Agreement.

1.1 “2001 Research Agreement” shall mean the JOINT INVENTION AND JOINT MARKETING AGREEMENT between and among MPG, MI, Whitehead, MIT and UMass dated September 19, 2001.

1.2 “2003 Therapeutics Agreement” shall mean the JOINT INVENTION AND JOINT MARKETING AGREEMENT FOR RNAI THERAPEUTIC PURPOSES between and among MPG, MI, MIT and Whitehead dated July 30, 2003.

1.3 “Affiliate” shall mean any corporation or other business entity that now or in the future directly or indirectly controls, is controlled by, or is under common control with, a Party or a third party (as the case may be as used in this Confidential Settlement Agreement). Control means direct or indirect ownership of, or other beneficial interest in, fifty percent (50%) or more of the voting stock, other voting interest, or income of a corporation or other business

entity, or possession of the power to elect or appoint fifty percent (50%) or more of the members of the governing body of the corporation or other business entity. A corporation or other business entity shall be an Affiliate only during such period of time that it meets the definition set forth in this Section 1.3.

1.4 “Alnylam License Agreement” shall mean the Co-Exclusive License Agreement between and among MI and Alnylam dated December 20, 2002, as amended, and as approved by Whitehead and MIT pursuant to the letter dated July 30, 2003.

1.5 “ Amendment to the Alnylam License Agreement ” shall mean the Amendment between and among Alnylam, MI, MIT and Whitehead attached hereto as Exhibit I.

1.6 “Assignment Agreement” shall mean the Assignment Agreement between and among MPG, Whitehead, MIT and UMass attached hereto as Exhibit A.

1.7 “University of Utah Claim” shall mean any Claim asserted by the University of Utah and/or Brenda L. Bass, Ph.D., or an assignee of either of them, and relating to or involving any patent or patent application in The Tuschl I Patent Family and/or The Tuschl II Patent Family, including any claim that Brenda L. Bass, Ph.D. should be named as an inventor or co-inventor of any patent or patent application in the Tuschl I Patent Family and/or the Tuschl II Patent Family, including without limitation any Claim under 35 U.S.C. § 256 and any declaratory judgment action challenging any such Claim.

1.8 “Claim” or “Claims” shall mean any and all claims, actions, causes of action, demands, costs, and charges of whatever nature, whether accrued now or hereafter, whether known or unknown, including without limitation any and all claims to recover attorneys’ fees and costs.

1.9 “Defendants” shall mean Whitehead, UMass and MIT collectively.

1.10 “Effective Date” shall mean March 14, 2011.

1.11 “Exclusive License Agreement” shall mean the Exclusive License Agreement to the US Tuschl II Patent Family between UMass and Alnylam attached hereto as Exhibit B.

1.12 “Litigation” shall mean the civil action entitled Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V., Max-Planck-Innovation GmbH, and Alnylam Pharmaceuticals, Inc. v. Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, and the Board of Trustees of the University of Massachusetts, pending in the United States District Court for the District of Massachusetts as Case No. 09-CV-11116-PBS.

1.13 “ Merck ” shall mean Merck & Co., Inc. and its Affiliates.

1.14 “Merck Option Agreement” shall mean Merck’s rights under the non-exclusive option agreement relating to the US Tuschl II Patent Family as provided for in Section 2.2 of the Exclusive License Agreement.

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1.15 “Party” shall mean MPG, MI, Alnylam, Whitehead, MIT, or UMass, and when used in the plural shall mean all of them.

1.16 “Plaintiffs” shall mean MPG, MI and Alnylam collectively.

1.17 “Prosecution” shall mean the process of interacting with a patent office such as the USPTO with respect to a patent application or patent, including but not limited to responding to office actions, conducting examiner interviews, filing continuing applications, drafting, amending and cancelling claims, pursuing appeals (including in a court, in the case of an appeal from or a challenge to a patent office action or decision), or otherwise seeking allowance of a patent application or seeking correction, reexamination, reissue, or patent term extension of an issued patent.

1.18 “Prosecution Guidelines” shall mean the Tuschl I and II Prosecution Guidelines attached as Exhibit C to this Confidential Settlement Agreement.

1.19 “UMass-Sirna Agreement” shall mean the License Agreement between UMass and Sirna Therapeutics, Inc., now Merck & Co., Inc. (“Merck”), dated September 8, 2003, as such license was in effect on the date on which the Litigation was initially filed.

1.20 “UMass’s Inventorship Claim” shall mean UMass’s Claim in the Litigation pursuant to 35 U.S.C. § 256 to have Phillip D. Zamore, Phillip A. Sharp, and/or David P. Bartel named as co-inventors of two issued patents in the U.S. Tuschl II Patent Family, and any other Claim that may now or hereafter exist to have any or all of Phillip D. Zamore, Phillip A. Sharp, or David P. Bartel named as an inventor on any application or patent in the Tuschl II Patent Family.

1.21 “USPTO” shall mean the United States Patent and Trademark Office.

1.22 “US Tuschl I Patent Family” shall mean any and all patents issued by, and patent applications filed in, the USPTO as set forth in the attached Exhibit D, entitled “RNA sequence-specific mediators of RNA interference,” naming as inventors Thomas Tuschl, David P. Bartel, Phillip A. Sharp, and Phillip D. Zamore, and any divisionals, continuations, continuation-in-part applications thereof, requests for continued examination, reissues or reexaminations of any of the foregoing filed in the USPTO.

1.23 “Non-US Tuschl I Patent Family” shall mean any and all patents issued by, and patent applications filed in, any country other than the United States as set forth in the attached Exhibit E, entitled “RNA sequence-specific mediators of RNA interference,” naming as inventors Thomas Tuschl, David P. Bartel, Phillip A. Sharp, and Phillip D. Zamore, and any divisionals, continuations, continuation-in-part applications thereof, requests for continued examination, reissues or reexaminations of any of the foregoing filed in any country other than the United States.

1.24 “The Tuschl I Patent Family” shall mean the US Tuschl I Patent Family and the Non-US Tuschl I Patent Family collectively.

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1.25 “US Tuschl II Patent Family” shall mean any and all patents issued by, and patent applications filed in, the USPTO as set forth in the attached Exhibit F, entitled “RNA Interference Mediating Small RNA Molecules,” naming as inventors Thomas Tuschl, Sayda Elbashir, and Winfried Lendeckel, and any divisionals, continuations, continuation-in-part applications thereof, requests for continued examination, reissues or reexaminations of any of the foregoing filed in the USPTO.

1.26 “Non-US Tuschl II Patent Family” shall mean any and all patents issued by, and patent applications filed in, any country other than the United States as set forth in the attached Exhibit G, entitled “RNA Interference Mediating Small RNA Molecules,” naming as inventors Thomas Tuschl, Sayda Elbashir, and Winfried Lendeckel, and any divisionals, continuations, continuation-in-part applications thereof, requests for continued examination reissues or reexaminations of any of the foregoing filed in any country other than the United States.

1.27 “The Tuschl II Patent Family” shall mean the US Tuschl II Patent Family and the Non-US Tuschl II Patent Family collectively.

1.28 “WGS Settlement Agreement” shall mean the Settlement Agreement between MI, MPG, and Alnylam, on one hand, and Wolf, Greenfield & Sacks, P.C., on the other hand, attached hereto as Exhibit H.

2. Patent Prosecution .

2.1 Prosecution of the US Tuschl I Patent Family . Max Planck shall have sole responsibility for Prosecution of the US Tuschl I Patent Family. Prosecution shall be conducted according to the principles set forth in the Prosecution Guidelines, which are incorporated herein. Max Planck shall (i) keep all other Parties reasonably and promptly informed as to Prosecution of the US Tuschl I Patent Family; (ii) furnish all other Parties copies of documents relevant to the Prosecution of the US Tuschl I Patent Family, including timely drafts of amendments and other responses to office actions reasonably in advance of filing; and (iii) allow all other Parties to comment on all substantive prosecution matters with respect to the Prosecution of the US Tuschl I Patent Family.

2.2 Prosecution of the Non-US Tuschl I Patent Family . UMass shall have sole responsibility for Prosecution of the Non-US Tuschl I Patent Family. Prosecution shall be conducted according to the principles set forth in the Prosecution Guidelines, which are incorporated herein. UMass shall (i) keep all other Parties reasonably and promptly informed as to Prosecution of the Non-US Tuschl I Patent Family; (ii) furnish all other Parties copies of documents relevant to the Prosecution of the Non-US Tuschl I Patent Family, including timely drafts of amendments and other responses to office actions reasonably in advance of filing; and (iii) allow all other Parties to comment on all substantive prosecution matters with respect to the Prosecution of the Non-US Tuschl I Patent Family.

2.3 Prosecution of the US Tuschl II Patent Family . Max Planck shall have sole responsibility for Prosecution of the US Tuschl II Patent Family. Prosecution shall be conducted according to the principles set forth in the Prosecution Guidelines, which are

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incorporated herein. Max Planck shall (i) keep all other Parties reasonably and promptly informed as to Prosecution of the US Tuschl II Patent Family; (ii) furnish all other Parties copies of documents relevant to the Prosecution of the US Tuschl II Patent Family, including timely drafts of amendments and other responses to office actions reasonably in advance of filing; and (iii) allow all other Parties to comment on all substantive prosecution matters with respect to the Prosecution of the US Tuschl II Patent Family.

2.4 Prosecution of the Non-US Tuschl II Patent Family . Max Planck shall have sole responsibility for Prosecution of the Non-US Tuschl II Patent Family. Prosecution shall be conducted according to the principles set forth in the Prosecution Guidelines, which are incorporated herein. Max Planck shall (i) keep all other Parties reasonably and promptly informed as to Prosecution of the Non-US Tuschl II Patent Family; (ii) furnish all other Parties copies of documents relevant to the Prosecution of the Non-US Tuschl II Patent Family, including timely drafts of amendments and other responses to office actions reasonably in advance of filing; and (iii) allow all other Parties to comment on all substantive prosecution matters with respect to the Prosecution of the Non-US Tuschl II Patent Family.

2.5 Outside Patent Prosecution Counsel . The Parties shall agree upon a law firm to handle Prosecution of both the US Tuschl I and the US Tuschl II Patent Families. Such law firm shall initially be Lando & Anastasi, LLP. In the event that such law firm withdraws or Max Planck decides to change the law firm prosecuting the US Tuschl I Patent Family and the US Tuschl II Patent Family, then Max Planck shall provide prompt notice of such event to MIT, UMass and Whitehead along with a recommended law firm to assume such prosecution from such point forward. Max Planck’s recommendation shall be subject to consent by MIT, UMass and Whitehead, such consent not to be unreasonably withheld or delayed. MPG (and/or MI, as appropriate), MIT, UMass and Whitehead shall each execute a Power of Attorney in favor of the agreed-upon law firm (or replacement law firm, as the case may be), as well as a reasonable conflict of interest waiver in the form requested by such law firm (or replacement law firm, as the case may be) that waives any conflict of interest in connection with the Prosecution of The Tuschl I and The Tuschl II Patent Families. The Parties shall also agree upon law firms to handle Prosecution of the Non-US Tuschl I and Non-US Tuschl II Patent Families and shall likewise execute Powers of Attorney and (if requested) reasonable conflict of interest waivers that waive any conflict of interest in connection with the Prosecution of The Tuschl I and The Tuschl II Patent Families in favor of such law firms. The Parties agree that the law firm of Nelson Mullins Riley & Scarborough LLP may handle Prosecution of the Non-US Tuschl I Patent Family and that they will execute Powers of Attorney and reasonable conflict of interest waivers in favor of such law firm that waive any conflict of interest in connection with the Prosecution of The Tuschl I and The Tuschl II Patent Families. The Parties agree that the law firm of Weickman & Weickman may handle Prosecution of the Non-US Tuschl II Patent Family and that they will execute Powers of Attorney and reasonable conflict of interest waivers that waive any conflict of interest in connection with the Prosecution of The Tuschl I and The Tuschl II Patent Families in favor of such law firm.

