Document:

exv10w26

Exhibit 10.26

Execution Version

FIRST AMENDMENT TO EMPLOYMENT AGREEMENT

     This First Amendment to Employment Agreement dated as of June 30, 2008 (this
“Amendment”) is entered into by and between Archemix Corp. (which, together with any parent
companies, subsidiaries, affiliates, successors and assigns shall be referred to as
“Archemix” or the “Company”), with its principal offices at 300 Third Street,
Cambridge, MA 02142, and Dr. Errol DeSouza (the “Executive”). Capitalized terms used but not
defined herein shall have the meanings ascribed to them in the Employment Agreement dated as of
March 7, 2003 by and between the Company and the Executive (the “Original Agreement”).

     WHEREAS, Section 9(c) of the Original Agreement provides that it may be amended only by
written agreement executed by the Company and the Executive; and

     WHEREAS, the Company the Executive desire to amend the Original Agreement as set forth below;

     NOW, THEREFORE, in consideration of the premises and the mutual covenants and agreements
herein contained, the parties hereby agree as follows:

     1. Amendments. Sections 2, 3 and 4 of the Original Agreement shall be deleted in
their entirety and replaced as set forth on Exhibit A hereto.

     2. Governing Law. This Amendment shall be governed by the internal laws of The
Commonwealth of Massachusetts, without regard to its principles of conflicts of laws, and shall
bind and inure to the benefit of the heirs, personal representatives, executors, administrators,
successors and assigns of the parties.

     3. Effect on Original Agreement. Except as specifically provided in this Amendment,
no other amendments, revisions or changes are made to the Original Agreement. All other terms and
conditions of the Original Agreement remain in full force and effect.

     4. Conforming References. Upon the effectiveness of this Amendment, each reference in
the Original Agreement to “this Agreement,” “hereunder,” “herein,” or other words of like import,
shall mean and be a reference to the Original Agreement as amended hereby.

     5. Counterparts. This Amendment may be executed in two or more counterparts, each of
which shall be deemed an original, but all of which together shall constitute one and the same
instrument.

 

 

SIGNATURE PAGE FOLLOWS

     IN WITNESS WHEREOF, the undersigned have duly executed this First Amendment to Employment
Agreement as of the day and year first above written.

	 	 	 	 	 	 	 
	 	 	ARCHEMIX CORP.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	     /s/ Peter Barrett
 

Peter Barrett
	 	 
	 

	 	 	 	Chairman, Compensation Committee	 	 
	 
	 	 	 	 	 	 
	 	 	EXECUTIVE	 	 
	 
	 	 	 	 	 	 
	 	 	     /s/ Errol B. De Souza	 	 
	 	 	 	 	 
	 	 	Dr. Errol B. De Souza	 	 

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EXHIBIT A

AMENDMENT TO EMPLOYMENT AGREEMENT

June 30, 2008

     2. Term of Employment; Definitions.

     (a) Employment At Will. The Executive’s employment hereunder will be on an “at-will”
basis and may be terminated by the Company or by the Executive at any time for any reason or for no
reason.

     (b) Definition of “Disability”. For purposes of this Agreement, “Disability” shall
mean the Executive’s failure due to illness, accident or any other physical or mental incapacity to
perform the essential functions of the Executive’s positions for ninety (90) consecutive days or an
aggregate of one hundred and twenty (120) days within any period of three hundred and sixty-five
(365) consecutive days during the term hereof. In the event Disability triggers payment of benefits
under Section 4 that are subject to Section 409A of the Internal Revenue Code of 1986, as amended
(“Section 409A”), Disability shall mean that, by reason of any medically determinable physical or
mental impairment that can be expected to result in death or can be expected to last for a
continuous period of not less than twelve (12) months, the Executive is unable to engage in any
substantial gainful activity or is receiving income replacement benefits for a period of not less
than three months under an accident and health plan covering employees of the Company

     (c) Definition of “Cause”. For purposes of this Agreement, “Cause” means any of the
following:

	 	(i)	 	a continuing failure by the Executive to render services to the
Company in accordance with the Executive’s assigned duties (other than such a
failure as a result of Disability);
	 
	 	(ii)	 	any act or omission by the Executive involving willful
misconduct or gross negligence which results in material harm to the
Company; 
	 
	 	(iii)	 	the Executive’s commission of any felony or any fraud,
financial wrongdoing, willful disloyalty, deliberate dishonesty or breach of
fiduciary duty in connection with the performance of the Executive’s
obligations to the Company AND which materially and adversely affects the
business activities, reputation, or goodwill of the Company;
	 
	 	(iv)	 	the Executive’s deliberate disregard of a Company rule or
policy which materially and adversely affects the business activities,
reputation, or goodwill of the Company; or

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	 	(vi)	 	the Executive’s material breach of this Agreement.

In the event of a termination for Cause, the Termination Notice given to the Executive by the
Company shall state that the termination of employment is “for Cause.” Such written notice shall
specify the particular act or acts, or failure to act, which is or are the basis for the decision
to so terminate the Executive’s employment for Cause. The Executive shall be given the opportunity
within thirty (30) calendar days of the receipt of such notice to meet with the Board to defend
such act or acts, or failure to act, and the Executive shall be given fifteen (15) days after such
meeting to cure such act (or failure to act) to the Board’s reasonable satisfaction. Upon failure
of the Executive, within such latter fifteen (15) day period, to so cure such act or failure to
act, the Executive’s employment by the Company shall be deemed terminated for Cause. All other
terminations initiated by the Company (other than due to Disability) shall be referred to as
termination without Cause.

     (d) Definition of “Good Reason”. For purposes of this Agreement, any termination of
employment initiated by the Executive within ninety (90) days following the occurrence, without the
Executive’s prior written consent, of any of the following events shall be a termination with Good
Reason and the Company shall be given at least thirty (30) days prior written notice of any such
Termination with Good Reason, and the Company shall have fifteen (15) days after such notice to
cure such occurrence.

	 	(i)	 	The appointment of a President or CEO other than the Executive
to serve in such position(s) during the term of the Executive’s employment
hereunder without the Executive’s consent;
	 
	 	(ii)	 	Any material reduction in the Executive’s responsibilities or
authority within the Company, including, without limitation, a change in the
lines of reporting such that the Executive no longer reports to the Board;
	 
	 	(iii)	 	A reduction in the Executive’s compensation except such a
reduction in connection with a reduction in compensation of other Company
executives at the level of senior management or with the Executive’s consent;
	 
	 	(iv)	 	A material breach of this Agreement by the Company;
	 
	 	(v)	 	Any failure by the Company to have this Agreement explicitly
assumed by a successor;
	 
	 	(vi)	 	Any material reduction in the Executive’s welfare benefits in
the aggregate (other than any across the board reduction imposed on
substantially all other members of the Company’s senior management); or
	 
	 	(vii)	 	Any relocation of the Executive’s principal office location to
a location more than thirty-five (35) miles from the Boston metropolitan area.

     All other terminations initiated by the Executive shall be considered termination without Good
Reason.

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     (e) Definition of “Change in Control”. For purposes of this Agreement, “Change in
Control” means an event or occurrence set forth in any one or more of the following in any one
transaction or series of transactions occurring within a 12-month period:

	 	(i)	 	the acquisition by an individual, entity or group (within the
meaning of Section 13(d) or 14(d) of the Securities Exchange Act of 1934, as
amended (the “Exchange Act”)) (a “Person”) of beneficial ownership of any
capital stock of the Company if, after such acquisition, such Person
beneficially owns (within the meaning of Rule 13d-3 promulgated under the
Exchange Act) more than 50% of the combined voting power of the
then-outstanding securities of the Company entitled to vote generally in the
election of directors (the “Outstanding Company Voting Securities”); provided,
however, that for purposes of this subsection (i), the following acquisitions
shall not constitute a Change in Control: (A) any acquisition directly from the
Company (excluding an acquisition pursuant to the exercise, conversion or
exchange of any security exercisable for, convertible into or exchangeable for
common stock or voting securities of the Company, unless the Person exercising,
converting or exchanging such security acquired such security directly from the
Company), (B) any acquisition by the Company, (C) any acquisition by any
employee benefit plan (or related trust) sponsored or maintained by the Company
or any corporation controlled by the Company, or (D) any acquisition of more
than 50% but less than 80% of the capital stock of the Company by one or more
financial investors, such as venture capital or private equity firms; or
	 
	 	(ii)	 	the consummation of a merger, consolidation, reorganization,
recapitalization or share exchange involving the Company, or a sale or other
disposition of assets of the Company having a total gross fair market value
equal to or more than 40% of the total gross fair market value of the assets of
the Company immediately before such sale or disposition (a “Business
Combination”), unless, immediately following such Business Combination, the
individuals and entities who were the beneficial owners of the Outstanding
Company Voting Securities immediately prior to such Business Combination
beneficially own, directly or indirectly, more than 50% of the combined voting
power of the then-outstanding securities of the resulting or acquiring
corporation in such Business Combination (which shall include, without
limitation, a corporation which as a result of such transaction owns the
Company or substantially all of the Company’s assets either directly or through
one or more subsidiaries) (such resulting or acquiring corporation is referred
to herein as the “Acquiring Corporation”).

In no event shall any of the forgoing events or occurrences constitute a Change in Control under
this Agreement if it results from the acquisition by any one person, or more than one person

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acting
as a group, owning more than 50% of the total fair market value or total voting power of
the Company’s stock, of additional stock of the Company. In all cases, the determination of
whether a Change of Control has occurred shall be interpreted in a manner consistent with the
definition of a change in control under Section 409A of the Internal Revenue Code of 1986, as
amended (“Section 409A”).

