Document:

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                                                                     Exhibit 4.3

                                                                       EXHIBIT G

                                 ARCHEMIX CORP.

                          REGISTRATION RIGHTS AGREEMENT

     This REGISTRATION RIGHTS AGREEMENT dated as of [_________] (the
"AGREEMENT") is made by and between Archemix Corp., a Delaware corporation (the
"COMPANY"), and Nuvelo, Inc., a Delaware corporation (the "INVESTOR").

     WHEREAS, the Company proposes to issue and sell to the Investor certain
shares of its common stock, par value $.001 per share ("COMMON STOCK") pursuant
to the Stock Purchase Agreement by and between the Company and Investor of even
date herewith (the "STOCK PURCHASE AGREEMENT") as provided in Section 7.3 of
that certain Amended and Restated Collaboration and License Agreement between
the Company and the Purchaser dated July [__}, 2006 (the "COLLABORATION
AGREEMENT");

     WHEREAS, as a condition to entering into the Stock Purchase Agreement, the
Investor has requested that the Company grant to it registration rights and
certain other rights and covenants set forth herein;

     NOW, THEREFORE, in consideration of the premises and mutual agreements set
forth herein and for other good and valuable consideration, the receipt and
sufficiency of which are hereby mutually acknowledged, and intending to be
legally bound hereby, the parties hereto agree as follows:

     1. Registration Rights. The Company and the Investor, as applicable,
covenant and agree as follows:

          1.1 Definitions. For purposes of this Agreement:

               (a) The term "ACT" means the Securities Act of 1933, as amended,
or any similar federal statute and the rules, regulations and policies of the
Commission thereunder, all as the same shall be in effect at the time.

               (b) The term "1934 ACT" means the Securities Exchange Act of
1934, as amended, or any similar federal statute and the rules, regulations and
policies of the Commission thereunder, all as the same shall be in effect at the
time.

               (c) The term "COMMON STOCK" shall have the meaning set forth in
the recitals.

               (d) The term "FORM S-1" means a registration statement on Form
S-1 or such other form under the Act as in effect on the date hereof, or any
registration form under the Act subsequently adopted by the SEC, which permits
the registration of securities under the Act for which no other form is
authorized or prescribed.

               (e) The term "FORM S-3" means a registration statement on Form
S-3 or such other form under the Act as in effect on the date hereof or any
registration form under the

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Act subsequently adopted by the SEC, which permits inclusion or incorporation of
substantial information by reference to other documents filed by the Company
with the SEC or relates to secondary offerings.

               (f) The term "HOLDER" means the Investor (so long as the Investor
holds Registrable Securities) and any person owning or having the right to
acquire Registrable Securities or any assignee thereof in accordance with
Section 1.10 hereof.

               (g) The term "QUALIFIED PUBLIC OFFERING" means the Company's firm
commitment underwritten initial public offering filed under the Act covering the
offer and sale of the Company's Common Stock, with gross offering proceeds to
the Company of not less than $30,000,000 exclusive of any amount issued to the
Investor pursuant to the Collaboration Agreement.

               (h) The terms "REGISTER", "REGISTERED," and "REGISTRATION" refer
to a registration effected by preparing and filing a registration statement,
other than a registration statement on Form S-4 on Form S-8 or successor or
comparable forms thereto, or similar document in compliance with the Act and the
declaration or ordering of effectiveness of such registration statement or
document.

               (i) The term "REGISTRABLE SECURITIES" means (i) any shares of
Common Stock issued to the Investor pursuant to the Stock Purchase Agreement,
(ii) any Common Stock of the Company issued as (or issuable upon the conversion
or exercise of any warrant, right or other security which is issued as) a
dividend or other distribution with respect to, or in exchange for or in
replacement of the shares referenced in (i) above, excluding in all cases,
however, any Registrable Securities sold by a person in a transaction in which
the rights under this Section 1 are not assigned; provided, however, that shares
of Common Stock which are Registrable Securities shall cease to be Registrable
Securities upon sale of such shares pursuant to a registration statement or Rule
144 under the Act or upon the eligibility for immediate sale of all Registrable
Securities under Rule 144(k) under the Act.

               (j) The term "SEC" means the Securities and Exchange Commission.

               (k) The term "SPECIAL REGISTRATION STATEMENT" means (i) a
registration statement relating to any employee benefit plan or (ii) with
respect to any corporate reorganization or transaction under Rule 145 of the
Act, any registration statements related to the issuance or resale of securities
issued in such a transaction or (iii) a registration related to stock issued
upon conversion of debt securities.

          1.2 Sale or Transfer of Shares; Legend.

               (a) The Registrable Securities shall not be sold or transferred
unless either (i) such shares first shall have been registered under the Act, or
(ii) the transfer complies with Rule 144, Rule 144A or an exemption from
registration under the Act, provided that, in the event of a sale pursuant to an
exemption under the Act, if requested by the Company, the Company shall have
been first furnished with an opinion of legal counsel, to the effect that such

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sale or transfer is exempt from the registration requirements of the Act,
provided further, however, that an opinion of counsel shall not be required for
sales under Rule 144 under the Act.