2.6 No Goldstein Petition. The Parties agree not to seek to withdraw the Powers of Attorney they execute pursuant to Section 2.5 above, whether through a petition filed in the USPTO pursuant to 37 CFR § 1.36 under In re Goldstein , 16 USPQ2d 1963 (Dep. Ass’t Com’r for Patents 1988), or otherwise. Further, each Party hereby consents to, and does, waive

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any conflict of interest of any attorney designated pursuant to Section 2.5 above in connection with the Prosecution of The Tuschl I and The Tuschl II Patent Families. Each Party further represents and warrants that it has consented to such conflict waiver after consultation with independent counsel and that the implications and risks of common representation in connection with the Prosecution of The Tuschl I and The Tuschl II Patent Families as provided for herein have been explained to them.

2.7 Costs of Patent Prosecution . As between Max Planck, Whitehead, MIT and UMass, Max Planck shall pay for all expenses, including attorneys’ fees, incurred in the Prosecution of the US Tuschl I Patent Family, the US Tuschl II Patent Family, and the Non-US Tuschl II Patent Family, PROVIDED THAT nothing herein shall be deemed to relieve any research reagent licensee of an existing obligation to pay, in addition to royalties, a portion of all fees and costs, including attorneys’ fees, incurred in the Prosecution of The Tuschl I Patent Family and The Tuschl II Patent Family under the terms set forth in the license agreements entered pursuant to the 2001 Research Agreement. As between Max Planck, Whitehead, MIT and UMass, UMass shall pay for all expenses, including attorneys’ fees, incurred in the Prosecution of the Non-US Tuschl I Patent Family, PROVIDED THAT nothing herein shall be deemed to relieve any research reagent licensee of an existing obligation to pay, in addition to royalties, a portion of all fees and costs, including attorneys’ fees, incurred in the Prosecution of The Tuschl I Patent Family under the terms set forth in the license agreements entered pursuant to the 2001 Research Agreement. For avoidance of doubt, this Section 2.7 does not authorize any Party to amend, and does not require any Party to consent to any amendment of, any license granted pursuant to the 2001 Research Agreement.

2.8 Amendment to 2001 Research Agreement . The third Whereas clause on page 1 of the 2001 Research Agreement is hereby amended to replace “MPG” with “MPG, M.I.T., Whitehead and UMass … “ with the remainder of that Whereas clause to remain unchanged. Section 1, entitled “Patent Management,” and Section 3(a) of the section entitled “Patent Maintenance,” of the 2001 Research Agreement are hereby superseded in their entirety and replaced by the provisions of Section 2.1 through 2.5 and 2.7 of this Confidential Settlement Agreement. Section 4, entitled “Sharing of Revenue,” of the 2001 Research Agreement is hereby amended to read as follows: “First, a five percent (5%) administration fee shall be deducted from all revenue and equity received by the licensing agent, whether M.I.T. or GI, from license fees and royalties from the PATENT PACKAGE. Then, the remaining revenue and equity shall be distributed by M.I.T. and GI on at least a quarterly basis as follows: (a) 50% shall be paid to GI, and shall be attributed to the MPG Invention. (b) 50% shall be paid to M.I.T., and shall be distributed in the following way by M.I.T.: …” Clauses (i), (ii), and (iii) of Section 4 remain unchanged.

2.9 Amendment to 2003 Therapeutics Agreement . Section 1, entitled “Patent Management,” and Section 2(a) of the section entitled “Patent Maintenance,” of the 2003 Therapeutics Agreement are hereby superseded in their entirety and replaced by the provisions of Sections 2.1 through 2.5 and 2.7 of this Confidential Settlement Agreement.

2.10 Allocation of Research Reagent Royalties . The Parties agree that, notwithstanding the provisions of Section 2.8 above, and notwithstanding the provisions of Section 4, entitled “Sharing of Revenue,” of the 2001 Research Agreement as amended above,

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Whitehead shall receive the first Five Hundred Thousand Dollars ($500,000) of royalty revenues received from the research licenses pursuant to the 2001 Research Agreement in each of calendar years 2011, 2012, 2013 and 2014, prior to any such royalties being otherwise disbursed or used by MIT or MI pursuant to the provisions of Section 4 of the 2001 Research Agreement, as amended above. Once Whitehead has received the first Five Hundred Thousand Dollars ($500,000) of royalty revenues in a calendar year, the remaining royalty revenues received in that calendar year shall be disbursed or used by MIT or MI pursuant to the provisions of Section 4 of the 2001 Research Agreement, as amended above, without any adjustment or offset of the amount due to Whitehead under such provisions as a result of the payments provided by this Section 2.10. For the sake of clarity, the Parties agree that, for calendar years 2011, 2012, 2013 and 2014, the deductions and distributions provided in Section 4 of the 2001 Research Agreement, as amended by Section 2.8 of this Confidential Settlement Agreement, shall only apply to royalty revenues in excess of Five Hundred Thousand Dollars ($500,000).

2.11 UMass Transfer of Royalties to Whitehead . (a) UMass agrees that it shall pay to Whitehead the sum of Five Hundred Thousand Dollars ($500,000) on or before December 31, 2015, either from the royalties received by UMass under the 2001 Research Agreement prior to that time or from another source that UMass, in its sole discretion, selects. UMass shall be obligated to make this payment to Whitehead on or before December 31, 2015, regardless of whether the royalties received by UMass under the 2001 Research Agreement prior to that time total less than Five Hundred Thousand Dollars ($500,000). (b) Without prejudice to Whitehead’s right to enforce the foregoing obligation set forth in Section 2.11(a) through legal action, UMass agrees, and hereby authorizes MIT, that in the event that UMass does not timely make the payment required by Section 2.11(a) to Whitehead, MIT should pay directly to Whitehead any and all royalties due to UMass under the 2001 Research Agreement starting on January 1, 2016, until such time as Whitehead has received the entire Five Hundred Thousand Dollars ($500,000) due to Whitehead under this Section 2.11.

2.12 Bayh-Dole Reports . To the extent that any periodic reports must be filed with the U.S. Government under the provisions of the Bayh-Dole Act in connection with the prosecution of The Tuschl I Patent Family, Max Planck agrees to timely provide MIT with the necessary information to prepare such reports and MIT agrees to prepare and file such reports on behalf of all of the co-owners of The Tuschl I Patent Family.

3. Other Agreements .

3.1 Assignment Agreement, Exclusive License Agreement, and Amendment to the Alnylam License Agreement . Not later than the Effective Date, MPG, Whitehead, MIT, and UMass shall execute and deliver the Assignment Agreement. Immediately following delivery of the Assignment Agreement, (i) Alnylam and UMass shall execute and deliver the Exclusive License Agreement, and (ii) Alnylam, MI, MIT and Whitehead shall execute and deliver the Amendment to the Alnylam License Agreement.

3.2 WGS Settlement Agreement . Not later than the Effective Date, MPG, MI, Alnylam and Wolf, Greenfield & Sacks, P.C. shall enter into the WGS Settlement Agreement.

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3.3 University of Utah Claim . The Parties acknowledge that the University of Utah has asserted that Brenda L. Bass, Ph.D., may be an inventor or co-inventor on one or more claims in the Tuschl I and/or Tuschl II Patent Families. Max Plank believes that the University of Utah Claim has no merit. Nevertheless, in order to clarify responsibilities for responding to any University of Utah Claim, the Parties agree as follows:

3.3.1 Subject to Section 3.3.3, commencing on the Effective Date, Alnylam shall defend and indemnify MPG, MI, Whitehead, MIT and UMass from any and all loss, cost, damage or expense (including but not limited to attorneys’ fees) incurred as a result of a University of Utah Claim.

3.3.2 Subject to Section 3.3.3, Alnylam shall have sole and exclusive control over any and all responses to a University of Utah Claim, including without limitation control over selection of counsel to represent MPG, MI, Whitehead, MIT and UMass in connection with a University of Utah Claim after good faith consideration of the views of Whitehead, MIT and UMass concerning the selection of counsel, sole and exclusive control over any litigation of such University of Utah Claim and all decisions in such litigation, as well as the authority to settle a University of Utah Claim without the consent of MPG, MI, MIT, Whitehead or UMass but after good faith consideration of the views of Whitehead, MIT and UMass concerning any settlement. Notwithstanding the foregoing, UMass shall have a right of prior approval over significant litigation decisions concerning, and settlement of, any non-patent claims or non-patent counterclaims to the extent they affect the interests of the Commonwealth of Massachusetts, such approval not to be unreasonably withheld or delayed, and counsel representing UMass must be approved by the Massachusetts Attorney General, be appointed as a Special Assistant Attorney General, and comply with the guidelines of the Massachusetts Attorney General with respect to that appointment. For avoidance of doubt, this Section 3.3.2. does not authorize any Party to amend, and does not require any Party to consent to any amendment of, the 2001 Research Agreement, the 2003 Therapeutic Agreement or the Alnylam License Agreement.

3.3.3 In the event there arises an actual or potential conflict of interest between a Party (the “Conflicted Party”) and Alnylam with respect to a University of Utah Claim such that representation of the Conflicted Party by the counsel retained by Alnylam would be inappropriate because of such conflict of interest, Alnylam shall not thereafter have control over the Conflicted Party’s response to, or litigation involving, such University of Utah Claim and the Conflicted Party shall be entitled to select its own counsel, which counsel shall be paid for by the Conflicted Party and not by Alnylam. Alnylam shall further obtain the consent of the Conflicted Party to settle a University of Utah Claim, which consent shall not be unreasonably withheld.

3.3.4 MPG, MI, Whitehead, MIT, and UMass shall cooperate fully with Alnylam in connection with any University of Utah Claim (including but not limited to the selection of counsel, subject to Section 3.3.3) and shall promptly provide reasonable access to all necessary documents, information,

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and persons under their control, and to render reasonable assistance in response to a request by Alnylam for such assistance, provided that Alnylam promptly reimburses MPG, MI, Whitehead, MIT, and UMass for any costs and expenses they reasonably incur in connection therewith, except in the event that MPG, MI, Whitehead, MIT and/or UMass retains their own counsel for such University of Utah Claim as provided in Section 3.3.3.

3.4 UMass Payments to Alnylam . In consideration of the rights granted under the Merck Option Agreement, UMass shall pay Alnylam (i) fifty percent (50%) of any additional payments or other consideration (exclusive of any milestone payments due under the UMass-Sirna Agreement) that UMass receives from Merck solely for rights to the US Tuschl II Family, and (2) four percent (4%) of royalty income (exclusive of any milestone payments due under the UMass-Sirna Agreement) that UMass receives from Merck solely for rights to the US Tuschl II Family. For the avoidance of any doubt, the Parties acknowledge and agree: (i) UMass shall have no obligation to make any payment to Alnylam in the event that UMass and Merck agree that the milestone payment provided for in the UMass-Sirna Agreement upon issuance of a patent in the US Tuschl I Patent Family shall be due if a patent issues in either the US Tuschl I Patent Family or the US Tuschl II Patent Family; (ii) if UMass increases the consideration it receives from Merck above the consideration described in the UMass-Sirna Agreement in exchange for rights to the US Tuschl II Patent Family, then Alnylam shall be entitled to fifty percent (50%) of such increased amount; and (iii) if UMass receives income under the UMass-Sirna Agreement solely as a result of the license of the US Tuschl II Patent Family (i.e., such payments would not have been made on account of the license to the US Tuschl I Patent Family), then Alnylam shall be entitled to four percent (4%) of such amount. UMass shall make such payments to Alnylam not later than sixty (60) days after receipt of the corollary payment from Merck.

3.5 No Termination of Merck Option Agreement . No challenge to the validity, enforceability, or inventorship of any application or patent in the Non-US Tuschl II Patent Family made by Merck outside of the United States shall have the effect of terminating Merck’s rights under Merck Option Agreement.

3.6 No Use of Merck License . Max Planck and Alnylam agree that neither the existence nor the terms of any license entered into by Merck pursuant to a Merck Option Agreement for rights to the US Tuschl II Patent Family shall be admissible for any purpose in any infringement action, opposition proceeding, nullity proceeding, or other judicial or administrative proceeding in which the validity of any member of the Tuschl II Patent Family may be challenged.