     3. Compensation.

     (a) Base Salary. Effective as of January 1, 2008, and during the period that the
Executive is employed by the Company, the Company will pay the Executive a base salary at the
annualized rate of not less than $458,650, less customary deductions for taxes, benefit
contributions and the like (the “Base Salary”). The Base Salary of the Executive for each calendar
year subsequent to 2008 will be reviewed by the Board and may be increased, but not decreased, in
the Board’s sole discretion. The Base Salary will be payable in substantially equal installments
in accordance with the Company’s payroll practices as in effect from time to time. The Executive
understands and acknowledges that the annualized amount of the Base Salary is set forth as a matter
of convenience and does not constitute nor will be deemed to constitute an agreement by the Company
to employ the Executive for any specific period of time.

     (b) Bonus. In addition to the Base Salary, the Executive shall be eligible to receive
a bonus for his service during 2008 and each subsequent calendar year equal to up to fifty percent
(50%) of the Base Salary for 2008 or such subsequent calendar year (the “Performance Bonus”). The
award and amount of any Performance Bonus shall be determined based on criteria set at the sole
discretion of the Compensation Committee of the Board. Any Performance Bonus will be determined
and distributed on or before the 15th day of the third month following the earlier of
the end of the fiscal year or the Executive’s cessation of employment.

     (c) Equity Compensation. Notwithstanding anything to the contrary in the individual
agreements governing the stock options issued to the Executive under the Company’s 2001 Employee,
Director and Consultant Stock Plan, as amended (the “Plan”), if the Executive ceases to be an
employee of the Company or of an Affiliate (for any reason other than termination of the
Executive’s employment for Cause), each stock option issued to the Executive may be exercised, if
it has not previously terminated, within thirty-six (36) months after the date the Executive ceases
to be an employee of the Company or an Affiliate, or within the originally prescribed term of such
option, whichever is earlier, but may not be exercised thereafter. In such event, each such option
shall be exercisable only to the extent that such option has become exercisable and is in effect at
the date of such cessation of employment. If any such option was an ISO, any portion exercised
after three (3) months from termination of employment will be a Non-Qualified Option and not an
ISO. Any terms not defined herein shall be defined as set forth in the Plan or applicable option
agreement.

     (d) Vacation. The Executive will be entitled to paid vacation in each calendar year
and paid holidays and personal days in accordance with the Company’s policies for its senior
executives as in effect from time to time.

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     (e) Fringe Benefits. The Executive will be entitled to participate in any employee
benefit plans which the Company provides or may establish for the benefit of its senior
executives generally (including, but not limited to, group life, disability, medical, dental
and other insurance, retirement, pension, profit-sharing and similar plans) (collectively, the
“Fringe Benefits”), provided that the Fringe Benefits will not include any stock option or similar
plans relating to the grant of equity securities of the Company except as provided herein. The
Executive’s eligibility to participate in the Fringe Benefits and receive benefits thereunder will
be subject to the plan documents governing such Fringe Benefits. Nothing contained herein will
require the Company to establish or maintain Fringe Benefits

     (f) Reimbursement of Expenses. During the term of this Agreement, the Company shall
reimburse the Executive, in accordance with the policies and practices of the Company in effect
from time to time during such term, for all reasonable and necessary traveling expenses and other
disbursement incurred by the Executive for or on behalf of the Company in connection with the
performance of the Executive’s duties hereunder upon presentation by the Executive to the Company
of appropriate receipts and documentation therefore, as the Company may reasonably deem to be
necessary. In addition, upon submission of reasonably detailed invoices, the Company will pay or
reimburse the Executive for up to $10,000 (on an after-tax basis) for financial planning services
each year that the Executive is employed pursuant to this Agreement. The Executive must submit any
request for reimbursement no later than ninety (90) days following the date that such business
expense is incurred in accordance with the Company’s reimbursement policy regarding same. The
Company may request additional documentation or a further explanation to substantiate any business
expense submitted for reimbursement and retains the discretion to approve or deny a request for
reimbursement. Any reimbursement in one calendar year shall not affect the amount that may be
reimbursed in any other calendar year, and a reimbursement (or right thereto) may not be exchanged
or liquidated for another benefit or payment. Any business expense reimbursements subject to
Section 409A of the Code shall be made no later than the end of the calendar year following the
calendar year in which such business expense is incurred by the Executive.

     4. Severance Compensation.

     (a) In the event of any termination of the Executive’s employment hereunder for any reason or
for no reason, the Company (i) will pay to the Executive (or to the Executive’s estate) (A) the
portion of the Executive’s Base Salary that has accrued prior to such termination and has not yet
been paid and (B) an amount equal to the value of the Executive’s accrued unused vacation days, and
(ii) will reimburse the Executive (or the Executive’s estate) for expenses properly incurred and
documented by the Executive on behalf of the Company prior to such termination in accordance with
Company policy (collectively, the “Accrued Obligations”). Such amounts will be paid within 10 days
in cash in lump sum after termination of employment.

     (b) Prior to a Change in Control, if the Executive’s employment is terminated by the Company
without Cause or by the Executive for Good Reason, then the Executive shall be entitled to receive
the following in addition to the Accrued Obligations; provided that Executive executes and submits
a general release of all claims against the Company (including its officers,

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directors, employees
and affiliates) in a form provided by the Company (a “General Release”) and substantially as
attached hereto as Appendix 1:

	 	(i)	 	Continued Salary. The Company will continue to pay to
the Executive his Base Salary for a minimum period of twelve (12) months, with
a continuance for each month or partial month that the Executive has not
obtained full-time employment, up to an aggregate total of eighteen (18) months
(the period of payment of Executive’s Base Salary after the twelfth month being
referred to herein as the “Salary Extension Period”); provided, however, that
in the event the Executive obtains full-time employment prior to the end of
eighteen (18) months with a salary (“New Salary”) that is less than his Base
Salary at the time of the termination of his employment, then for each such
month or partial month through the eighteenth month, the Company will pay the
Executive the difference between his Base Salary and his New Salary. Such
payments shall be payable in accordance with the Company’s payroll practices as
in effect from time to time; provided, however, that if Executive wishes to
exercise any vested stock options issued to him under the Plan (including,
without limitation, options accelerated pursuant to clause (iv) below), then
the Company will pay him in a lump sum the amount of funds required to do so
(subject to the withholding and other normal payroll deductions) and Executive
will use such funds to exercise such options. The amount paid pursuant to the
preceding proviso shall be applied to the latest Base Salary payments due in
the twelve (12) month period following termination;
	 
	 	(ii)	 	Bonus. Within thirty (30) days after such termination
of employment, the Company will pay to the Executive the full amount of his
target Performance Bonus for the calendar year in which the termination occurs;
within thirty (30) days after the 12 month anniversary of such termination of
employment the Company will pay to the Executive the full amount of his target
Performance Bonus for the calendar year in which the termination occurs; and if
there is any Salary Extension Period, the Company will pay to the Executive
within thirty (30) days after the end of the Salary Extension Period, a prorata
portion of his target Performance Bonus for the calendar year in which the
termination occurs determined by multiplying the full amount of his target
Performance Bonus for the calendar year in which the termination occurs by the
quotient obtained by dividing the number of months in the Salary Extension
Period by 12;
	 
	 	(iii)	 	Continued Health Insurance. The Company will continue
to provide the Executive with group health insurance and continue to pay the
amount of the premium as in effect on the date of such termination for the same
period of time as the Base Salary is continued pursuant to Section 4(b)(i),
commencing on the effective date of such termination, subject to applicable law
and the terms of the respective policies. The foregoing will

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	 	 	 	constitute
continuation coverage under the Consolidated Omnibus Budget Reconciliation Act
(“COBRA”), will be subject to the Executive’s valid election of such
continuation benefits under COBRA, will be administered
in accordance with the requirements of COBRA and will not be construed to
extend any period of continuation coverage required by law; and

	 	(iv)	 	Accelerated Vesting. Any unvested portion of any stock
options issued to the Executive under the Plan will immediately vest with
respect to an additional number of shares that would have vested over the
thirty-six (36) month period following the termination of employment.

     (c) Upon or subsequent to a Change in Control, if the Executive’s employment is terminated by
the Company without Cause or by the Executive for Good Reason, and provided that the Executive
executes and submits a General Release, then the Executive shall be entitled to receive the
following, in addition to the Accrued Obligations:

	 	(i)	 	Continued Salary. The Company will pay to the
Executive an amount equal to eighteen (18) months of Base Salary;
	 
	 	(ii)	 	Bonus. Within thirty (30) days after such termination
of employment, the Company will pay to the Executive the full amount of his
target Performance Bonus for the calendar year in which the termination occurs;
and within thirty (30) days after the eighteen (18) month anniversary of such
termination of employment the Company will pay to the Executive one hundred
fifty percent (150%) of the full amount of his target Performance Bonus for
the calendar year in which the termination occurs;
	 
	 	(iii)	 	Continued Health Insurance. The Company will continue
to provide the Executive with group health insurance and continue to pay the
amount of the premium as in effect on the date of such termination for a period
of eighteen months, commencing on the effective date of such termination,
subject to applicable law and the terms of the respective policies. The
foregoing will constitute continuation coverage under the Consolidated Omnibus
Budget Reconciliation Act (“COBRA”), will be subject to the Executive’s valid
election of such continuation benefits under COBRA, will be administered in
accordance with the requirements of COBRA and will not be construed to extend
any period of continuation coverage (e.g., COBRA) required by law; and
 
	 
	 	(iv)	 	Accelerated Vesting. Any unvested portion of any stock
options issued to the Executive under the Plan will immediately vest.

     (d) In the event of the termination of the Executive’s employment hereunder by Company for
Cause, the Company will pay the Accrued Obligations to the Executive.