4. Survival of the 2001 Research Agreement and 2003 Therapeutics Agreement . Except as explicitly amended by this Confidential Settlement Agreement, the 2001 Research Agreement and the 2003 Therapeutics Agreement remain in force and effect. The Parties further covenant and agree that the allocation and distribution of revenue and equity under the 2001 Research Agreement as amended by this Confidential Settlement Agreement and under the 2003 Therapeutics Agreement as amended by this Confidential Settlement Agreement shall remain unchanged regardless of the issuance or non-issuance of patents in either The Tuschl I Patent Family or The Tuschl II Patent Family.

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5. Challenges to The Tuschl I and The Tuschl II Patent Families .

5.1 No Challenges . Alnylam, Max Planck, Whitehead, MIT and UMass and their Affiliates shall not voluntarily challenge or cause to be challenged the validity, enforceability or inventorship of any patents in The Tuschl I Patent Family or The Tuschl II Patent Family before any court, agency, or other tribunal (including the USPTO).

5.2 No Participation . Alnylam, Max Planck, Whitehead, MIT and UMass and their Affiliates shall not initiate, or knowingly support or assist any third party with, any legal or administrative proceeding that seeks to invalidate, revoke, reexamine, challenge inventorship or render unenforceable any patents in The Tuschl I Patent Family or The Tuschl II Patent Family, including any proceeding before the USPTO. As used in the preceding sentence, “knowingly” shall mean knowing that the participation or assistance, at the time it is given, relates to any actual or prospective legal or administrative proceeding that seeks to invalidate, revoke, reexamine, or render unenforceable any patents in The Tuschl I Patent Family or The Tuschl II Patent Family, including any proceeding before the USPTO. Nothing herein shall preclude a Party from participating in such a proceeding to support the validity or enforceability of any patent in The Tuschl I Patent Family or The Tuschl II Patent Family. No Party shall be deemed to have violated any provision of this Section 5 based solely on activities: (i) undertaken by one or more of its licensees or Merck, without any support of such activities by the Party; (ii) undertaken at the request of a licensee, of a license granted pursuant to the 2001 Research Agreement, to the extent such activities are required by the license agreement as it currently provides as of the Effective Date; or (iii) required by a lawful subpoena or court order. For avoidance of doubt, this Section 5.2 does not authorize any Party to amend, and does not require any Party to consent to any amendment of, any license granted pursuant to the 2001 Research Agreement.

5.3 Compelled Testimony . Sections 5.1 and 5.2 shall not apply to any testimony, documents or other evidence provided in response to a subpoena or order issued by any court, tribunal, or agency.

6. No Further Conveyances of Rights . (a) UMass, MIT and Whitehead each covenant and agree, other than as expressly provided for, or agreed to, in: the 2001 Research Agreement, the 2003 Therapeutics Agreement, the Alnylam License Agreement or the two non-asserts attached to the August 6, 2004 letter from MIT to Kevin Nash of Dharmacon, (i) not to dedicate to the public nor to convey to any entity whatsoever, including to any of its or their Affiliates, whether by assignment, license or otherwise, any interest in the US Tuschl II Patent Family without the prior written consent of Max Planck; and (ii) not to make any representation in any form or manner that any patent application or patent in the US Tuschl II Patent Family may be used for research purposes. (b) Under no circumstance shall UMass, MIT or Whitehead disclaim or otherwise relinquish ownership of any US Tuschl II Patent without the prior written consent of Max Planck. In the event that UMass, MIT or Whitehead does disclaim or otherwise relinquish its ownership interest in any US Tuschl II Patent, such Party shall be deemed to have disclaimed and relinquished its ownership interest in every patent in the US Tuschl II Patent Family and every patent in The Tuschl I Patent Family in order to maintain common ownership between The Tuschl I Patent Family and The Tuschl II Patent Family. (c) For purposes of clarity, this Section 6 does not affect or limit the rights and abilities of any licensing agent under the

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2001 Research Agreement or the 2003 Therapeutics Agreement to negotiate and enter into licenses with any third party on behalf of the parties to those agreements, subject to existing contractual obligations.

7. Releases, Covenants Not to Sue, and Dismissals .

7.1 Releases by Plaintiffs . Plaintiffs, on behalf of themselves and their predecessors, successors, assigns, and Affiliates, do hereby now and forever release and discharge Defendants, and their predecessors, successors, assigns, and Affiliates, and each of their respective current and former trustees, officers, directors, employees, agents, attorneys, and representatives, from: (i) any and all Claims concerning any act or omission occurring prior to the execution of this Confidential Settlement Agreement that are related to, or connected in any way with, the Tuschl I Patent Family, the Tuschl II Patent Family, UMass’s Inventorship Claim, or the Litigation, including without limitation any and all claims that were raised or could have been raised in the Litigation, any and all claims for breach of the 2001 Research Agreement, the 2003 Therapeutics Agreement, or the Alnylam License Agreement; and (ii) any and all Claims to recover attorneys’ fees and costs, or to be defended, indemnified, or held harmless, in connection with The Tuschl I and/or The Tuschl II Patent Families, (including without limitation the Prosecution of The Tuschl I and/or The Tuschl II Patent Families), UMass’s Inventorship Claim, the Litigation, the 2001 Research Agreement, the 2003 Therapeutics Agreement, or the Alnylam License Agreement,.

7.2 Releases by Defendants . Defendants, on behalf of themselves and their predecessors, successors, assigns, and Affiliates (collectively, the “Releasing Entities”), do hereby now and forever release and discharge Plaintiffs, and their predecessors, successors, assigns, and Affiliates, and each of their respective current and former trustees, officers, directors, employees, agents, attorneys, and representatives, from: (i) any and all Claims concerning any act or omission occurring prior to the execution of this Confidential Settlement Agreement that are related to, or connected in any way with, The Tuschl I Patent Family, The Tuschl II Patent Family, UMass’s Inventorship Claim, or the Litigation, including without limitation any and all claims that were raised or could have been raised in the Litigation, any and all claims for breach of the 2001 Research Agreement, the 2003 Therapeutics Agreement, or the Alnylam License Agreement; and (ii) any and all Claims to recover attorneys’ fees and costs, or to be defended, indemnified, or held harmless, in connection with The Tuschl I Patent Family, The Tuschl II Patent Family (including without limitation the Prosecution of The Tuschl I Patent Family or The Tuschl II Patent Family), UMass’s Inventorship Claim, the Litigation, the 2001 Research Agreement, the 2003 Therapeutics Agreement, or the Alnylam License Agreement, provided, however, that the release contained in this Section 7.2 shall not extend to any claim for indemnification under Section 7.1 of the Alnylam License Agreement for a claim brought against Whitehead or MIT by a non-Releasing Entity other than a claim seeking to recover attorneys’ fees and costs in connection with the Litigation or a claim seeking to recover attorneys’ fees and costs incurred prior to the Effective Date in connection with the Prosecution of The Tuschl I Patent Family or The Tuschl II Patent Family.

7.3 Releases by Whitehead . Whitehead, on behalf of itself and its predecessors, successors, assigns, and Affiliates, does hereby now and forever release and discharge UMass and MIT, and their predecessors, successors, assigns, and Affiliates, and each

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of their respective current and former trustees, officers, directors, employees, agents, attorneys, and representatives, from: (i) any and all Claims concerning any act or omission occurring prior to the execution of this Confidential Settlement Agreement that are related to, or connected in any way with, the Tuschl I Patent Family, the Tuschl II Patent Family, UMass’s Inventorship Claim, or the Litigation, including without limitation any and all claims that were raised or could have been raised in the Litigation, any and all claims for breach of the 2001 Research Agreement, the 2003 Therapeutics Agreement, or the Alnylam License Agreement; and (ii) any and all Claims to recover attorneys’ fees and costs, or to be defended, indemnified, or held harmless, in connection with The Tuschl I and/or The Tuschl II Patent Families, (including without limitation the Prosecution of The Tuschl I and/or The Tuschl II Patent Families), UMass’s Inventorship Claim, the Litigation, the 2001 Research Agreement, the 2003 Therapeutics Agreement, or the Alnylam License Agreement.

7.4 Releases by UMass and MIT . UMass and MIT, on behalf of themselves and their predecessors, successors, assigns, and Affiliates, do hereby now and forever release and discharge Whitehead and each other, and their predecessors, successors, assigns, and Affiliates, and each of their respective current and former trustees, officers, directors, employees, agents, attorneys, and representatives, from: (i) any and all Claims concerning any act or omission occurring prior to the execution of this Confidential Settlement Agreement that are related to, or connected in any way with, the Tuschl I Patent Family, the Tuschl II Patent Family, UMass’s Inventorship Claim, or the Litigation, including without limitation any and all claims that were raised or could have been raised in the Litigation, any and all claims for breach of the 2001 Research Agreement, the 2003 Therapeutics Agreement, or the Alnylam License Agreement; and (ii) any and all Claims to recover attorneys’ fees and costs, or to be defended, indemnified, or held harmless, in connection with The Tuschl I and/or The Tuschl II Patent Families, (including without limitation the Prosecution of The Tuschl I and/or The Tuschl II Patent Families), UMass’s Inventorship Claim, the Litigation, the 2001 Research Agreement, the 2003 Therapeutics Agreement, or the Alnylam License Agreement.

7.5 Covenant Not to Sue . The Parties and their Affiliates shall not now or at any time in the future initiate any legal proceeding anywhere in the world asserting any Claim released pursuant to Sections 7.1 through 7.4. Any Party that breaches (or whose Affiliate breaches) the obligations under this Section 7.5 (i) consents to the dismissal of such legal proceeding and to the entry of a permanent injunction restraining the breaching Party (or Affiliate) from initiating any future legal proceeding asserting any Claim released pursuant to this Confidential Settlement Agreement; and (ii) shall be liable to the other Party and its Affiliates for their reasonable attorneys’ fees and costs incurred in securing the dismissal of such legal proceeding and the entry of such permanent injunction.

7.6 Dismissal of Litigation . Not later than three (3) business days after the Effective Date, the Parties shall file a Stipulated Order of Dismissal, in the form of Exhibit J attached hereto, requesting the court to dismiss with prejudice the Litigation and all claims and counterclaims asserted therein.

7.7 No Licenses or Releases to Unnamed Third Parties . For the sake of clarity, the Parties acknowledge and agree that this Confidential Settlement Agreement grants no license to and releases no Claims against any other third party not specifically provided for in this Confidential Settlement Agreement or the Exhibits thereto.

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8. Further Assurances . Each Party covenants and agrees that it shall execute and deliver such other documents as may be required to implement any provision of this Agreement.

9. Limitation of Remedies . UNLESS A REPRESENTATION OR WARRANTY OF A PARTY IN THIS CONFIDENTIAL SETTLEMENT AGREEMENT IS KNOWINGLY FALSE, IN NO OTHER EVENT SHALL THE PARTIES, THEIR TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, DIRECT OR INDIRECT, FOR A BREACH OF THIS CONFIDENTIAL SETTLEMENT AGREEMENT, INCLUDING ECONOMIC DAMAGES, ATTORNEYS’ FEES (EXCEPT AS SET FORTH IN SECTION 7.5), DIRECT OR INDIRECT, OR INJURY TO PROPERTY OR LOST PROFITS, REGARDLESS OF WHETHER THE PARTY OR PARTIES SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.

10. Confidentiality .

10.1 Limitations on Disclosure . The Parties and their counsel shall take reasonable measures to ensure that the terms of this Confidential Settlement Agreement remain strictly confidential and are not disclosed to any third party, except as specifically set forth in Sections 10.1.1 through 10.1.6.

10.1.1 Pursuant to Order . The terms of this Confidential Settlement Agreement may be disclosed pursuant to any order or subpoena requiring disclosure in any legal proceeding, but only so long as the Party that has the disclosure requirement provides the other Parties with written notice of such requirement not later than ten business days after first learning of such order or subpoena.

10.1.2 Professional Advisers . The terms of this Confidential Settlement Agreement may be disclosed to any Party’s attorney, accountant, auditor, or insurer, but only so long as any such person or entity is informed of this confidentiality provision and agrees in writing to take reasonable measures to keep the terms of this Confidential Settlement Agreement strictly confidential and prevent their disclosure to any third party except as permitted by Section 10.1.5.

10.1.3 Merck . The terms of this Confidential Settlement Agreement may be disclosed to Merck, but only so long as Merck is informed of this confidentiality provision and agrees in writing to take reasonable measures to keep the terms of this Confidential Settlement Agreement strictly confidential and prevent their disclosure to any third party except as permitted by Section 10.1.5 and 10.1.6.

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10.1.4 Licensees . A redacted version of this Confidential Settlement Agreement may be disclosed to any licensee of a license agreement entered into pursuant to the 2001 Research Agreement solely to the extent required by such license agreement with any of the Parties, provided that all terms and provisions of this Confidential Settlement Agreement that need not be disclosed to such licensee are redacted, and further provided that the disclosing Party takes reasonable measures to keep the terms of this Confidential Settlement Agreement strictly confidential and prevent their disclosure to any third party except as permitted by Section 10.1.5. Prior to making any such disclosure, the Party intending to make the disclosure shall provide the other Parties with a redacted version of this Confidential Settlement Agreement to be disclosed pursuant to this Section 10.1.4 and give the other Parties a reasonable opportunity to object to the content of the redacted document on the ground that it would disclose more information than authorized by this Section 10.1.

10.1.5 Required by Law . The terms of this Confidential Settlement Agreement may be disclosed as required by law, including but not limited to any disclosure required to be made pursuant to the reporting obligations applicable to nonprofit corporations or recipients of federal funds or as required by the Securities and Exchange Commission or other such regulatory authorities, or as required by the Office of the Attorney General of the Commonwealth of Massachusetts. Prior to making any such disclosure, the Party intending to make the disclosure shall provide the other Parties with a redacted version of this Confidential Settlement Agreement to be disclosed pursuant to this Section 10.1.5 and give the other Parties a reasonable opportunity to object to the content of the redacted document on the ground that it would disclose more information than authorized by this Section 10.1.5.

10.1.6 Public Information . Any term of this Confidential Settlement Agreement may be disclosed publicly only to the extent such term is publicly known or widely disseminated to the public, other than through the wrongful act of the Party or its Affiliates, prior to the disclosure by the Party.

10.2 Media Inquiries . Notwithstanding the generality of the restrictions imposed by Section 10.1, a Party may disclose that there has been a settlement of the Parties’ disputes, the terms of which settlement are confidential, and Alnylam may issue the press release attached hereto as Exhibit K. No other statements or releases to the press shall be made by any Party concerning the terms of this Confidential Settlement Agreement, except that the Parties may disclose the information contained in Alnylam’s press release and may disclose that pursuant to the settlement, The Tuschl II Patent Family became co-owned by MPG, Whitehead, MIT and UMass.

11. Final and Binding Agreement . Each Party agrees that it has made such investigation of all matters pertaining to this Confidential Settlement Agreement that such Party deems necessary. Each Party agrees that it is not relying in any manner on any statement, promise, representation or omission, whether oral or written, express or implied, made by any person or entity, not specifically set forth in this Confidential Settlement Agreement (or in an

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exhibit attached hereto), including but not limited to any statement, promise, representation or omission concerning The Tuschl I Patent Family, The Tuschl II Patent Family or the Litigation. Each Party acknowledges that, after execution of this Confidential Settlement Agreement, such Party may discover facts different from or in addition to those which it now knows or believes to be true. Nevertheless, each Party agrees that this Confidential Settlement Agreement shall be and remain in full force and effect in all respects, notwithstanding such different or additional facts. This Confidential Settlement Agreement is intended to be, and is, final and binding on all Parties, regardless of any allegation of misrepresentation, mistake of law or fact, or any other circumstances whatsoever, unless a Party knowingly made a false representation or warranty in this Confidential Settlement Agreement.

12. Assignment . This Confidential Settlement Agreement is personal to the Parties and no rights or obligations under this Confidential Settlement Agreement may be assigned by any Party without the prior written consent of the other Parties.

13. Compromise Agreement . This Confidential Settlement Agreement is a compromise and settlement of disputed Claims and is not intended to be, nor shall be construed as, any admission of liability or wrongdoing by any Party.

14. Warranties and Representations .

14.1 No Assignment of Claims . Each Party warrants and represents that such Party has not sold, assigned, conveyed, pledged, encumbered, or otherwise in any way transferred to any person or entity any Claim released by such Party pursuant to this Confidential Settlement Agreement.

14.2 No Assignment of Patent Ownership . Each Party warrants and represents that such Party has not sold, assigned, conveyed, pledged, encumbered, or otherwise in any way transferred to any person or entity any ownership or partial ownership interest in the Tuschl I Patent Family as of the Effective Date.

14.3 Independent Advice . Each Party warrants and represents that it has received or had the opportunity to obtain independent legal advice from such Party’s attorney with respect to the rights and obligations arising from, and the advisability of executing, this Confidential Settlement Agreement.

14.4 Due Authorization . Each Party warrants and represents that such Party is fully entitled and duly authorized to enter into and deliver this Confidential Settlement Agreement. In particular, and without limiting the generality of the foregoing, each Party warrants and represents that it is fully entitled to grant the releases, enter into the covenants, and undertake the obligations set forth herein.

14.5 Corporate Power . The Parties warrant and represent that they are duly organized and validly existing, and that they have full corporate power and authority to enter into this Confidential Settlement Agreement and carry out the provisions hereof.

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14.6 Survival of Warranties . All warranties and representations set forth in this Confidential Settlement Agreement (and in any exhibit attached hereto) shall survive the execution and delivery of this Confidential Settlement Agreement.

14.7 Licenses Granted Under 2001 Research Agreement .

14.7.1 MIT License Grants . MIT warrants and represents that the only licenses that MIT has granted pursuant to the 2001 Research Agreement under which a current or former licensee currently has any rights or Claims are licenses to Ambion (now a wholly owned subsidiary of Life Technologies), Dharmacon (now a wholly owned subsidiary of ThermoFisher Scientific), Qiagen, Sigma Aldrich Co. and Merck & Co. Inc.

14.7.2 Max Planck License Grants . Max Planck warrants and represents that it has not granted any licenses pursuant to the 2001 Research Agreement under which a current or former licensee currently has any rights or Claims.

15. General Provisions .

15.1 Choice of Law . This Confidential Settlement Agreement shall be governed by and construed in accordance with the internal substantive laws of the Commonwealth of Massachusetts as applied to contracts made and wholly performed within the Commonwealth of Massachusetts without regard to its principles of choice of law. Each Party agrees that it shall not argue to any court or other tribunal that the substantive laws of the state Commonwealth of Massachusetts do not govern the construction or enforcement of this Confidential Settlement Agreement.

15.2 No Oral Modification . No provision of this Confidential Settlement Agreement can be waived, modified, amended, or supplemented except in a writing that expressly references this Confidential Settlement Agreement and is signed by an authorized representative of each Party to be bound.

15.3 No Construction Against Drafter . Because all Parties have participated in drafting, reviewing, and editing the language of this Confidential Settlement Agreement, no presumption for or against any Party arising out of drafting all or any part of this contract shall be applied in any action whatsoever.

15.4 No Third-Party Beneficiaries . The Parties agree that there are no third-party beneficiaries of any kind to this Confidential Settlement Agreement.

15.5 Entire Agreement . This Confidential Settlement Agreement, along with the Prosecution Guidelines attached as Exhibit A hereto, constitutes the entire agreement and understanding between the Parties and supersedes all prior agreements and understandings as to its subject matter, whether written or oral, with the exception of (1) the Exclusive License Agreement; (2) the Assignment Agreement; (3) the 2001 Research Agreement, as amended by this Confidential Settlement Agreement and the Exclusive License Agreement; (4) the 2003 Therapeutics Agreement, as amended by this Confidential Settlement Agreement and the Exclusive License Agreement; (5) the Alnylam License Agreement; and (6) the Amendment to the Alnylam License Agreement.

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15.6 Severability . Should a provision of this Confidential Settlement Agreement be found to be void, illegal or unenforceable, the remaining provisions of this Confidential Settlement Agreement will not cease to be effective. The Parties shall negotiate in good faith to replace such void, illegal or unenforceable provision by a new provision which reflects, to the extent possible, the original intent of the Parties.

15.7 Headings . The subject headings used in this Confidential Settlement Agreement are included for purposes of convenience only, and shall not affect the construction or interpretation of any provisions of this document.

15.8 Notices . Any notices to be given under this Agreement shall be delivered personally, or sent by registered or certified mail, courier, fax or e-mail, to the party at its address below or at such other address as may be supplied in writing.

Notices as described above shall be provided to the following:

If to MAX PLANCK :

Managing Director

Max Planck Innovation GmbH

Amalienstr. 33

80799 Munich

Germany

If to ALNYLAM :

Alnylam Pharmaceuticals, Inc.

300 Third Street

Cambridge, MA 02142

Attn: General Counsel

If to MIT :

Massachusetts Institute of Technology

77 Massachusetts Ave.

Cambridge, MA 02139-4307

Attn: Office of the General Counsel

If to WHITEHEAD :

Vice President

Whitehead Institute

Nine Cambridge Center

Cambridge, MA 02142-1493

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If to UMASS :

Office of Technology Management

University of Massachusetts

222 Maple Avenue

Higgins Building, Suite 114

Shrewsbury, MA 01545

Attn: Executive Director

15.9 Execution in Counterparts . This Confidential Settlement Agreement may be executed and delivered in any number of counterparts. When each Party has signed and delivered at least one counterpart to all other Parties, each counterpart shall be deemed an original and all counterparts, taken together, shall constitute one and the same agreement, which shall be binding and effective on the Parties hereto. This Confidential Settlement Agreement shall not become binding on the Parties hereto unless it has been executed by authorized representatives of all Parties.

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IN WITNESS WHEREOF, the Parties have approved and executed this Confidential Settlement Agreement as of the Effective Date.

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EXHIBIT A

Exhibit A

ASSIGNMENT

WHEREAS, MAX-PLANCK-GESELLSCHAFT ZUR FÖRDERUNG DER WISSENSCHAFTEN E.V., a corporation duly organized and existing under the laws of Germany (“MPG”), represents and warrants that it is the owner of 100% of the entire right, title and interest in and to the TUSCHL II UNITED STATES PATENTS AND PATENT APPLICATIONS, defined as the patents and patent applications filed in the United States Patent and Trademark Office set forth in the attached Schedule A, entitled “RNA Interference Mediating Small RNA Molecules” by Thomas Tuschl, Sayda Elbashir, and Winfried Lendeckel, and any divisionals, continuations, continuation-in-part applications directed to the same subject matter, continued prosecution applications, reissues or reexaminations of any of the foregoing filed in the United States Patent and Trademark Office. (For the avoidance of doubt, TUSCHL II UNITED STATES PATENTS AND PATENT APPLICATIONS does not include any Tuschl II patents or patent applications filed outside of the United States, and no rights or interest in any such patents or patent applications are granted under this Assignment.)

WHEREAS, MASSACHUSETTS INSTITUTE OF TECHNOLOGY, a corporation duly organized and existing under the laws of the Commonwealth of Massachusetts (“M.I.T.”), WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH, a Delaware corporation (“WHITEHEAD”), and the UNIVERSITY OF MASSACHUSETTS, a public institution of higher education duly organized and existing under the laws of the Commonwealth of Massachusetts (“UMASS”), each wish to acquire an undivided share of all right, title and interest in and to the TUSCHL II UNITED STATES PATENTS AND PATENT APPLICATIONS.