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     (e) In the event of the termination of the Executive’s employment due to Disability or death,
the Executive (or his estate or representatives) shall be entitled to receive all Accrued
Obligations. In addition, the unvested portion of any stock options issued to the Executive under
the Plan will immediately vest with respect to an additional number of shares that would have
vested over the twelve (12) month period following the termination of employment.

     (f) Notwithstanding the forgoing, if any benefits provided under this Section 4 are deferred
compensation under Section 409A, any termination of employment triggering payment of such benefit
must be a “separation from service” under Section 409A before payment of such benefits under the
terms of this Agreement may commence. Further, if the Executive is a “specified employee” under
Section 409A as of the date of his or her termination of employment hereunder, then, to the extent
necessary to avoid the imposition of excise taxes or other penalties under Section 409A, the
payment of benefits by the Company under this Agreement, if any, that were scheduled to be paid to
the Executive during the first six (6) months following the date of his or her termination of
employment shall not be paid until the date that is the first business day following the last day
of the six (6)-month period following the Executive’s termination of employment, at which time such
delayed deferred compensation payments shall be paid in a lump sum. The terms of this Agreement
shall be interpreted in a manner consistent with the provisions of Section 409A. Regardless of the
forgoing or any other provision in this Agreement, the Company makes no guarantees as to the tax
consequences related to any payments under this Agreement or otherwise under Section 409A.

     (g) Notwithstanding the forgoing, if any benefits provided under this Section 4, taken
together with any other payments or distributions by the Company to or for the benefit of the
executive, otherwise would constitute in whole or in part an “excess parachute payment” under
Section 280G of the Code, the payments to the Executive under this Agreement shall be reduced to
the extent necessary to avoid the application of Section 280G. The Company may elect, in the
alternative, to seek stockholder approval in accordance with Section 280G with respect to such
payments, provided that in no event shall the Company be deemed to have guaranteed any particular
outcome with respect to such stockholder vote. The Company shall not be deemed to have guaranteed
any particular tax consequences under Section 280G to the Executive.

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APPENDIX 1

GENERAL RELEASE

     1. General Release. In consideration of the payments and benefits to be made under that
certain Employment Agreement dated as of March 7, 2003, as amended by the First Amendment to
Employment Agreement dated as of June 30, 2008, (the “Agreement”), Errol DeSouza (the “Executive”),
with the intention of binding the Executive and the Executive’s heirs, executors, administrators
and assigns, does hereby release, remise, acquit and forever discharge Archemix Corp. (the
“Company”) and each of its subsidiaries and affiliates (the “Company Affiliated Group”), their
present and former officers, directors, executives, agents, attorneys, employees and employee
benefits plans (and the fiduciaries thereof), and the successors, predecessors and assigns of each
of the foregoing (collectively, the “Company Released Parties”), of and from any and all claims,
actions, causes of action, complaints, charges, demands, rights, damages, debts, sums of money,
accounts, financial obligations, suits, expenses, attorneys’ fees and liabilities of whatever kind
or nature in law, equity or otherwise, whether accrued, absolute, contingent, unliquidated or
otherwise and whether now known or unknown, suspected or unsuspected which the Executive,
individually or as a member of a class, now has, owns or holds, or has at any time heretofore had,
owned or held, against any Company Released Party in any capacity, including, without limitation,
any and all non-waivable claims (i) arising out of or in any way connected with the Executive’s
service to any member of the Company Affiliated Group (or the predecessors thereof) in any
capacity, or the termination of such service in any such capacity, (ii) for severance or vacation
benefits, unpaid wages, salary or incentive payments, (iii) for breach of contract, wrongful
discharge, impairment of economic opportunity, defamation, intentional infliction of emotional harm
or other tort and (iv) for any violation of applicable state and local labor and employment laws
(including, without limitation, all laws concerning unlawful and unfair labor and employment
practices), any and all claims based on the Executive Retirement Income Security Act of 1974
(“ERISA”), any and all claims arising under the civil rights laws of any federal, state or local
jurisdiction, including, without limitation, Title VII of the Civil Rights Act of 1964 (“Title
VII”), the Americans with Disabilities Act (“ADA”), the Age Discrimination in Employment Act
(“ADEA”), Sections 503 and 504 of the Rehabilitation Act, and any and all claims under any
whistleblower laws or whistleblower provisions of other laws, excepting only:

	 	(a)	 	rights of the Executive under this General Release and the
Agreement;
	 
	 	(b)	 	rights of the Executive relating to equity awards held by the
Executive as of his or her Date of Termination (as defined in the Agreement);
	 
	 	(c)	 	the right of the Executive to receive COBRA continuation
coverage in accordance with applicable law;

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	 	(d)	 	rights to indemnification the Executive may have (i) under
applicable corporate law, (ii) under the by-laws or certificate of
incorporation of any
Company Released Party or (iii) as an insured under any director’s and
officer’s liability insurance policy now or previously in force;
	 
	 	(e)	 	claims (i) for benefits under any health, disability,
retirement, deferred compensation, life insurance or other, similar Executive
benefit plan or arrangement of the Company Affiliated Group and (ii) for earned
but unused vacation pay through the Date of Termination in accordance with
applicable Company policy; and
	 
	 	(f)	 	claims for the reimbursement of unreimbursed business expenses
incurred prior to the Date of Termination pursuant to applicable Company
policy.

     2. No Admissions. The Executive acknowledges and agrees that this General Release is not to be
construed in any way as an admission of any liability whatsoever by any Company Released Party, any
such liability being expressly denied.

     3. Application to all Forms of Relief. This General Release applies to any relief no matter
how called, including, without limitation, wages, back pay, front pay, compensatory damages,
liquidated damages, punitive damages for pain or suffering, costs and attorney’s fees and expenses.

     4. Specific Waiver; Exclusions. The Executive specifically acknowledges that his or her
acceptance of the terms of this General Release is, among other things, a specific waiver of his or
her rights, claims and causes of action under Title VII, ADEA, ADA and any state or local law or
regulation in respect of discrimination of any kind; provided, however, that nothing herein shall
be deemed, nor does anything herein purport, to constitute or require a waiver of any right or
claim or cause of action which by law the Executive is not permitted to waive.

     5. No Complaints or Other Claims. The Executive acknowledges and agrees that neither he/she
nor any of his/her agents or assigns has, with respect to any transaction or state of facts
existing prior to the date hereof, filed any complaints, charges or lawsuits against any Company
Released Party with any governmental agency, court or tribunal.

     6. Additional Obligations And Covenants. In consideration of the payments and benefits
offered to be made under the Agreement, and for other good and valuable consideration, receipt of
which is hereby acknowledged by the Executive, the Executive agrees to the following additional
obligations and covenants:

	 	(a)	 	Confidentiality. The Executive shall not, without the prior written
consent of the Company or as may otherwise be required by law or any legal
process, communicate to anyone other than the Company and those designated by the
Company or on behalf of the Company in the furtherance of its business, any 

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	 	 	 	trade
secrets, confidential information, knowledge or data relating to any member of the
Company Affiliated Group, obtained by the Executive during the Executive’s
employment by the Company that is not generally available
public knowledge (other than by acts by the Executive in violation of this
General Release).

	 	(b)	 	Return of Company Material. The Executive represents that, as of the
date he or she signs this Agreement, he or she has returned to the Company all
Company Material (as defined below). For purposes of this Section 6(b), “Company
Material” means any documents, files and other property and information of any
kind belonging or relating to (i) any member of the Company Affiliated Group, (ii)
the current and former suppliers, creditors, directors, officers, employees,
agents and customers of any of them or (iii) the businesses, products, services
and operations (including without limitation, business, financial and accounting
practices) of any of them, in each case whether tangible or intangible (including,
without limitation, credit cards, building and office access cards, keys, computer
equipment, cellular telephones, pagers, electronic devices, hardware, manuals,
files, documents, records, software, customer data, research, financial data and
information, memoranda, surveys, correspondence, statistics and payroll and other
employee data, and any copies, compilations, extracts, excerpts, summaries and
other notes thereof or relating thereto), excluding only information (x) that is
generally available public knowledge or (y) that relates to the Executive’s
compensation or Executive benefits.
	 
	 	(c)	 	Cooperation. Following the Termination Date, the Executive shall
reasonably cooperate with the Company upon reasonable request of the Board and be
reasonably available to the Company with respect to matters arising out of the
Executive’s services to the Company Affiliated Group.
	 
	 	(d)	 	Nondisparagement. The Executive agrees not to communicate negatively
about or otherwise disparage any Company Released Party or the products or
businesses of any of them in any way whatsoever.
	 
	 	(e)	 	Nonsolicitation. The Executive agrees that for the period of time
beginning on the date hereof and ending on the second anniversary of the
Executive’s Date of Termination, the Executive shall not, either directly or
indirectly, solicit, entice, persuade, induce or otherwise attempt to influence
any person who is employed by any member of the Company Affiliated Group to
terminate such person’s employment by such member of the Company Affiliated Group.
The Executive also agrees that for the same period of time he or she shall not
assist any person or entity in the recruitment of any person who is employed by
any member of the Company Affiliated Group. The Executive’s provision of a

11

 

	 	 	 	reference to or in respect of any individual shall not be a violation this Section
6(e).

     7. Conditions of General Release.

	 	(a)	 	Terms and Conditions. From and after the Date of Termination, the
Executive shall abide by all the terms and conditions of this General Release and
the terms and any conditions set forth in any employment or confidentiality
agreements signed by the Executive, which is incorporated herein by reference.
	 
	 	(b)	 	No Representation. The Executive acknowledges that, other than as set
forth in this General Release and the Agreement, (i) no promises have been made to
him or her and (ii) in signing this General Release the Executive is not relying
upon any statement or representation made by or on behalf of any Company Released
Party and each or any of them concerning the merits of any claims or the nature,
amount, extent or duration of any damages relating to any claims or the amount of
any money, benefits, or compensation due the Executive or claimed by the
Executive, or concerning the General Release or concerning any other thing or
matter.
	 