WHEREAS, MPG wishes to transfer, convey and assign to each of M.I.T., WHITEHEAD and UMASS an undivided share of all right, title and interest in and to the

TUSCHL II UNITED STATES PATENTS AND PATENT APPLICATIONS, and to retain all remaining right, title and interest in and to the TUSCHL II UNITED STATES PATENTS AND PATENT APPLICATIONS for itself, so that MPG, M.I.T., WHITEHEAD and UMASS shall be joint owners of the TUSCHL II UNITED STATES PATENTS AND PATENT APPLICATIONS.

NOW THEREFORE, for good and valuable consideration, the adequacy of which is hereby acknowledged, MPG hereby transfers, conveys and assigns to each of M.I.T., WHITEHEAD and UMASS an undivided share of all right, title and interest in and to the TUSCHL II UNITED STATES PATENTS AND PATENT APPLICATIONS, including but not limited to the right to sue for past, present and future infringement of same. MPG retains an undivided share of all right, title and interest in and to the TUSCHL II UNITED STATES PATENTS AND PATENT APPLICATIONS.

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IN WITNESS WHEREOF, THROUGH the signatures of their authorized representatives below, the parties hereto have caused this Assignment to be made and executed as of this 14th day of March, 2011.

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EXHIBIT B

EXHIBIT B

Exhibit B has been filed separately as Exhibit 10.2 to the Company’s Current Report on Form 8-K filed on October 2, 2015 and is incorporated herein by reference.

EXHIBIT C

Exhibit C

Tuschl I and II Prosecution Guidelines

General Principle :

Maximize the commercial potential of the T1 and T2 inventions by prosecuting their respective United States patent applications in a manner that leads to valid and enforceable T1 and T2 claims that are not substantially different in scope than those currently pending.

Specifics

1. The parties shall agree to execute the necessary documents to create common ownership of the T1 and T2 patent families in the United States. When common ownership is established, except as provided for herein, no party may dedicate to the public or convey to any other party by assignment, license or otherwise any interest that they acquired in T2 nor may they make any statements that T2 intellectual property is free to be used for research purposes.

2. Prosecution of T1 and T2 United States applications shall be undertaken in a coordinated manner, controlled by Max Planck consistent with the guidelines set forth in this document. The other parties shall have the right to comment on all substantive prosecution matters and such comments shall be considered in good faith by Max Planck. A law firm to be agreed upon by the parties would prosecute T1 outside of the United States. UMass shall control prosecution of T1 outside the US in accordance with these guidelines, using such law firm to oversee such prosecution. The other parties shall have the right to comment on all substantive prosecution matters and such comments shall be considered in good faith by UMass.

3. Max Planck shall diligently prosecute the T1 claims as broadly as possible including to cover multiple structures of RNA molecules and shall not narrow the claim scope, either through claim amendment or statements made during prosecution, of any issued or pending T1 claims case without the consent of the other co-owners, not to be unreasonably withheld, nor prosecute the T2 claims to the intentional detriment of T1 and vice versa.

4. A third party gatekeeper/arbiter shall be identified along with a simple, speedy dispute resolution mechanism in the event there is disagreement among the parties regarding the implementation of these rules and guidelines. The arbiter shall initially be [TO BE AGREED BY THE PARTIES]. When a dispute arises among the parties, the arbiter shall consider in good faith the position(s) of each party in the dispute which the parties shall have at least fifteen (15) days to submit to such arbiter. The arbiter shall render his/her decision in an unbiased manner in accordance with the General Principles and Specifics set forth in this document within five (5) business days of receiving all relevant documentation from the parties and, at the arbiter’s discretion, discussion with the parties; provided, however, that the arbiter shall hold no ex parte meetings or substantive conversations with the parties without the consent of all of the parties. In the event that the arbiter is no longer willing or capable of serving in this function, a replacement shall be selected as follows: each of the parties shall nominate five potential replacements and any potential arbiter appearing on each of the relevant lists shall be the arbiter and the parties shall attempt in good faith to secure such arbiter’s services. In the event that there is more than one arbiter that appears on each such list, the parties shall agree in good faith

which arbiter to approach first. In the event that there are no arbiters in common, the parties shall repeat the process until an arbiter appears on each such list or all of the parties can otherwise agree on an arbiter.

5. As soon as practical, an interview shall be arranged with the T1 and T2 patent examiners jointly to discuss both patent families in a coordinated fashion to help optimize the prosecution strategy going forward. A representative of each T1 owner shall be entitled to attend the interview.

6. A prosecution roadmap shall be created consistent with the guidelines above, for each pending patent family, taking into consideration the specific issues raised in each case and subject to the right of the other parties to comment and the dispute resolution mechanism. The parties acknowledge that any such roadmap is subject to change and must be flexible.

7. Where required, terminal disclaimers will be filed in both T1 and T2 patent applications.

Exhibit D

Exhibit D

US Tuschl I Patent Family

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EXHIBIT H

Exhibit H

SETTLEMENT AGREEMENT

This Settlement Agreement is entered into as of the Effective Date by and between Max-Planck-Gesellschaft zur Förderung der Wissenschaften e. V. (“MPG”), Max-Planck-Innovation GmbH (“MI”) (collectively referred to herein as “Max Planck”), and Alnylam Pharmaceuticals, Inc. (“Alnylam”), on the one hand, and Wolf, Greenfield & Sacks, PC (“Wolf Greenfield”), on the other hand.

This Settlement Agreement is made with respect to the lettered recitals below. The Definitions set forth in Section 1 below apply to the recitals.

A. WHEREAS, MPG and Wolf Greenfield are parties to the Litigation;

B. WHEREAS, the Parties deem it to be in their best interests and to their mutual advantage to settle their disputes on the terms and conditions set forth in this Settlement Agreement, without admitting liability;

NOW, THEREFORE, in consideration of all of the terms and conditions of this Settlement Agreement, the Parties agree as follows:

1. Definitions . The following words and phrases shall have the meanings set forth below solely for purposes of this Settlement Agreement.

1.1 “Claims” shall mean any and all claims, counterclaims, actions, causes of action, demands, costs, and charges of whatever nature, whether known or unknown, including without limitation any and all claims to recover attorneys’ fees and costs.

1.2 “Effective Date” shall mean March 14, 2011.

1.3 “Litigation” shall mean the civil action entitled Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. v. Wolf, Greenfield & Sacks, PC , pending in the United States District Court for the District of Massachusetts as Civil Action No. 1:09-CV-11168-PBS.

1.4 “Party” shall mean MPG, MI, Alnylam or Wolf Greenfield, and when used in the plural shall mean all of them.

2. Releases, Covenants Not to Sue, and Dismissals .

2.1 Releases by MPG, MI and Alnylam . MPG, MI, and Alnylam, on behalf of themselves and their predecessors, successors, and assigns, do hereby now and forever release and discharge Wolf Greenfield, and its predecessors, successors, and assigns, and each of its respective current and former shareholders, trustees, officers, directors, employees, agents, attorneys, insurers and representatives (but only in the representatives’ capacities as such), from any and all Claims concerning any act or omission occurring prior to or on the Effective Date, including without limitation any and all Claims arising under, related to, or connected in any way with the Litigation.

2.2 Releases by Wolf Greenfield . Wolf Greenfield, on behalf of itself and its predecessors, successors, and assigns, does hereby now and forever release and discharge MPG, MI, and Alnylam and their predecessors, successors, and assigns, and each of their respective current and former shareholders, trustees, officers, directors, employees, agents, attorneys, insurers and representatives (but only in the representatives’ capacities as such), from any and all Claims concerning any act or omission occurring prior to or on the Effective Date, including without limitation any and all Claims arising under, related to, or connected in any way with the Litigation.

2.3 Covenant Not to Sue . The Parties shall not now or at any time in the future initiate any legal proceeding anywhere in the world asserting any Claim released pursuant to Sections 7.1 and 17.2. Any Party that breaches the obligations under this Section 7.5 (i) consents to the dismissal of such legal proceeding and to the entry of a permanent injunction restraining the breaching Party from initiating any future legal proceeding asserting any Claim released pursuant to this Settlement Agreement; and (ii) shall be liable to the other Party for their reasonable attorneys’ fees and costs incurred in securing the dismissal of such legal proceeding and the entry of such permanent injunction.

2.4 Dismissal of Litigation . Not later than three business days after the earlier of (i) the entry by the District Court of the Vacatur requested in the Joint Stipulated Motion filed pursuant to Section 2.5; or (ii) sixty (60) days after the Effective Date, the Parties shall file a Stipulated Order of Dismissal, in the form of Exhibit A attached hereto, requesting the District Court to dismiss with prejudice the Litigation and all Claims asserted therein.

2.5 Joint Stipulated Motion for Vacatur . Not later than three business days after the Effective Date, MPG and Wolf Greenfield shall file the Joint Stipulated Motion for Vacatur of the Court’s September 14, 2010 Memorandum and Order (Dkt #108), in the form attached as Exhibit B hereto.

3. Further Assurances . Each Party covenants and agrees that it shall execute and deliver such other documents as may be required to implement any provision of this Settlement Agreement.

4. Limitation of Remedies . IN NO EVENT SHALL THE PARTIES, THEIR TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, FOR A BREACH OF THIS SETTLEMENT AGREEMENT, INCLUDING ECONOMIC DAMAGES, ATTORNEYS’ FEES (EXCEPT AS PROVIDED IN SECTION 7.5), DIRECT OR INDIRECT, OR INJURY TO PROPERTY OR LOST PROFITS, REGARDLESS OF WHETHER THE PARTY OR PARTIES SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.

5. Confidentiality .

5.1 Limitations on Disclosure . The Parties and their counsel shall take all reasonable measures to ensure that the terms of this Settlement Agreement remain strictly confidential and are not disclosed to any third party, except as follows:

5.1.1 Pursuant to Order. The terms of this Settlement Agreement may be disclosed pursuant to any order or subpoena requiring disclosure in any legal proceeding, so long as the Party that has the disclosure requirement provides the other Parties with written notice of such requirement not later than ten business days after first learning of such order or subpoena.

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5.1.2 Professional Advisers . The terms of this Settlement Agreement may be disclosed to any Party’s attorney, accountant, auditor, or insurer, but only so long as any such person or entity is informed of this confidentiality provision and agrees in writing to take all reasonable measures to keep the terms of this Settlement Agreement strictly confidential and prevent their disclosure to any third party except as permitted by Section 5.1.3.

5.1.3 Required by Law. The terms of this Settlement Agreement may be disclosed as required by law, including but not limited to any disclosure required to be made pursuant to the reporting obligations applicable to nonprofit corporations or recipients of federal funds or as required by the Securities Exchange Commission or other such regulatory authorities.

6. Final and Binding Agreement . Each Party agrees that it has made such investigation of all matters pertaining to this Settlement Agreement that such Party deems necessary. Each Party agrees that it is not relying in any manner on any statement, promise, representation or omission, whether oral or written, express or implied, made by any person or entity, not specifically set forth in this Settlement Agreement. Each Party acknowledges that, after execution of this Settlement Agreement, such Party may discover facts different from or in addition to those which it now knows or believes to be true. Nevertheless, each Party agrees that this Settlement Agreement shall be and remain in full force and effect in all respects, notwithstanding such different or additional facts. This Settlement Agreement is intended to be, and is, final and binding on all Parties, regardless of any allegation of misrepresentation, fraud, mistake of law or fact, or any other circumstances whatsoever.

7. Assignment . This Settlement Agreement is personal to the Parties and no rights or obligations under this Settlement Agreement may be assigned by any Party without the prior written consent of the other Parties.

8. Compromise Agreement . This Settlement Agreement is a compromise and settlement of disputed Claims and is not intended to be, nor shall be construed as, any admission of liability or wrongdoing by any Party.

9. Warranties and Representations.

9.1 No Assignment of Claims . Each Party warrants and represents that such Party has not sold, assigned, conveyed, pledged, encumbered, or otherwise in any way transferred to any person or entity any Claim released by such Party pursuant to this Settlement Agreement.

9.2 Independent Advice . Each Party warrants and represents that it has received or had the opportunity to obtain independent legal advice from such Party’s attorney with respect to the rights and obligations arising from, and the advisability of executing, this Settlement Agreement.