	 	(c)	 	Injunctive Relief. In the event of a breach or threatened breach by
the Executive of any provision of this General Release, the Executive agrees that
the Company shall be entitled to injunctive relief in a court of appropriate
jurisdiction to remedy any such breach or threatened breach, the Executive
acknowledging that damages would be inadequate or insufficient.

     8. Voluntariness. The Executive agrees that he or she is relying solely upon his or her own
judgment; that the Executive is over eighteen years of age and is legally competent to sign this
General Release; that the Executive is signing this General Release of his or her own free will;
that the Executive has read and understood the General Release before signing it; and that the
Executive is signing this General Release in exchange for consideration that he or she believes is
satisfactory and adequate.

     9. Legal Counsel. The Executive acknowledges that he or she has been informed of the right to
consult with legal counsel and has been encouraged to do so.

     10. Complete Agreement/Severability. This General Release (excepting                     , which are
incorporated by reference and shall survive the signing of this document) constitutes the complete
and final agreement between the parties and supersedes and replaces all prior or contemporaneous
agreements, negotiations, or discussions relating to the subject matter of this General Release.
All provisions and portions of this General Release are severable. If any provision or portion of
this General Release or the application of any provision or portion of the General Release shall be
determined to be invalid or unenforceable to any extent or for any reason, all other provisions and
portions of this General Release shall remain in full force and shall continue to be enforceable to
the fullest and greatest extent permitted by law.

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     11. ADEA/OWBP Acceptance and Revocation Period. It is the Company’s desire and intent to make
certain that the Executive fully understands the provisions and effects of this General Release To
that end, he or she has been encouraged and given the opportunity to consult with legal counsel for
the purpose of reviewing the terms of this document. Also, because the
Executive is over the age of 40, and consistent with the provisions of the ADEA, which prohibits
discrimination on the basis of age, the Executive acknowledges that he or she has been given a
period of twenty-one (21) days within which to consider this General Release, unless applicable law
requires a longer period, in which case the Executive shall be advised of such longer period and
such longer period shall apply. The Executive may accept this General Release at any time within
this period of time by signing the General Release and returning it to the Company. This General
Release shall not become effective or enforceable until seven (7) calendar days after the Executive
signs it. The Executive may revoke his or her acceptance of this General Release at any time within
that seven (7) calendar day period by sending written notice to the Company. Such notice must be
received by the Company within the seven (7) calendar day period in order to be effective and, if
so received, would void this General Release for all purposes.

     Consistent with the provisions of the ADEA and other federal discrimination laws, nothing in
this General Release shall be deemed to prohibit the Executive from challenging the validity of
this release under the federal age or other discrimination laws (the “Federal Discrimination Laws”)
or from filing a charge or complaint of age or other employment related discrimination with the
Equal Employment Opportunity Commission (“EEOC”), or from participating in any investigation or
proceeding conducted by the EEOC. Further, nothing in this General Release shall be deemed to
limit the Company’s right to seek immediate dismissal of such charge or complaint on the basis that
the Executive’s signing of this General Release constitutes a full release of any individual rights
under the Federal Discrimination Laws, or to seek restitution to the extent permitted by law of the
economic benefits provided to the Executive under the Agreement in the event that the Executive
successfully challenges the validity of this release and prevail in any claim under the Federal
Discrimination Laws.

     12. Governing Law; Jurisdiction. Except for issues or matters as to which federal law is
applicable, this General Release shall be governed by and construed and enforced in accordance with
the laws of the Commonwealth of Massachusetts without giving effect to the conflicts of law
principles thereof. Both parties agree that any action, demand, claim or counterclaim relating to
the terms and provisions of this Agreement , or to its breach, shall be commenced in a court of
competent jurisdiction in Massachusetts and that venue shall lie exclusively in Middlesex or
Suffolk County, Massachusetts. Both parties further agree that any action, demand, claim or
counterclaim shall be resolved by a judge alone, and both parties hereby waive and forever renounce
the right to a trial before a civil jury.

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     IN WITNESS WHEREOF, the Executive has executed this General Release as of the date last set
forth below.

	 	 	 	 	 	 	 	 	 
	 	 	ARCHEMIX CORP.	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	By: 	 	 	 	 	 	 
	 	 	 	 	 	 
	 

	 	 	Name:	 	 	 	 
	 

	 	 	Title:	 	 	 	 
	 

	 	 	Date:	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	EXECUTIVE	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	Signature:
	 	 
	 

	 	 	 	 	 	 	 	 
	 	 	Printed Name:
	 	 
	 

	 	 	 	 	 	 	 	 
	 	 	Date:
	 	 
	 

	 	 	 	 	 	 	 	 

14exv10w31

Exhibit 10.31

FORM OF

ARCHEMIX CORP.

CHANGE IN CONTROL AGREEMENT

     THIS CHANGE IN CONTROL AGREEMENT (this “Agreement”), by and between Archemix Corp., a Delaware
corporation (the “Company”), and                      (the “Executive”), is made as of
September 30, 2008 (the “Effective Date”).

     WHEREAS, the Company recognizes that the possibility of a Change in Control (as defined in
Section 1.1) of the Company exists and that such possibility, and the uncertainty and questions
which it may raise among key personnel, may result in the departure or distraction of key personnel
to the detriment of the Company and its stockholders, and

     WHEREAS, the Board of Directors of the Company (the “Board”) has determined that appropriate
steps should be taken to reinforce and encourage the continued employment and dedication of the
Company’s key personnel without distraction from the possibility of a Change in Control of the
Company and related events and circumstances.

     NOW, THEREFORE, as an inducement for and in consideration of the Executive remaining in its
employ, the Company agrees that the Executive shall receive the benefits set forth in this
Agreement in the event the Executive’s employment with the Company is terminated under the
circumstances described below in connection with a Change in Control.

     1. Key Definitions.

     As used herein, the following terms shall have the following respective meanings:

     1.1 “Anticipatory Termination” means a termination of the employment of Executive by the
Company under the following circumstances: (a) a Change in Control occurs, (b) the Executive’s
employment with the Company is terminated prior to the date on which the Change in Control occurs,
and (c) it is reasonably demonstrated by the Executive that such termination of employment (i) was
at the request of a third party who has taken steps reasonably calculated to effect a Change in
Control or (ii) otherwise arose in connection with or in anticipation of a Change in Control.

     1.2 “Change in Control” means an event or occurrence set forth in any one or more of the
following in any one transaction or series of transactions occurring within a 12-month period:

	 	(a)	 	the acquisition by an individual, entity or group (within the
meaning of Section 13(d) or 14(d) of the Securities Exchange Act of 1934, as
amended (the “Exchange Act”)) (a “Person”) of beneficial ownership of any
capital stock of the Company if, after such acquisition, such Person
beneficially owns (within the meaning of Rule 13d-3 promulgated under the
Exchange Act) more than 50% of the combined voting power of the

1

 

	 	 	 	then-outstanding securities of the Company entitled to vote generally in the
election of directors (the “Outstanding Company Voting Securities”);
provided, however, that for purposes of this subsection (a), the following
acquisitions shall not constitute a Change in Control: (i) any acquisition
directly from the Company (excluding an acquisition pursuant to the
exercise, conversion or exchange of any security exercisable for,
convertible into or exchangeable for common stock or voting securities of
the Company, unless the Person exercising, converting or exchanging such
security acquired such security directly from the Company), (ii) any
acquisition by the Company, or (iii) any acquisition by any employee benefit
plan (or related trust) sponsored or maintained by the Company or any
corporation controlled by the Company; or

	 	(b)	 	the consummation of a merger, consolidation, reorganization,
recapitalization or share exchange involving the Company, or a sale or other
disposition of assets of the Company having a total gross fair market value
equal to or more than 40% of the total gross fair market value of the assets of
the Company immediately before such sale or disposition (a “Business
Combination”), unless, immediately following such Business Combination, the
individuals and entities who were the beneficial owners of the Outstanding
Company Voting Securities immediately prior to such Business Combination
beneficially own, directly or indirectly, more than 50% of the combined voting
power of the then-outstanding securities of the resulting or acquiring
corporation in such Business Combination (which shall include, without
limitation, a corporation which as a result of such transaction owns the
Company or substantially all of the Company’s assets either directly or through
one or more subsidiaries) (such resulting or acquiring corporation is referred
to herein as the “Acquiring Corporation”).

          In no event shall any of the forgoing events or occurrences constitute a Change in Control
under this Agreement if it results from the acquisition by any one person, or more than one
person acting as a group, owning more than 50% of the total fair market value or total voting
power of the Company’s stock, of additional stock of the Company. In all cases, the
determination of whether a Change of Control has occurred shall be interpreted in a manner
consistent with the definition of a change in control under Section 409A of the Internal Revenue
Code of 1986, as amended (“Section 409A”).

     1.3 “Change in Control Date” means the first date during the Term (as defined in Section 2,
including any extension thereof) on which a Change in Control occurs.

     1.4 “Cause” means any of the following:

	 	(a)	 	a continuing failure by the Executive to render services to the
Company in accordance with the Executive’s assigned duties (other than such a
failure as a result of Disability);

2

 

	 	(a)	 	any act or omission by the Executive involving willful
misconduct or gross negligence which results in material harm to the
Company; 

	 	(a)	 	the Executive’s commission of any felony or any fraud,
financial wrongdoing, willful disloyalty, deliberate dishonesty or breach of
fiduciary duty in connection with the performance of the Executive’s
obligations to the Company AND which materially and adversely affects the
business activities, reputation, or goodwill of the Company;
	 
	 	(a)	 	the Executive’s deliberate disregard of a Company rule or
policy which materially and adversely affects the business activities,
reputation, or goodwill of the Company; or
	 
	 	(vi)	 	the Executive’s material breach of this Agreement.

In the event of a termination for Cause, the Termination Notice given to the Executive by the
Company shall state that the termination of employment is “for Cause.” Such written notice shall
specify the particular act or acts, or failure to act, which is or are the basis for the decision
to so terminate the Executive’s employment for Cause. The Executive shall be given the opportunity
within thirty (30) calendar days of the receipt of such notice to meet with the Board to defend
such act or acts, or failure to act, and the Executive shall be given fifteen (15) days after such
meeting to cure such act (or failure to act) to the Board’s reasonable satisfaction. Upon failure
of the Executive, within such latter fifteen (15) day period, to so cure such act or failure to
act, the Executive’s employment by the Company shall be deemed terminated for Cause. All other
terminations initiated by the Company (other than due to Disability) shall be referred to as
termination without Cause.

     1.5 “Disability” means the Executive’s failure due to illness, accident or any other physical
or mental incapacity to perform the essential functions of the Executive’s positions for ninety
(90) consecutive days or an aggregate of one hundred and twenty (120) days within any period of
three hundred and sixty-five (365) consecutive days during the term hereof. In the event Disability
triggers payment of benefits under Section 4 that are subject to Section 409A of the Internal
Revenue Code of 1986, as amended (“Section 409A”), Disability shall mean that, by reason of any
medically determinable physical or mental impairment that can be expected to result in death or can
be expected to last for a continuous period of not less than twelve (12) months, the Executive is
unable to engage in any substantial gainful activity or is receiving income replacement benefits
for a period of not less than three months under an accident and health plan covering employees of
the Company.

     1.6 “Good Reason” means the occurrence, without the Executive’s written consent, of any of the
events or circumstances set forth in clauses (a) through (e) below.

	 	(a)	 	any material diminution in the Executive’s duties, authority or
responsibilities as in effect immediately prior to the earliest to occur of (i)
the Change in Control Date, (ii) the date of the execution by the Company of
the initial written agreement or instrument providing for the Change in Control
or (iii) the date of the adoption by the Board of Directors of a

3

 

	 	 	 	resolution providing for the Change in Control (with the earliest to occur
of such dates referred to herein as the “Measurement Date”); provided that a
change in title or role reflecting the difference in size or structure of an
Acquiring Corporation shall not be Good Reason if the Executive’s duties,
authority or responsibilities within the portion of the business of the
Acquiring Corporation represented by the business of the Company are not
materially diminished;

	 	(b)	 	any material diminution in the Executive’s duties, authority or
responsibilities prior to the date set forth in clause (a) that the Executive
can reasonably demonstrate (i) was at the request of a third party who has
taken steps reasonably calculated to effect a Change in Control or (ii)
otherwise arose in connection with or in anticipation of a Change in Control;
	 
	 	(c)	 	a material reduction in the Executive’s compensation as in
effect on the Measurement Date, except such a reduction (i) with the
Executive’s consent, or (ii) in connection with a reduction in compensation of
other Company executives at the level of senior management (a “Broad Executive
Reduction”) other than a Broad Executive Reduction that Executive can
reasonably demonstrate (x) was at the request of a third party who has taken
steps reasonably calculated to effect a Change in Control or (y) otherwise
arose in connection with or in anticipation of a Change in Control;
	 
	 	(d)	 	a material breach of this Agreement by the Company or any
successor to the Company;
	 
	 	(e)	 	any material reduction in the aggregate in the Executive’s
pension, retirement or benefit plans or programs (including without limitation
any 401(k), life insurance, medical, health and accident or disability plan and
any vacation program or policy) (a “Benefit Plan”) in which the Executive
participates or which is applicable to the Executive immediately prior to the
Measurement Date, unless an equitable arrangement (embodied in an ongoing
substitute or alternative plan) has been made with respect to such plan or
program; except for any across the board reduction imposed on substantially
all other members of the Company’s senior management (a “Broad Executive
Benefit Reduction”) other than a Broad Executive Benefit Reduction that
Executive can reasonably demonstrate (i) was at the request of a third party
who has taken steps reasonably calculated to effect a Change in Control or (ii)
otherwise arose in connection with or in anticipation of a Change in Control;
or
	 
	 	(f)	 	any relocation of the Executive’s principal office location to
a location more than 35 miles from the Boston, Massachusetts metropolitan area.

4

 

     The Executive’s right to terminate his or her employment for Good Reason shall not be affected
by his or her incapacity due to physical or mental illness.

     1.7 “Reverse Merger” means the consummation of a merger or share exchange involving the
Company as the result of which the equity of the Company (including outstanding warrants and stock
options) is converted into the ownership of (or the right to receive upon exercise) at least 50% of
the equity of the resulting or acquiring corporation.

     1.8 “Reverse Merger Date” means the first date during the Term (as defined in Section 2) on
which a Reverse Merger occurs. Anything in this Agreement to the contrary notwithstanding, if (a) a
Reverse Merger occurs, (b) the Executive’s employment with the Company is terminated prior to the
date on which the Reverse Merger occurs, and (c) it is reasonably demonstrated by the Executive
that such termination of employment (i) was at the request of a third party who has taken steps
reasonably calculated to effect a Reverse Merger or (ii) otherwise arose in connection with or in
anticipation of a Reverse Merger, then for all purposes of this Agreement the “Reverse Merger Date”
shall mean the date immediately prior to the date of such termination of employment.

     1.9 “Severance Term” shall mean nine (9) months.

     2. Term of Agreement. This Agreement, and all rights and obligations of the parties
hereunder, shall take effect upon the Effective Date and shall expire upon the first to occur of
(a) the expiration of the Term (as defined below) if a Change in Control has not occurred during
the Term, (b) the fulfillment by the Company of all of its obligations under this Agreement
following the 12-month anniversary of the Change in Control Date, if the Executive is still
employed by the Company as of such date, (c) the fulfillment by the Company of all of its
obligations under this Agreement if the Executive’s employment with the Company terminates on or
within 12 months following the Change in Control Date, (d) immediately prior to effectiveness of
the Company’s initial public offering registered under the Securities Act of 1933, or (e) three (3)
months after the consummation of a Reverse Merger with a corporation subject to reporting
obligations under the Securities Exchange Act of 1934. “Term” shall mean the period commencing as
of the Effective Date and continuing in effect through December 31, 2010; provided, however, that
on January 1, 2011 and each January 1 thereafter, the Term shall be automatically extended for one
additional year beyond its then Term (as previously extended) unless, not later than 90 days prior
to any such January 1, the Company shall have given the Executive written notice that the Term will
not be extended; provided, further, however, in the event that a definitive agreement relating to
any transaction that would result in a Change in Control is entered into during the Term but not
consummated prior to the scheduled expiration of the Term (or any extension thereof), the Term
shall be automatically extended until the earlier to occur of (i) the termination such definitive
agreement or (ii) the consummation of the Change in Control contemplated thereby.

     3. Employment Status; Termination Following a Change of Control.

     3.1 Not an Employment Contract. The Executive acknowledges that this Agreement does not
constitute a contract of employment or impose on the Company any obligation to retain the Executive
as an employee and that this Agreement does not prevent the Executive from terminating employment
at any time. Except in the case of an Anticipatory Termination, if the

5

 

Executive’s employment with the Company terminates for any reason and subsequently a Change in
Control shall occur, the Executive shall not be entitled to any benefits hereunder. This Agreement
deals only with termination of employment under the specific circumstances set forth herein and
does not deal with termination of employment under any other circumstances. Nothing in this
Agreement shall be deemed to amend or modify the terms of any separate employment agreement to
which the Executive and the Company are party.

     3.2 Termination of Employment.

	 	(a)	 	If a Change of Control Date occurs during the Term (or any
extension thereof), any termination of the Executive’s employment by the
Company or by the Executive on or within twelve (12) months following the
Change of Control Date (other than due to the death of the Executive)
shall be communicated by a written notice to the other party hereto (the
“Notice of Termination”), given in accordance with Section 7. Any Notice of
Termination shall: (i) indicate the specific termination provision (if any) of
this Agreement relied upon by the party giving such notice, (ii) to the extent
applicable, set forth in reasonable detail the facts and circumstances claimed
to provide a basis for termination of the Executive’s employment under the
provision so indicated and (iii) specify the Date of Termination (as defined
below). The effective date of an employment termination (the “Date of
Termination”) shall be the close of business on the date specified in the
Notice of Termination (which date may not be less than fifteen (15) days or
more than thirty (30) days after the date of delivery of such Notice of
Termination) in the case of a termination other than termination due to the
Executive’s death, a termination by the Company for Cause or a termination by
the Executive for Good Reason. In the case of the Executive’s death, the Date
of Termination shall be the date of the Executive’s death. In the event the
Company fails to satisfy the requirements of Section 3.2(a) regarding a Notice
of Termination, the purported termination of the Executive’s employment
pursuant to such Notice of Termination shall not be effective for purposes of
this Agreement.
	 
	 	(b)	 	The failure by the Executive or the Company to set forth in the
Notice of Termination any fact or circumstance which contributes to a showing
of Good Reason or Cause shall not waive any right of the Executive or the
Company, respectively, hereunder or preclude the Executive or the Company,
respectively, from asserting any such fact or circumstance in enforcing the
Executive’s or the Company’s rights hereunder.
	 
	 	(c)	 	Any Notice of Termination for Cause given by the Company must
be given within 90 days of the occurrence (or if later, the discovery) of the
event(s) or circumstance(s) which constitute(s) Cause. Such Notice of
Termination for Cause shall provide the Executive with thirty (30) days to
remedy such events or circumstances (the “Cause Cure Period”), if such events
or circumstances may be subject to being remedied. Any event or

6

 

	 	 	 	circumstance that is remedied by the Executive within the Cause Cure Period
shall not be deemed to constitute Cause.