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9.3 Due Authorization . Each Party warrants and represents that such Party is fully entitled and duly authorized to enter into and deliver this Settlement Agreement. In particular, and without limiting the generality of the foregoing, each Party warrants and represents that it is fully entitled to grant the releases, enter into the covenants, and undertake the obligations set forth herein.

9.4 Corporate Power . The Parties warrant and represent that they are duly organized and validly existing, and that they have full corporate power and authority to enter into this Settlement Agreement and carry out the provisions hereof.

9.5 Survival of Warranties . All warranties and representations set forth in this Agreement shall survive the execution and delivery of this Settlement Agreement.

10. General Provisions .

10.1 Choice of Law . This Settlement Agreement shall be governed by and construed in accordance with the internal substantive laws of the Commonwealth of Massachusetts as applied to contracts made and wholly performed within the Commonwealth of Massachusetts without regard to its principles of choice of law. Each Party agrees that it shall not argue to any court or other tribunal that the substantive laws of the state Commonwealth of Massachusetts do not govern the construction or enforcement of this Settlement Agreement.

10.2 No Oral Modification . No provision of this Settlement Agreement can be waived, modified, amended, or supplemented except in a writing that expressly references this Settlement Agreement and is signed by an authorized representative of each Party to be bound.

10.3 No Construction Against Drafter . Because all Parties have participated in drafting, reviewing, and editing the language of this Settlement Agreement, no presumption for or against any Party arising out of drafting all or any part of this contract shall be applied in any action whatsoever.

10.4 Entire Agreement . This Settlement Agreement constitutes the entire agreement and understanding between the Parties and supersedes all prior agreements and understandings as to its subject matter.

10.5 Headings . The subject headings used in this Settlement Agreement are included for purposes of convenience only, and shall not affect the construction or interpretation of any provisions of this document.

10.6 Notices . Any notices to be given under this Agreement shall be delivered personally, or sent by registered or certified mail, courier, fax or e-mail, to the party at its address below or at such other address as may be supplied in writing.

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Notices as described above shall be provided to the following:

If to Max Planck :

Managing Director

Max Planck Innovation GmbH

Amalienstr. 33

80799 Munich

Germany

If to Alnylam:

Alnylam Pharmaceuticals, Inc.

300 Third Street

Cambridge, MA 02142

Attn: General Counsel

If to Wolf Greenfield

Jason Honeyman

WOLF, GREENFIELD & SACKS, PC

600 Atlantic Avenue

Boston, Massachusetts 02210-2206

Phone: (617) 646-8222

Fax: (617) 646-8646

jhoneyman@wolfgreenfield.com

10.7 Execution in Counterparts . This Settlement Agreement may be executed and delivered in any number of counterparts. When each Party has signed and delivered at least one counterpart to all other Parties, each counterpart shall be deemed an original and all counterparts, taken together, shall constitute one and the same agreement, which shall be binding and effective on the Parties hereto. This Settlement Agreement shall not become binding on the Parties hereto unless it has been executed by authorized representatives of all Parties.

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IN WITNESS WHEREOF, the Parties have approved and executed this Settlement Agreement as of the Effective Date.

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Exhibit A to Settlement Agreement

MAX-PLANCK-GESELLSCHAFT ZUR FOERDERUNG DER

WISSENSCHAFTEN E.V. AND WOLF GREENFIELD & SACKS, PC’S

[PROPOSED] STIPULATED ORDER OF DISMISSAL

Pursuant to Federal Rule of Civil Procedure 41(a), Plaintiff Max-Planck-Gesellschaft zur Foerderung der Wissenschaften e.V. (“Max Planck”) and Defendant Wolf Greenfield & Sacks, PC (“Wolf Greenfield”), by their attorneys, hereby stipulate and agree that this action be dismissed in its entirety with prejudice and that all rights of appeal are waived. Each party shall bear its own costs and attorney’s fees.

Exhibit 10.2

EXCLUSIVE LICENSE AGREEMENT FOR TUSCHL II UNITED STATES

PATENTS AND PATENT APPLICATIONS

This Exclusive License Agreement for Tuschl II United States Patents and Patent Applications (“Agreement”) is made as of March 14, 2011 (“Effective Date”), by and between Alnylam Pharmaceuticals, Inc. (“Alnylam”) and University of Massachusetts (“UMass”).

This Agreement is made with respect to the following recitals:

WHEREAS, Max-Planck-Gesellschaft zur Föerderung der Wissenschaften e.V. (“Max-Planck”), is an owner of rights in and to the patents and patent applications defined herein as the US Tuschl II Patent Family;

WHEREAS, pursuant to that certain Assignment Agreement made and entered into as of March 14, 2011, UMass has become a co-owner of the US Tuschl II Patent Family;

WHEREAS, UMass has the right to grant licenses under the US Tuschl II Patent Family;

WHEREAS, Alnylam desires to obtain a license with the right to grant sublicenses under the US Tuschl II Patent Family, and UMass desires to grant such license subject to the conditions set forth herein;

NOW, THEREFORE, Alnylam and UMass hereby agree as follows:

1. Definitions . The following words and phrases shall have the meanings set forth below solely for purposes of this Agreement.

1.1. “Affiliate” shall mean any corporation or other business entity that now or in the future directly or indirectly controls, is controlled by, or is under common control with, a Party or a Third Party (as the case may be under this Agreement). Control means direct or indirect ownership of, or other beneficial interest in, fifty percent (50%) or more of the voting stock, other voting interest, or income of a corporation or other business entity, or possession of the power to elect or appoint fifty percent (50%) or more of the members of the governing body of the corporation or other business entity. A corporation or other business entity shall be an Affiliate only during such period of time that it meets the definition set forth in this Section 1.1.

1.2. “Collaboration Partner” shall mean an entity involved in a bona fide collaboration with Merck or any of Merck’s Affiliates sublicensed in accordance herewith. A bona fide collaboration shall mean a collaboration with Merck or any of its Affiliates sublicensed in accordance herewith, where such collaboration is entered into after Merck’s commencement of GLP toxicology testing of the Licensed Product required for the filing of an Investigational New Drug Application and involves the development of a Licensed Product in the Field, in which Merck plays an integral role in the experimentation and a dominant or co-equal role in the decision-making, relating to the development of such Licensed Product in the Field. Merck’s or any of its properly-sublicensed Affiliates’ experimentation relating to the discovery and development of a Licensed Product in the

Field prior to the commencement of a collaboration shall be deemed to have been conducted in the course of the collaboration for purposes of determining whether the collaboration constitutes a bona fide collaboration.

1.3. “Confidentiality Agreement” shall mean a document in the form attached as Exhibit B hereto.

1.4. “Distributor” shall mean an entity that purchases Licensed Products (whether in packaged form or bulk form) from Merck, one of its Affiliates, or a Collaboration Partner, and resells such Licensed Products to Third Parties in a manner consistent with normal trade practices in the pharmaceutical industry.

1.5. “ Excluded Targets ” shall mean any Target for which Alnylam has, prior to the Effective Date, granted a Third Party exclusive rights under the US Tuschl II Patent Family, unless such Target has ceased to be an Excluded Target pursuant to Section 2.2 hereof.

1.6. “ Field ” shall mean all uses other than the commercial sale or use as a research reagent, including in a kit format, for research or educational purposes, including without limitation,

1.7. “Gatekeeper” shall mean an independent attorney, not employed by Alnylam, registered to practice before the United States Patent and Trademark Office who shall be mutually agreed upon by UMass and Alnylam, and who shall be bound by the Confidentiality Agreement and perform the services identified in Section 2.3 of this Agreement.

1.8. “ Licensed Product ” shall mean any product or part thereof in the Field, the manufacture, use or sale of which would, absent the license granted hereunder, infringe one or more claims of an issued patent in the US Tuschl II Patent Family.

1.9. “Merck” shall mean Merck & Co., Inc.

1.10. “Merck License Agreement” shall mean a non-exclusive license agreement entered into by Merck under the terms and restrictions provided for in Section 2.2 of this Agreement.

1.11. “Party” shall mean Alnylam or UMass, and when used in the plural shall mean both all of them.

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1.12. “ Sublicensee ” shall mean any corporation, firm, partnership, limited liability company, or other legal entity or business association other than an Affiliate of Alnylam that sells or intends to commercialize Licensed Products under a sublicense from Alnylam to develop, make, use and sell Licensed Products. Sublicensee shall not include a distributor. For the purpose of this Agreement, Sublicensee shall also include the assignees of Alnylam to which Alnylam has sub-assigned its ownership position in the Tuschl II United States Patents and Patent Applications in certain countries.

1.13. “ Target ” shall mean (a) a polypeptide or entity comprising a combination of at least one polypeptide and other macromolecules, that is a site or potential site of therapeutic intervention by a therapeutic agent; or a nucleic acid which is required for expression of such polypeptide; (b) variants of a polypeptide, cellular entity or nucleic acid described in clause (a); or (c) a defined non-peptide entity, including a microorganism, virus, bacterium or single cell parasite; provided that the entirety of the genome of a virus shall be regarded as a single Target.

1.14. “ Term ” shall mean the period commencing on the Effective Date and concluding on the expiration or abandonment of all issued patents and filed patent applications in the US Tuschl II Patent Family.

1.15. “ Third Party ” shall mean any corporation, firm, partnership, limited liability company, or other legal entity or business association other than Alnylam, an Affiliate of Alnylam, or a Sublicensee.

1.16. “US Tuschl I Patent Family” shall mean any and all patents issued by, and patent applications filed in, the USPTO as set forth in the attached Exhibit C, entitled “RNA sequence-specific mediators of RNA interference,” naming as inventors Thomas Tuschl, David P. Bartel, Phillip A. Sharp, and Phillip D. Zamore, and any divisionals, continuations, continuation-in-part applications thereof, requests for continued examination, reissues or reexaminations of any of the foregoing filed in the USPTO.

1.17. “ US Tuschl II Patent ” shall mean any patent within the scope of rights covered by Section 1.18 that is issued by the United States Patent and Trademark Office.

1.18. “ US Tuschl II Patent Family ” shall mean any and all patents issued by, and patent applications filed, in the USPTO as set forth in the attached Exhibit A, entitled “RNA Interference Mediating Small RNA Molecules,” naming as inventors by Thomas Tuschl, Sayda Elbashir, and Winfried Lendeckel, and any divisionals, continuations, continuation-in-part applications thereof, requests for continued examination, reissues or reexaminations of any of the foregoing filed in the USPTO.

2. Grant of Rights .

2.1. Exclusive License . Except as expressly set forth in Section 2.2, UMass grants to Alnylam for the Term an exclusive, unrestricted, royalty-free license, with the right to grant sublicenses, under the US Tuschl II Patent Family including without limitation the right to make, have made, sell, have sold, offer for sale, import and use any Licensed Product.