	 	(d)	 	Any Notice of Termination for Good Reason given by the
Executive must be given within ninety (90) days of the occurrence of the
event(s) or circumstance(s) which constitute(s) Good Reason. Such Notice of
Termination for Good Reason shall provide the Company with thirty (30) days to
remedy such events or circumstances (the “Good Reason Cure Period”), if such
action may be subject to being remedied. Any event or circumstance that is
remedied by the Company within the Good Reason Cure Period shall not be deemed
to constitute Good Reason.

     4. Benefits to Executive.

     4.1 Benefits in Connection with a Change in Control. If a Change in Control Date occurs
during the Term (or any extension thereof) and there is an Anticipatory Termination or the
Executive’s employment with the Company terminates on or within 12 months following the
consummation of the Change in Control associated with such Change in Control Date, the Executive
shall be entitled to the following benefits:

	 	(a)	 	Termination Without Cause or for Good Reason. If (w) there is
an Anticipatory Termination, (x) the Executive is not offered continued
employment by the Acquiring Corporation or (y) the Executive’s employment with
the Company is terminated by the Company (other than for Cause, Disability or
Death) or by the Executive for Good Reason on or within 12 months following the
consummation of the Change in Control, then the Executive shall be entitled to
the following benefits:

	 	(i)	 	the Company shall pay to the Executive the
following amounts:

	 	(1)	 	in a lump sum, in cash,
within 30 days after the Date of Termination, the sum of (A)
any unpaid portion of the Executive’s base salary through the
Date of Termination, (B) a pro rata current year bonus amount
(calculated by dividing the number of full and partial months
of the current fiscal year in which the Executive is employed
through the Date of Termination by 12, and multiplying this
fraction by the amount of the current annual bonus target, or
if not yet set, the amount of the annual bonus payment paid to
the Executive in the preceding year), and (C) the amount of
any accrued vacation pay, in each case to the extent not
previously paid (the sum of the amounts described in clauses
(A), (B), and (C) shall be hereinafter referred to as the
“Accrued Obligations”); and

7

 

	 	(2)	 	in a lump sum, in cash,
within 30 days after the Date of Termination, the sum of (A)
the Executive’s current base salary for the Severance Term;
and (B) (i) the amount of the current annual bonus target, or
if not yet set, the amount of the annual bonus payment paid to
the Executive in the preceding year multiplied by (ii) the
quotient of the number of months in the Severance Term divided
by twelve (12); and

	 	(ii)	 	for the Severance Term after the Date of
Termination or such longer period as may be provided by the terms of
the appropriate plan, program, practice or policy, the Company shall
provide health insurance continuation benefits under the Consolidated
Omnibus Budget Reconciliation Act of 1985 (“COBRA”) at the Company’s
cost to the Executive and the Executive’s family at least equal to
those which would have been provided to them if the Executive’s
employment had not been terminated, in accordance with the applicable
Benefit Plans in effect on the Measurement Date and upon the
Executive’s valid COBRA election; provided, however, that if the
Executive becomes reemployed with another employer and is eligible to
receive health insurance benefits from such employer on terms at least
as favorable to the Executive and his or her family as those being
provided by the Company, then the Company shall no longer be required
to provide those particular benefits to the Executive and his or her
family; and
	 
	 	(iii)	 	to the extent not previously paid or provided,
the Company shall timely pay or provide to the Executive any other
amounts or benefits required to be paid or provided or which the
Executive is eligible to receive following the Executive’s termination
of employment under any plan, program, policy, practice, contract or
agreement of the Company and its affiliated companies (such other
amounts and benefits shall be hereinafter referred to as the “Other
Benefits”).

	 	(b)	 	Resignation without Good Reason; Termination for Death or
Disability. If the Executive voluntarily terminates his or her employment with
the Company on or within 12 months following the consummation of the Change in
Control, excluding a termination for Good Reason, or if the Executive’s
employment with the Company is terminated by reason of the Executive’s death or
Disability on or within 12 months following the Change in Control Date, then
the Company shall (i) pay the Executive (or his or her estate, if applicable),
in a lump sum in cash within 30 days after the Date of Termination, the Accrued
Obligations other than the pro rata current year bonus amount, and (ii) timely
pay or provide to the Executive the Other Benefits.

8

 

	 	(c)	 	Termination for Cause. If the Company terminates the
Executive’s employment with the Company for Cause during the Term (or any
extension thereof) or on or within 12 months following the Change in Control
Date, then the Company shall only pay the Executive such amounts, and provide
such benefits, as is required by law.

     4.2 Vesting of Stock Options and Restricted Stock in Connection with a Change in Control. (a)
If (i) a Change in Control Date occurs during the Term (or any extension thereof) and (A) there is
an Anticipatory Termination or (B) the Executive’s employment with the Company terminates on or
within 12 months following the consummation of the Change in Control associated with such Change in
Control Date, and (ii) all of the Unvested Securities held by the Executive will not be exchanged
or replaced in the Change in Control with vested securities on comparable terms as the class of
shares underlying the Unvested Securities, then the Company shall cause 50% of the portion of
Executive’s Unvested Securities which are not exchanged or replaced to become vested and
exercisable (and no longer subject to repurchase) immediately prior to the occurrence of the Change
in Control.

     (b) In the event of an Anticipatory Termination, the period in which the Executive may
exercise the Executive’s Unvested Securities shall be extended until thirty (30) days after the
consummation of the Change in Control, but in no event beyond the original term of such option.

     4.3 Mitigation. The Executive shall not be required to mitigate the amount of any payment or
benefits provided for in this Section 4 by seeking other employment or otherwise. Further, the
amount of any payment or benefits provided for in this Section 4 shall not be reduced by any
compensation earned by the Executive as a result of employment by another employer, by retirement
benefits, by offset against any amount claimed to be owed by the Executive to the Company or
otherwise, except as provided in Section 4.1(a)(ii).

     4.4 Benefits in Connection with a Reverse Merger. (a) In connection with a Reverse Merger
that occurs during the Term, notwithstanding anything to the contrary implied or expressed in the
Stock Plan, the Company’s Certificate of Incorporation, any stock option agreement or other
agreement, the Executive shall receive that number of shares of common stock and options
exercisable for share of common stock (in relative proportion to the Executive’s holdings of shares
of common stock and stock options in the Company immediately prior to the Reverse Merger Date) in
the surviving company in the Reverse Merger necessary such that the Executive’s proportionate
ownership of the equity distributed to or otherwise received by holders of shares of common stock
and stock options in the Company in connection with the Reverse Merger is at least equal to the
Executive’s proportionate ownership of the shares of common stock and stock options in the Company
prior to the Reverse Merger.

     (b) If a Reverse Merger occurs during the Term and (i) the Executive’s employment is
terminated by the Company or the resulting or acquiring corporation without Cause on or within
twelve (12) months following the Reverse Merger Date and the Executive’s position is filled by a
person employed in a substantially similar position prior to the Reverse Merger by the other party
to the Reverse Merger, or (ii) Executive’s employment is terminated by the Executive for Good
Reason on or within three (3) months following the Reverse Merger Date, then the

9

 

Executive shall be entitled to the benefits set forth in Section 4.1(a) and 4.2(a) (and shall be
subject to the corresponding obligations and provisions set forth in this Agreement) as if a Change
in Control had occurred.

     4.5 Release. As a condition to Executive receiving the benefits under Section 4.1(a), Section
4.2 or Section 4.4, the Executive must first execute and deliver to Company a general release of
claims against the Company and its affiliates in a form substantially similar to the general
release attached hereto as Exhibit A, and such release, by its terms, has become irrevocable.

     4.6 Application of Section 409A. Notwithstanding the forgoing, if any benefits provided under
this Section 4 are deferred compensation under Section 409A, the following shall apply:

     (a) Any termination of employment triggering payment of such benefit must be a “separation
from service” under Section 409A before payment of such benefits under the terms of this Agreement
may commence (but the absence of such a separation shall not limit the Executive’s right to
eventual payment based on the termination at such time as the termination is a “separation from
service” under Section 409A).

     (b) If the Executive is a “specified employee” under Section 409A as of the date of his or her
termination of employment hereunder, then, to the extent necessary to avoid the imposition of
excise taxes or other penalties under Section 409A, the payment of benefits by the Company under
this Agreement, if any, that were scheduled to be paid to the Executive during the first six (6)
months following the date of his or her termination of employment shall not be paid until the
earlier of the Executive’s death and the date that is the first business day following the 6-month
anniversary of the Executive’s termination of employment, at which time such delayed deferred
compensation payments shall be paid in a lump sum and the remainder of the benefit payments, if
any, shall thereafter be paid in accordance with their normal schedule.

     (c) The parties shall cooperate fully with each other to ensure compliance with Section 409A
of the Code, including without limitation, adopting amendments to this Agreement and any other
arrangements subject to Section 409A and operating the Agreement and other arrangements in
accordance with Section 409A.

     4.7 Application of Section 280G. Notwithstanding the forgoing, if any benefits provided
under this Section 4, taken together with any other payments or distributions by the Company to or
for the benefit of the executive, otherwise would constitute in whole or in part an “excess
parachute payment” under Section 280G of the Code, the payments to the Executive under this
Agreement shall be reduced to the extent necessary to avoid the application of Section 280G.
Immediately prior to a Change in Control or Reverse Merger, the Company will seek stockholder
approval in accordance with Section 280G with respect to any such payments so that the so-called
“golden parachute” provisions of Section 280G of the Code do not apply to any such payments,
provided that in no event shall the Company be deemed to have guaranteed any particular outcome
with respect to such stockholder vote.