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2.2. Merck License Agreement . Notwithstanding the license set forth in Section 2.1, UMass reserves the right to convey an option (and corresponding licenses) to Merck (and to no other person or entity) to acquire from UMass one or more non-exclusive licenses to make, have made, sell, have sold, offer for sale, import and use any Licensed Product, except with respect to Excluded Targets, under the US Tuschl II Patent Family, provided that the agreement conveying the option and any agreement granting any such license shall include provisions to the effect that (i) Merck shall have no right to grant any sublicenses, except to (a) an Affiliate (which sublicense shall automatically terminate at the time that the entity to which the sublicense was granted ceases to be an Affiliate of Merck); and (b) a Collaboration Partner, Distributor, or a contractor working under the direction of Merck or a Merck Affiliate to the extent such contractor assists in performing the activities licensed hereunder, and in such cases only with respect to the specific Licensed Product that is the subject of the particular collaboration, distribution or services agreement; (ii) the option agreement and all licenses shall automatically terminate if Merck files a legal proceeding in the USPTO, a United States court, or an arbitral forum, challenging the validity, enforceability or inventorship of any application or patent in the US Tuschl II Patent Family, except if Merck is sued for infringement of a US Tuschl II Patent; and (iii) the license cannot be assigned except to an Affiliate or in connection with a merger, acquisition, or sale of all or substantially all of the assets of Merck or an Affiliate relating to the subject matter of the US Tuschl II Patent Family, which sale includes the assignment of the License Agreement dated September 8, 2003, between UMass and Sirna Therapeutics, Inc. Nothing contained in this Section 2.2 shall be construed to prevent Merck from asserting non-infringement as a defense in any legal proceeding involving a patent or application in the US Tuschl II Patent Family, or to assert any defense in a legal proceeding outside the United States involving a patent or application that is not a member of the US Tuschl II Patent Family. UMass acknowledges and agrees that (a) it shall have no right to grant to Merck any rights under the US Tuschl II Patent Family with respect to any Excluded Targets, and (b) any non-exclusive license granted to Merck pursuant to this Section 2.2 shall expressly provide that Merck is prohibited from granting any sublicense, covenant not to sue, or freedom to operate under any application or patent in the US Tuschl II Patent Family except as set forth in clause (i) above. Alnylam represents and warrants that, as of the Effective Date, there are forty-one (41) Excluded Targets. Alnylam shall allow UMass to designate a single outside attorney (the “UMass Attorney”) who agrees to be bound by the Confidentiality Agreement to inspect at Alnylam’s offices, at a reasonable time and with reasonable advance notice, documents sufficient to confirm that, as of the Effective Date, there are forty-one (41) Excluded Targets. Alnylam agrees that, if at any time after the Effective Date, a Target ceases to be subject to exclusive rights granted to another entity under the US Tuschl II Patent Family, then such Target shall no longer be an Excluded Target.

2.3. Provisions Concerning Excluded Targets . Alnylam shall provide the Gatekeeper with a certified list of Excluded Targets within one month of the Effective Date. The Gatekeeper shall maintain such list in a secure location during the Term of this Agreement. Alnylam shall update the list of Excluded Targets during the Term of the Agreement by promptly informing the Gatekeeper when a Target has been removed from the list. Merck may, from time to time, provide to the Gatekeeper in confidence a list of proposed Targets. Within fourteen (14) business days following the Gatekeeper’s receipt of such list from Merck, the Gatekeeper shall notify Merck in writing which, if any, of the

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Targets identified on such list are Excluded Targets, and hence would be excluded from the Merck License Agreement. If the Gatekeeper has questions as to whether a proposed Target is an Excluded Target, the Gatekeeper may, in his or her sole discretion, pose appropriate scientific questions to an independent expert, which expert shall first enter into and be bound by the Confidentiality Agreement. In the event that the Gatekeeper informs Merck that any proposed Target is an Excluded Target, the UMass Attorney may thereafter inspect all documents on which the Gatekeeper relied in determining that the proposed Target is an Excluded Target, and the Gatekeeper shall disclose to the UMass Attorney any advice received from any independent scientific expert. If wishes to exercise its option to enter into a Merck License Agreement provided for in (and subject to the terms and restrictions of) Section 2.2 above, UMass, Merck, Alnylam and the Gatekeeper shall each enter into the Confidentiality Agreement. (i) In the event that the Merck License Agreement is to cover all Targets except Excluded Targets, the Gatekeeper shall provide UMass with the list of Excluded Targets within seven (7) business days of receiving notice from UMass of Merck’s request to exercise its option to enter into a Merck License Agreement and the Confidentiality Agreement executed by authorized representatives of UMass and Merck. The list of Excluded Targets shall be attached as an exhibit to the Merck License Agreement, which shall expressly provide that no rights are granted with respect to all such Excluded Targets (as required by Section 2.2) and which list shall remain subject to the terms of the Confidentiality Agreement. (ii) In the event that the Merck License Agreement is to be limited to a particular Target or Targets only, UMass shall thereupon provide to the Gatekeeper in confidence a list of the proposed Targets to be covered by the Merck License Agreement. Within fourteen (14) business days following the Gatekeeper’s receipt of such list from UMass, the Gatekeeper shall notify UMass in writing which, if any, of the Targets identified on such list are Excluded Targets, and hence must be excluded from the Merck License Agreement. Such writing shall be subject to the terms of the Confidentiality Agreement. If the Gatekeeper has any questions as to whether a proposed Target is an Excluded Target, the Gatekeeper may, in his or her sole discretion, pose appropriate scientific questions to an independent expert, which expert shall first enter into and be bound by the Confidentiality Agreement. In the event that the Gatekeeper informs Merck that any proposed Target is an Excluded Target, the UMass Attorney may thereafter inspect all documents on which the Gatekeeper relied in determining that the proposed Target is an Excluded Target, and the Gatekeeper shall disclose to the UMass Attorney any advice received from any independent scientific expert. UMass may grant Merck a license with respect to any Targets not identified by the Gatekeeper as Excluded Targets, subject to the terms and restrictions of Section 2.2.

2.4. Retained Research Rights. UMass shall retain the right to practice the inventions claimed in the US Tuschl II Patent Family for research, teaching, education, non-commercial collaboration and publication purposes. Alnylam acknowledges that the U.S. federal government retains a royalty-free, non-exclusive, non-transferable license to practice any government-funded invention claimed in any patent or application in the US Tuschl II Patent Family for government purposes.

2.5. No Further Conveyances of Rights . (a) Except as expressly set forth in Section 2.2, UMass covenants and agrees (i) not to dedicate to the public nor to convey to any entity whatsoever, including to any of its or their Affiliates or other Third Parties, whether by assignment, license or otherwise, any interest in the US Tuschl II Patent Family;

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and (ii) not to make any representation in any form or manner that any patent application or patent in the US Tuschl II Patent Family may be used for research purposes other than as expressly agreed to pursuant to the September 2001 Joint Invention and Joint Marketing Agreement. (b) Under no circumstance shall UMass disclaim or otherwise relinquish ownership of any US Tuschl II Patent without the prior written consent of Max Planck. In the event that UMass does disclaim or otherwise relinquish its ownership interest in any US Tuschl II Patent, in addition to any other rights and remedies available to the Parties, UMass shall be deemed to have disclaimed and relinquished its ownership interest in every patent and application in the US Tuschl II Patent Family and in every patent and application in the US Tuschl I Patent Family such that common ownership is maintained between the US Tuschl I Patent Family and the US Tuschl II Patent Family.

2.6. No Additional Rights . Nothing in this Agreement shall be construed to confer any rights upon Alnylam by implication, estoppel, or otherwise as to any intellectual property rights, including without limitation patents and patent applications, trademarks, copyrights and know-how, of UMass other than the US Tuschl II Patent Family, regardless of whether such intellectual property rights shall be dominant or subordinate to any patent application or patent in the US Tuschl II Patent Family.

3. Patent Enforcement .

3.1. Notice . Each Party shall notify the other Party promptly in writing of any infringement of any US Tuschl II Patent that becomes known to any of them, including without limitation the receipt of any Paragraph IV notice letter under the Drug Price Competition and Patent Term Restoration Act of 1984 (commonly referred to as the Hatch-Waxman Act). In no event shall such notice be given more than 60 calendar days after learning of any infringement.

3.2. Control of Patent Enforcement . Alnylam shall have the right to bring suit for infringement of any claim in any US Tuschl II Patent, to enjoin infringement, to collect damages, profits and awards of whatever nature recoverable for such infringement, to defend against any challenge to validity of such patent, and to pursue any such litigation until a final judgment, from which no further appeal may be taken and no further review may be sought.

3.2.1. Upon reasonable prior notice, Alnylam may join UMass as a party if necessary in any such litigation brought in the United States against a for-profit commercial entity (the US Commercial Infringement Litigation”), provided that the complaint satisfies all pleading obligations and the requirements of Rule 11 of the Federal Rules of Civil Procedure. Alnylam shall select counsel to represent Alnylam and UMass in connection with such US Commercial Infringement litigation, provided that UMass shall have a right of prior approval with respect to counsel for UMass, such approval not to be unreasonably withheld or delayed. Counsel representing UMass must be appointed a Special Assistant Attorney General and comply with the guidelines of the Massachusetts Attorney General with respect to that appointment. Alnylam shall have control over all decisions in, and any settlement of, any such US Commercial Infringement Litigation, provided that UMass shall have a right of prior approval over significant litigation decisions concerning, and settlement of, any non-patent claims or non-patent counterclaims to the extent they affect the interests

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of the Commonwealth of Massachusetts, such approval not to be unreasonably withheld or delayed. Alnylam shall reasonably consult with UMass and keep it informed concerning developments in the US Commercial Litigation.

3.2.2. In the event there arises an actual or potential conflict of interest between Alnylam and UMass with respect to the US Commercial Infringement Litigation such that representation of UMass by the counsel retained by Alnylam is inappropriate, Alnylam shall not thereafter have control over decisions in the litigation affecting UMass, and UMass shall be entitled to select its own counsel, which counsel shall be paid for by the UMass and not by Alnylam. Alnylam shall further obtain the prior consent of UMass to settle such litigation, which consent shall not be unreasonably withheld.

3.2.3. Alnylam shall hold UMass harmless from, and indemnify it against, any costs, expenses, or liability the UMass may incur in connection with any action taken under this Section 3; provided that Alnylam shall be obligated to reimburse UMass for costs and expenses incurred during the prosecution or defense of any such litigation only if reasonably incurred by UMass for purposes of such action.

3.3. Alnylam Fees . Any and all fees, costs and expenses incurred by Alnylam, including, without limitation, attorney’s fees, court costs and disbursements, in connection with any action taken under this Section 3 shall be paid by Alnylam.

3.4. Cooperation . UMass shall cooperate fully with Alnylam in connection with any action under this Section 3 and agrees to promptly provide reasonable access to all necessary documents, information, and persons under its control, and to render reasonable assistance in response to a request by Alnylam for such assistance, all at Alnylam’s expense.

3.5. Consent . UMass shall not be entitled to bring a suit for infringement of any US Tuschl II Patent without the express written consent of Alnylam, which Alnylam may withhold in its sole discretion.

4. Confidentiality

4.1. Limitations on Disclosure . The Parties and their counsel shall take reasonable measures to ensure that the terms of this Exclusive License Agreement remain strictly confidential and are not disclosed to any third party, except as specifically set forth in Sections 4.2.1 through 4.2.5.

4.1.1. Pursuant to Order . The terms of this Confidential Settlement Agreement may be disclosed pursuant to any order or subpoena requiring disclosure in any legal proceeding, but only so long as the Party that has the disclosure requirement provides the other Parties with written notice of such requirement not later than ten business days after first learning of such order or subpoena.

4.1.2. Professional Advisers . The terms of this Exclusive License Agreement may be disclosed to any Party’s attorney, accountant, auditor, or insurer, but only so long as any such person or entity is informed of this confidentiality provision and agrees in writing to take reasonable measures to keep the terms of this Exclusive License Agreement strictly confidential and prevent their disclosure to any third party except as permitted by Sections 4.1.4 and 4.1.5.

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4.1.3. Merck. The terms of this Exclusive License Agreement may be disclosed to Merck, but only so long as Merck is informed of this confidentiality provision and agrees in writing to take reasonable measures to keep the terms of this Exclusive License Agreement strictly confidential and prevent their disclosure to any third party except as permitted by Sections 4.1.4 and 4.1.5.

4.1.4. Required by Law . The terms of this Exclusive License Agreement may be disclosed as required by law, including but not limited to any disclosure required to be made pursuant to the reporting obligations applicable to nonprofit corporations or recipients of federal funds or as required by the Securities and Exchange Commission or other such regulatory authorities, or as required by the Office of the Attorney General of the Commonwealth of Massachusetts. Prior to making any such disclosure, the Party intending to make the disclosure shall provide the other Party with a redacted version of this Exclusive License Agreement to be disclosed pursuant to this Section 4.1.4 and give the other Party a reasonable opportunity to object to the content of the redacted document on the ground that it would disclose more information than authorized by this Section 4.1.4.