10

 

     5. Settlement of Disputes; Arbitration. All claims by the Executive for benefits under this
Agreement shall be directed to and determined by the Board of Directors of the Company and shall be
in writing. Any denial by the Board of Directors of a claim for benefits under this Agreement shall
be delivered to the Executive in writing and shall set forth the specific reasons for the denial
and the specific provisions of this Agreement relied upon. The Board of Directors shall afford a
reasonable opportunity to the Executive for a review of the decision denying a claim. Any further
dispute or controversy arising under or in connection with this Agreement shall be settled
exclusively by arbitration in Boston, Massachusetts, in accordance with the rules of the American
Arbitration Association then in effect. Judgment may be entered on the arbitrator’s award in any
court having jurisdiction.

     6. Successors.

     6.1 Successor to Company. This Agreement will bind and inure to the benefit of the Company’s
successors and permitted assigns The Company shall require any Acquiring Corporation or any other
successor (whether direct or indirect, by purchase, merger, consolidation or otherwise) to
expressly assume and agree to perform this Agreement to the same extent that the Company would be
required to perform it if no such succession had taken place. Executive shall have the right to
require the Company or any successor to confirm in writing such successor’s assumption and
agreement to so perform this Agreement. Failure of the Company to obtain an assumption of this
Agreement at or prior to the effectiveness of any succession shall be a material breach of this
Agreement and shall constitute Good Reason if the Executive elects to terminate employment, except
that for purposes of implementing the foregoing, the date on which any such succession becomes
effective shall be deemed the Date of Termination. As used in this Agreement, “Company” shall mean
the Company as defined above and any successor to its business or assets as aforesaid which assumes
and agrees to perform this Agreement, by operation of law or otherwise.

     6.2 Successor to Executive. This Agreement shall inure to the benefit of and be enforceable by
the Executive’s personal or legal representatives, executors, administrators, successors, heirs,
distributees, devisees and legatees. If the Executive should die while any amount would still be
payable to the Executive or his or her family hereunder if the Executive had continued to live, all
such amounts, unless otherwise provided herein, shall be paid in accordance with the terms of this
Agreement to the executors, personal representatives or administrators of the Executive’s estate.

     7. Notice. All notices, instructions and other communications given hereunder or in
connection herewith shall be in writing. Any such notice, instruction or communication shall be
sent either (i) by registered or certified mail, return receipt requested, postage prepaid, or (ii)
prepaid via a reputable nationwide overnight courier service, in each case addressed (a) to the
Company, at 300 Third Street, Cambridge, MA 02142, Attn: Chief Executive Officer, and (b) to the
Executive at the address for notices indicated below (or to such other address as either the
Company or the Executive may have furnished to the other in writing in accordance herewith). Any
such notice, instruction or communication shall be deemed to have been delivered five business days
after it is sent by registered or certified mail, return receipt requested, postage prepaid, or one
business day after it is sent via a reputable nationwide overnight courier service. Either party
may give any notice, instruction or other communication hereunder using any other means, but no
such notice, instruction or other communication shall be

11

 

deemed to have been duly delivered unless and until it actually is received by the party for whom
it is intended.

     8. Miscellaneous.

     8.1 Employment by Affiliate. For purposes of this Agreement, the Executive’s employment with
the Company shall not be deemed to have terminated solely as a result of the Executive continuing
to be employed by an affiliate of the Company.

     8.2 Severability. The invalidity or unenforceability of any provision of this Agreement shall
not affect the validity or enforceability of any other provision of this Agreement, which shall
remain in full force and effect.

     8.3 Injunctive Relief. The Company and the Executive agree that any breach of this Agreement
by the Company is likely to cause the Executive substantial and irrevocable damage and therefore,
in the event of any such breach, in addition to such other remedies which may be available, the
Executive shall have the right to seek specific performance and injunctive relief.

     8.4 Governing Law. The validity, interpretation, construction and performance of this
Agreement shall be governed by the internal laws of the Commonwealth of Massachusetts, without
regard to conflicts of law principles.

     8.5 Waivers. No waiver by the Executive at any time of any breach of, or compliance with, any
provision of this Agreement to be performed by the Company shall be deemed a waiver of that or any
other provision at any subsequent time.

     8.6 Counterparts. This Agreement may be executed in counterparts, each of which shall be
deemed to be an original but both of which together shall constitute one and the same instrument.

     8.7 Section 409A. The terms of this Agreement shall be interpreted in a manner consistent
with the provisions of Section 409A. Regardless of the forgoing or any other provision in this
Agreement, the Company makes no guarantees as to the tax consequences related to any payments under
this Agreement or otherwise under Section 409A.

     8.8 Tax Withholding. Any payments provided for hereunder shall be paid net of any applicable
tax withholding required under federal, state or local law.

     8.9 Entire Agreement. This Agreement sets forth the entire agreement of the parties hereto in
respect of the subject matter contained herein and supersedes all prior agreements, promises,
covenants, arrangements, communications, representations or warranties, whether oral or written, by
any officer, employee or representative of any party hereto in respect of the subject matter
contained herein, except for                      (“Surviving Agreements”); and any prior agreement
of the parties hereto in respect of the subject matter contained herein other than the Surviving
Agreements is hereby terminated and cancelled. Notwithstanding the foregoing, this Agreement shall
have no effect on the Executive’s rights under any subsequent agreement between Executive and the
Company or under any management incentive plan adopted by the Company.

12

 

     8.10 Headings. The headings in this Agreement are for purposes of reference only and shall
not limit or otherwise affect the meaning of any provision of this Agreement.

     8.11 Amendments. This Agreement may be amended or modified only by a written instrument
executed by both the Company and the Executive.

     IN WITNESS WHEREOF, the parties hereto have executed this Change in Control Agreement as of
the day and year first set forth above.

	 	 	 	 	 	 	 	 	 
	 	 	ARCHEMIX CORP.	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	By:
	 	 
	 	 	 	 	 	 	 
	 

	 	 	 Name:	 	 	 
	 

	 	 	 Title:	 	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	EXECUTIVE	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	Signature:
	 	 
	 

	 	 	 	 	 	 

	 	 
	 	 	Printed Name: 	 	 	 
	 

	 	 	 	 	 	 

	 	 
	 	 	Address:
	 	 
	 

	 	 	 	 	 	 

	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	 	 	 

13

 

EXHIBIT A

GENERAL RELEASE

     1. General Release. In consideration of the payments and benefits to be made under that
certain Change in Control Agreement, dated                     , 2008, (the “Agreement”),
                                         (the “Executive”), with the intention of binding the Executive
and the Executive’s heirs, executors, administrators and assigns, does hereby release, remise,
acquit and forever discharge Archemix Corp. (the “Company”) and each of its subsidiaries and
affiliates (the “Company Affiliated Group”), their present and former officers, directors,
executives, agents, attorneys, employees and employee benefits plans (and the fiduciaries thereof),
and the successors, predecessors and assigns of each of the foregoing (collectively, the “Company
Released Parties”), of and from any and all claims, actions, causes of action, complaints, charges,
demands, rights, damages, debts, sums of money, accounts, financial obligations, suits, expenses,
attorneys’ fees and liabilities of whatever kind or nature in law, equity or otherwise, whether
accrued, absolute, contingent, unliquidated or otherwise and whether now known or unknown,
suspected or unsuspected which the Executive, individually or as a member of a class, now has, owns
or holds, or has at any time heretofore had, owned or held, against any Company Released Party in
any capacity, including, without limitation, any and all non-waivable claims (i) arising out of or
in any way connected with the Executive’s service to any member of the Company Affiliated Group (or
the predecessors thereof) in any capacity, or the termination of such service in any such capacity,
(ii) for severance or vacation benefits, unpaid wages, salary or incentive payments, (iii) for
breach of contract, wrongful discharge, impairment of economic opportunity, defamation, intentional
infliction of emotional harm or other tort and (iv) for any violation of applicable state and local
labor and employment laws (including, without limitation, all laws concerning unlawful and unfair
labor and employment practices), any and all claims based on the Executive Retirement Income
Security Act of 1974 (“ERISA”), any and all claims arising under the civil rights laws of any
federal, state or local jurisdiction, including, without limitation, Title VII of the Civil Rights
Act of 1964 (“Title VII”), the Americans with Disabilities Act (“ADA”), the Age Discrimination in
Employment Act (“ADEA”), Sections 503 and 504 of the Rehabilitation Act, and any and all claims
under any whistleblower laws or whistleblower provisions of other laws, excepting only:

	 	(a)	 	rights of the Executive under this General Release and the
Agreement;
	 
	 	(b)	 	[rights of the Executive under the Company’s Management
Incentive Plan];[to be included with proper reference if any such plan exists]
	 
	 	(c)	 	rights of the Executive relating to equity awards held by the
Executive as of his or her Date of Termination (as defined in the Agreement);
	 
	 	(d)	 	the right of the Executive to receive COBRA continuation
coverage in accordance with applicable law;
	 
	 	(e)	 	rights to indemnification the Executive may have (i) under
applicable corporate law, (ii) under the by-laws or certificate of
incorporation of any

 

 

	 	 	 	Company Released Party or (iii) as an insured under any director’s and
officer’s liability insurance policy now or previously in force;

	 	(f)	 	claims (i) for benefits under any health, disability,
retirement, deferred compensation, life insurance or other, similar Executive
benefit plan or arrangement of the Company Affiliated Group, (ii) for earned
but unpaid salary and awarded bonus amounts through the Date of Termination and
(iii) for earned but unused vacation pay through the Date of Termination in
accordance with applicable Company policy; and
	 
	 	(g)	 	claims for the reimbursement of unreimbursed business expenses
incurred prior to the Date of Termination pursuant to applicable Company
policy.