4.1.5. Public Information . Any term of this Confidential Settlement Agreement may be disclosed publicly only to the extent such term is publicly known or widely disseminated to the public, other than through the wrongful act of the Party or its Affiliates, prior to the disclosure by the Party.

5. Miscellaneous Provisions .

5.1.1. Non-Use of UMass Trademarks . Neither Alnylam nor its Affiliates and Sublicensees shall use the name of “University of Massachusetts,” or any variation, adaptation, or abbreviation thereof, or of any of its trustees, officers, faculty, students, employees, or agents, or any trademark owned by any of them, in any promotional material or other public announcement or disclosure, without the prior written consent of the UMass or in the case of an individual, the consent of that individual. The foregoing notwithstanding, Alnylam may state generally that it has a license from UMass under the US Tuschl II Patent Family, subject only to UMass’s reserved rights to convey non-exclusive licenses to Merck.

5.1.2. Termination . This license is non-revocable and cannot be terminated under any circumstances.

5.1.3. Limitation of Remedies . IN NO EVENT SHALL THE PARTIES, THEIR TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES AND AFFILIATES, BE LIABLE FOR SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, DIRECT OR INDIRECT, RELATING TO THIS AGREEMENT, INCLUDING ECONOMIC DAMAGES, ATTORNEYS’ FEES, OR INJURY TO PROPERTY OR LOST PROFITS, REGARDLESS OF WHETHER THE PARTY OR PARTIES SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.

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5.2. Notices . Any notices required or permitted under this Agreement and all correspondence hereunder shall be in English and in writing, shall specifically refer to this Agreement, and shall be sent by a method providing confirmation of delivery to the following addresses or facsimile numbers of the parties:

If to UMass:

Office of Technology Management

University of Massachusetts

222 Maple Avenue

Higgins Building, Suite 114

Shrewsbury, MA 01545

Attn: Executive Director

If to Alnylam:

Alnylam Pharmaceuticals, Inc.

300 Third Street

Cambridge, MA 02142

Attn: General Counsel

5.3. Governing Law . This Agreement shall be construed, governed, interpreted and applied in accordance with the laws of the Commonwealth of Massachusetts, even if the laws of the Commonwealth would select a different governing law.

5.4. Compliance with Laws . Alnylam shall use commercially reasonable efforts to comply with all local, state, federal, and international laws and regulations relating to the development, manufacture, use and sale of Licensed Products.

5.5. Indemnification. Alnylam shall indemnify, defend, and hold harmless UMass and its trustees, officers, faculty, students, employees, and agents and their respective successors, heirs and assigns (the “indemnitees”), against any liability, damage, loss, or expense (including reasonable attorneys’ fees and expenses) incurred by or imposed upon any of the indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including without limitation actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) concerning (i) any use of the inventions claimed in the US Tuschl II Patent Family by Alnylam or its sublicensees, or (ii) any product, process, or service that is developed, made, used, sold, or performed by Alnylam or its sublicensees pursuant to any right or license granted to Alnylam under this Agreement. Alnylam shall obtain and carry in full force and effect commercial general liability insurance, including product liability and errors and omissions insurance, which shall protect Alnylam and its indemnitees, including UMass, with respect to events covered by this Section.

5.6. Integration . This Agreement supersedes all prior written agreements and all prior written and contemporaneous oral agreements with respect to the subject matter hereof.

5.7. Amendment and Waiver . This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any

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waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar.

5.8. Severability . Should one of the provisions of this Agreement be held void, invalid or unenforceable, the remaining provisions of this Agreement will not cease to be effective. The parties shall negotiate in good faith to replace such void, invalid or unenforceable provision by a new provision which reflects, to the extent possible, the original intent of the parties.

5.9. Headings . All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.

IN WITNESS WHEREOF, the parties have caused this Agreement to be executed by their duly authorized representatives.

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EXHIBIT A

CONFIDENTIALITY AGREEMENT

Reference is made to that certain Exclusive License Agreement for Tuschl II United States Patents and Patent Applications (the “Exclusive License Agreement”) made as of March 14, 2011 by and between Alnylam Pharmaceuticals, Inc. (“Alnylam”) and University of Massachusetts (“UMass”). All capitalized terms not defined herein are defined in the Exclusive License Agreement. All parties that either have executed this Confidentiality Agreement or an undertaking thereto are defined, collectively, as the “Parties.”

WHEREAS, Alnylam may provide confidential and proprietary information identifying Targets and Excluded Targets (the “Alnylam Target Information”) to UMass, Merck & Co., Inc. (“Merck”), or the Gatekeeper, or any and all of them; and

WHEREAS, Merck may provide confidential and proprietary information identifying proposed Targets (the “Merck Target Information”) to the Gatekeeper; and

WHEREAS, it is understood and agreed by the Parties that such disclosures are solely in connection with the Exclusive License Agreement and not for any other purpose (the “Purposes”);

NOW, THEREFORE , the Parties hereto agree as follows:

1. Target Information . The Parties acknowledge and agree that the “Alnylam Target Information” is and will remain Alnylam’s confidential, proprietary information; and that the “Merck Target Information” is and will remain Merck’s confidential, proprietary information. The Alnylam Target Information and the Merck Target Information are defined, collectively, as the “Target Information.”

2. Treatment of Target Information . The Party receiving Target Information not otherwise known to it prior to disclosure is defined as the “Receiving Party.” The Party disclosing Target Information is defined as the “Disclosing Party.” All Target Information disclosed to the Receiving Party under the Exclusive License Agreement shall be governed by the following provisions:

a. Target Information may be used by solely in connection with the Purposes identified above.

b. No Receiving Party shall disclose or permit disclosure of any Target Information of the Disclosing Party to third parties or to employees of the Receiving Party, other than designated directors, officers, employees and agents who are required to have the information in order to perform the Parties’ authorized activities in connection with the Exclusive License Agreement. Each Receiving Party has had or will have its designated directors, officers, employees and agents who have access to Target Information of the Disclosing Party sign the undertaking annexed hereto as Schedule 1, and, upon request, shall notify the Disclosing Party in writing of the names of each person who has signed such agreements. Each Receiving Party agrees that it shall take all reasonable and necessary measures to protect the secrecy of and avoid disclosure or unauthorized use of Target

Information of the Disclosing party. Such measures shall include, but not be limited to, the highest degree of care that the Receiving Party utilizes to protect its own information of a similar nature, which shall be no less than reasonable care. Each Party agrees to notify the other in writing of any actual or suspected misuse, misappropriation, or unauthorized disclosure of Target Information of the Disclosing Party which may come to the Receiving Party’s attention and to cooperate with the Disclosing Party to stop and prevent such activities.

c. Unless otherwise agreed to by the Parties, Target Information disclosed under the Exclusive License Agreement shall at all times remain, as between the Parties, the property of the Disclosing Party. No license to use any trade secrets, copyrights, or other intellectual property rights is granted by this Agreement.

d. The Party providing the information shall determine the manner and form in which the Target Information will be disclosed.

e. In the event that the Receiving Party or any of its employees or agents become legally compelled (by deposition, interrogatory, request for documents, subpoena, civil investigative demand, court order, or similar process) to disclose any of the Target Information of the Disclosing Party, that Party or person from whom such information is being sought shall provide the other Party with prompt prior written notice of such requirement so that the other Party may seek a protective order or other appropriate remedy and/or waive compliance with the terms of this Agreement. In the event that such protective order or other remedy is not obtained, or the Disclosing Party waives compliance with the provisions hereof, the Receiving Party and its employees and agents agree to provide the Disclosing Party with information about what Target Information will be disclosed and to furnish only that portion of the Target Information of the Disclosing Party which is legally required to be furnished. The Receiving Party shall consult with Disclosing Party and exercise in good faith all reasonable efforts to mutually agree with the Disclosing Party regarding the nature, extent, and form of such production.

f. No Receiving Party will disclose to any person not a Party to this Agreement or authorized to review the Target information either the Target Information or the fact that the Receiving Party is in possession of the Target Information.

g. Public Information . The confidentiality provisions of this Agreement shall not apply to any Target Information that is published or becomes generally known to the public other than through the wrongful act of a Party hereto.

3. Disclosure to UMass Pursuant to Section 2.2 of the Exclusive License Agreement . If disclosure of Alnylam Target Information is made to UMass pursuant to Section 2.2 of the Exclusive License Agreement, in addition to the other provisions of this Confidentiality Agreement, such disclosure also shall be governed by the provisions of this Section 3 of this Confidentiality Agreement:

a. Prior to reviewing the Alnylam Target Information, the outside attorney designated by UMass shall sign the undertaking attached as Schedule 1 hereto.

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b. The Alnylam Target Information may not be copied or reproduced by any means.

c. The outside attorney may not disclose the Alnylam Target Information to anyone but may simply confirm or deny that as of the Effective Date, there are forty-one (41) Excluded Targets.

4. Disclosure to Gatekeeper Pursuant to Section 2.3 of the Exclusive License Agreement . If disclosure of Target Information is made to the Gatekeeper pursuant to Section 2.3 of the Exclusive License Agreement, in addition to the other provisions of this Confidentiality Agreement, such disclosure also shall be governed by the provisions of Section 4 of this Confidentiality Agreement:

a. Prior to receiving the Target Information, the Gatekeeper shall sign the undertaking attached as Schedule 1 hereto.

b. The Target Information may not be copied or reproduced by any means except as absolutely necessary to transmit the Target Information to the Receiving Party and for the Gatekeeper to comply with the requirements of Section 2.3 of the Exclusive License Agreement.

c. Notwithstanding Section 6 hereof, the Gatekeeper may not assign this Agreement to anyone without the written consent of all Parties.

5. Term . The Target Information shall remain governed by the terms of this Agreement during the Term of the Exclusive License Agreement.

6. Assignment, Successors and Assigns . No Party may assign this Agreement without the prior written consent of all Parties, except that Merck may assign it in connection with a merger, acquisition, or sale of substantially all the assets of the business relating to the Tuschl I and Tuschl II Patent Families. Nothing in this Agreement, express or implied, is intended to confer upon any Party other than the Parties hereto any rights, remedies, obligations, or liabilities under or by reason of this Agreement, except as expressly provided in this Agreement.

7. Amendment . This Confidentiality Agreement may be amended, modified, canceled, and/or waived only by a written instrument that expressly refers to this Confidentiality Agreement and is executed subsequent to the effective date of this Agreement by duly authorized representatives of each of the Parties hereto.

8. Authority . Each of the undersigned represents that he or she has been duly authorized to execute this Confidentiality Agreement on behalf of his or her respective clients or entities.

9. Damages Insufficient . Each Party hereto expressly agrees that due to the unique nature of the Disclosing Party’s Target Information, monetary damages would be inadequate to compensate the Disclosing Party for any breach by the Receiving Party of its covenants and agreements set forth in this Agreement. Accordingly, each Party agrees and acknowledges that any such violation or threatened violation shall cause irreparable injury to

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the Disclosing Party and that, in addition to any other remedies that may be available, in law, in equity or otherwise, the Disclosing Party shall be entitled to seek injunctive relief against the threatened breach of this Agreement or the continuation of any such breach by the Receiving Party, without the necessity of proving irreparable harm

10. Choice of Law . This Confidentiality Agreement shall be governed by, construed, and enforced in accordance with the laws of the Commonwealth of Massachusetts, without giving effect to its choice of law provisions.

11. Counterparts . This Confidentiality Agreement may be executed in counterparts, each of which counterpart shall be original, but together shall constitute one and the same instrument.

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SCHEDULE 1

UNDERTAKING

I, the undersigned, hereby agree and acknowledge that I am over the age of 18 and have read the Confidentiality Agreement and the Exclusive License Agreement and agree to be bound by the terms thereof. Specifically, I understand that by signing this Undertaking, I am bound by each of the terms of the Confidentiality Agreement. I represent and warrant that I have had the opportunity to consult with an attorney concerning the provisions of the Confidentiality Agreement and my responsibilities and have either done so or have elected not to do so.

1.

Exhibit C to Exclusive License Agreement:

US TUSCHL II PATENT FAMILY

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