     2. No Admissions. The Executive acknowledges and agrees that this General Release is not to be
construed in any way as an admission of any liability whatsoever by any Company Released Party, any
such liability being expressly denied.

     3. Application to all Forms of Relief. This General Release applies to any relief no matter
how called, including, without limitation, wages, back pay, front pay, compensatory damages,
liquidated damages, punitive damages for pain or suffering, costs and attorney’s fees and expenses.

     4. Specific Waiver; Exclusions. The Executive specifically acknowledges that his or her
acceptance of the terms of this General Release is, among other things, a specific waiver of his or
her rights, claims and causes of action under Title VII, ADEA, ADA and any state or local law or
regulation in respect of discrimination of any kind; provided, however, that nothing herein shall
be deemed, nor does anything herein purport, to constitute or require a waiver of any right or
claim or cause of action which by law the Executive is not permitted to waive.

     5. No Complaints or Other Claims. The Executive acknowledges and agrees that neither he/she
nor any of his/her agents or assigns has, with respect to any transaction or state of facts
existing prior to the date hereof, filed any complaints, charges or lawsuits against any Company
Released Party with any governmental agency, court or tribunal.

     6. Additional Obligations And Covenants. In consideration of the payments and benefits
offered to be made under the Agreement, and for other good and valuable consideration, receipt of
which is hereby acknowledged by the Executive, the Executive agrees to the following additional
obligations and covenants:

	 	(a)	 	Confidentiality. The Executive shall not, without the prior written
consent of the Company or as may otherwise be required by law or any legal
process, communicate to anyone other than the Company and those designated by the
Company or on behalf of the Company in the furtherance of its business, any trade
secrets, confidential information, knowledge or data relating to any member of the
Company Affiliated Group, obtained by the Executive during the Executive’s
employment by the Company that is not generally available

A-2

 

	 	 	 	public knowledge (other than by acts by the Executive in violation of this
General Release).

	 	(b)	 	Return of Company Material. The Executive represents that, as of the
date he or she signs this Agreement, he or she has returned to the Company all
Company Material (as defined below). For purposes of this Section 6(b), “Company
Material” means any documents, files and other property and information of any
kind belonging or relating to (i) any member of the Company Affiliated Group, (ii)
the current and former suppliers, creditors, directors, officers, employees,
agents and customers of any of them or (iii) the businesses, products, services
and operations (including without limitation, business, financial and accounting
practices) of any of them, in each case whether tangible or intangible (including,
without limitation, credit cards, building and office access cards, keys, computer
equipment, cellular telephones, pagers, electronic devices, hardware, manuals,
files, documents, records, software, customer data, research, financial data and
information, memoranda, surveys, correspondence, statistics and payroll and other
employee data, and any copies, compilations, extracts, excerpts, summaries and
other notes thereof or relating thereto), excluding only information (x) that is
generally available public knowledge or (y) that relates to the Executive’s
compensation or Executive benefits.
	 
	 	(c)	 	Cooperation. Following the Termination Date, the Executive shall
reasonably cooperate with the Company upon reasonable request of the Board and be
reasonably available to the Company with respect to matters arising out of the
Executive’s services to the Company Affiliated Group, at the expense of the
Company.
	 
	 	(d)	 	Nondisparagement. The Executive agrees not to communicate negatively
about or otherwise disparage any Company Released Party or the products or
businesses of any of them in any way whatsoever. The Company agrees not to
communicate negatively about or otherwise disparage the Executive.
	 
	 	(e)	 	Nonsolicitation. The Executive agrees that for the period of time
beginning on the date hereof and ending on the first anniversary of the
Executive’s Date of Termination, the Executive shall not, either directly or
indirectly, solicit, entice, persuade, induce or otherwise attempt to influence
any person who is employed by any member of the Company Affiliated Group to
terminate such person’s employment by such member of the Company Affiliated Group.
The Executive also agrees that for the same period of time he or she shall not
assist any person or entity in the recruitment of any person who is employed by
any member of the Company Affiliated Group. The Executive’s provision of a
reference to or in respect of any individual shall not be a violation this 

Section
6(e).

A-3

 

     7. Conditions of General Release.

	 	(a)	 	Terms and Conditions. From and after the Date of Termination, the
Executive shall abide by all the terms and conditions of this General Release and
the terms and any conditions set forth in any employment or confidentiality
agreements signed by the Executive, which is incorporated herein by reference.
	 
	 	(b)	 	No Representation. The Executive acknowledges that, other than as set
forth in this General Release, [the Management Incentive Plan] [to be included
with proper reference if any such plan exists] and the Agreement, (i) no promises
have been made to him or her and (ii) in signing this General Release the
Executive is not relying upon any statement or representation made by or on behalf
of any Company Released Party and each or any of them concerning the merits of any
claims or the nature, amount, extent or duration of any damages relating to any
claims or the amount of any money, benefits, or compensation due the Executive or
claimed by the Executive, or concerning the General Release or concerning any
other thing or matter.
	 
	 	(c)	 	Injunctive Relief. In the event of a breach or threatened breach by
the Executive of any provision of this General Release, the Executive agrees that
the Company shall be entitled to seek injunctive relief in a court of appropriate
jurisdiction to remedy any such breach or threatened breach, the Executive
acknowledging that damages may be inadequate or insufficient.

     8. Voluntariness. The Executive agrees that he or she is relying solely upon his or her own
judgment; that the Executive is over eighteen years of age and is legally competent to sign this
General Release; that the Executive is signing this General Release of his or her own free will;
that the Executive has read and understood the General Release before signing it; and that the
Executive is signing this General Release in exchange for consideration that he or she believes is
satisfactory and adequate.

     9. Legal Counsel. The Executive acknowledges that he or she has been informed of the right to
consult with legal counsel and has been encouraged to do so.

     10. Complete Agreement/Severability. This General Release (excepting                     , which are
incorporated by reference and shall survive the signing of this document) constitutes the complete
and final agreement between the parties and supersedes and replaces all prior or contemporaneous
agreements, negotiations, or discussions relating to the subject matter of this General Release.
All provisions and portions of this General Release are severable. If any provision or portion of
this General Release or the application of any provision or portion of the General Release shall be
determined to be invalid or unenforceable to any extent or for any reason, all other provisions and
portions of this General Release shall remain in full force and shall continue to be enforceable to
the fullest and greatest extent permitted by law.

     11. ADEA/OWBP Acceptance and Revocation Period. It is the Company’s desire and intent to make
certain that the Executive fully understands the provisions and effects of this General Release.
To that end, he or she has been encouraged and given the opportunity to

A-4

 

consult with legal counsel for the purpose of reviewing the terms of this document. Also, because
the Executive is over the age of 40, and consistent with the provisions of the ADEA, which
prohibits discrimination on the basis of age, the Executive acknowledges that he or she has been
given a period of twenty-one (21) days within which to consider this General Release, unless
applicable law requires a longer period, in which case the Executive shall be advised of such
longer period and such longer period shall apply. The Executive may accept this General Release at
any time within this period of time by signing the General Release and returning it to the Company.
This General Release shall not become effective or enforceable until seven (7) calendar days after
the Executive signs it. The Executive may revoke his or her acceptance of this General Release at
any time within that seven (7) calendar day period by sending written notice to the Company. Such
notice must be received by the Company within the seven (7) calendar day period in order to be
effective and, if so received, would void this General Release for all purposes.

     Consistent with the provisions of the ADEA and other federal discrimination laws, nothing in
this General Release shall be deemed to prohibit the Executive from challenging the validity of
this release under the federal age or other discrimination laws (the “Federal Discrimination Laws”)
or from filing a charge or complaint of age or other employment related discrimination with the
Equal Employment Opportunity Commission (“EEOC”), or from participating in any investigation or
proceeding conducted by the EEOC. Further, nothing in this General Release shall be deemed to
limit the Company’s right to seek immediate dismissal of such charge or complaint on the basis that
the Executive’s signing of this General Release constitutes a full release of any individual rights
under the Federal Discrimination Laws, or to seek restitution to the extent permitted by law of the
economic benefits provided to the Executive under the Agreement in the event that the Executive
successfully challenges the validity of this release and prevail in any claim under the Federal
Discrimination Laws.

     12. Governing Law; Jurisdiction. Except for issues or matters as to which federal law is
applicable, this General Release shall be governed by and construed and enforced in accordance with
the laws of the Commonwealth of Massachusetts without giving effect to the conflicts of law
principles thereof. Both parties agree that any action, demand, claim or counterclaim relating to
the terms and provisions of this Agreement, or to its breach, shall be commenced in a court of
competent jurisdiction in Massachusetts and that venue shall lie exclusively in Middlesex or
Suffolk County, Massachusetts. Both parties further agree that any action, demand, claim or
counterclaim shall be resolved by a judge alone, and both parties hereby waive and forever renounce
the right to a trial before a civil jury.

A-5

 

     IN WITNESS WHEREOF, the Executive has executed this General Release as of the date last set
forth below.

	 	 	 	 	 	 	 	 	 
	 	 	ARCHEMIX CORP.	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	By:
	 	 
	 	 	 	 	 	 	 
	 

	 	 	 	Name:	 	 	 	 
	 

	 	 	 	Title:	 	 	 	 
	 

	 	 	 	Date:	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	EXECUTIVE	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	Signature:
	 	 
	 

	 	 	 	 	 	 	 	 
	 	 	Printed Name:	 	 	 	 
	 

	 	 	 	 	 	 	 	 
	 	 	Date:
	 	 
	 

	 	 	 	 	 	 	 	 

A-6

 

Schedule I

Gregg Beloff

Page Bouchard

James Gilbert

Glenn Goddard

John Harre

Duncan Higgons

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