               (b) Each certificate representing the Registrable Securities
shall bear a legend substantially in the following form:

     "THE SHARES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER
     THE SECURITIES ACT OF 1933 OR ANY STATE SECURITIES LAW AND THEY MAY NOT BE
     OFFERED, SOLD, TRANSFERRED, HYPOTHECATED OR OTHERWISE ASSIGNED BY ANY
     PERSON, INCLUDING A PLEDGEE, UNLESS (1) EITHER (a) SUCH SHARES FIRST SHALL
     HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR (b)
     THE TRANSFER COMPLIES WITH RULE 144, RULE 144A OR AN EXEMPTION FROM
     REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND, IF
     REQUESTED BY THE COMPANY, THE COMPANY SHALL HAVE RECEIVED AN OPINION OF
     COUNSEL SATISFACTORY TO THE COMPANY THAT AN EXEMPTION FROM REGISTRATION
     UNDER SUCH ACTS IS THEN AVAILABLE, PROVIDED, HOWEVER, THAT AN OPINION OF
     COUNSEL SHALL NOT BE REQUIRED FOR SALES MADE UNDER RULE 144 AND (2) THERE
     SHALL HAVE BEEN COMPLIANCE WITH ALL APPLICABLE STATE SECURITIES LAWS.

The foregoing legend shall be removed from the certificates representing any
Registrable Securities, at the request of the holder thereof, at such time as
they become eligible for resale pursuant to Rule 144(k) under the Act.

          1.3 "Piggyback" Registration.

               (a) Registration Statement. Following the consummation of a
Qualified Public Offering, if (but without any obligation to do so) the Company
shall determine to register (including for this purpose a registration effected
by the Company for stockholders other than the Holders) any of its stock or
other securities under the Act in connection with the public offering of such
securities solely for cash (other than a registration or Form S-4 or S-8 or
relating solely to the sale of securities to participants in a stock plan or a
registration relating solely to a Rule 145 transaction or a registration on any
form which does not include substantially the same information as would be
required to be included in a registration statement covering the sale of the
Registrable Securities), the Company shall, at such time, promptly give each
Holder written notice of such registration. Upon the written request of each
Holder given within fifteen (15) days after receipt of such notice by the Holder
in accordance with Section 2.5, the Company shall, subject to the provisions of
this Section 1.3, use its reasonable best efforts to include in such
registration all of the Registrable Securities that each such Holder has
requested to be registered.

               (b) Company Deferral. In connection with any offering not
involving an underwriting of shares of the Company's capital stock, if the
Company shall furnish to the Holders a certificate signed by the Chairman of the
Company stating that in the good faith

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judgment of the Board of Directors, it would be seriously detrimental to the
Company and its stockholders for all of the Holders' shares to be included in
the registration statement to be filed and it is therefore essential to defer
the inclusion of all or some of the Holders' Registrable Securities in such
registration statement, the Company shall have the right to reduce such number
of shares as the Board of Directors determines, in its good faith judgment, are
necessary, provided, however, that if the number of Registrable Securities to be
included in the registration statement in accordance with the foregoing is less
than the total number of shares which the Holders of Registrable Securities have
requested to be included, then the number of shares that may be included in the
registration statement shall be allocated, first, to the Company; second, to
holders of shares of capital stock (other than a Holder) with registration
rights under that certain Second Amended and Restated Registration Rights
Agreement dated as of March 31, 2004 by and among the Company and the Purchasers
named therein, as amended from time to time (the "EXISTING REGISTRATION RIGHTS
AGREEMENT"); and third to the Holders on a pro rata basis based on the total
number of Registrable Securities held by each Holder.

               (c) Underwriting Requirements. In connection with any offering
involving an underwriting of shares of the Company's capital stock, the Company
shall not be required under this Section 1.3 to include any of the Holders'
Registrable Securities in such underwriting unless such Holders accept the terms
of the underwriting as agreed upon between the Company and the underwriters
selected by the Company. If the total amount of securities, including
Registrable Securities, requested by stockholders to be included in an offering
exceeds the amount that the underwriters determine, in good faith, is compatible
with the success of the offering, then the Company shall be required to include
in the offering only that number of such securities, including Registrable
Securities, which the underwriters determine in good faith will not jeopardize
the success of the offering. If the number of Registrable Securities to be
included in the underwriting in accordance with the foregoing is less than the
total number of shares which the Holders of Registrable Securities have
requested to be included, then the number of shares that may be included in the
underwriting shall be allocated, first, to the Company; second, to holders of
shares of capital stock (other than a Holder) with registration rights under the
Existing Registration Rights Agreement; and third to the Holders on a pro rata
basis based on the total number of Registrable Securities held by each Holder.

               (d) Withdrawal. Notwithstanding the foregoing provisions, the
Company may withdraw any registration statement referred to in this Section 1.3
for any reason without thereby incurring any liability to the holders of
Registrable Securities.

          1.4 Demand Registration. In case the Company shall, at any time
following the one year anniversary of the closing of a Qualified Public
Offering, receive from any Holder or Holders of Registrable Securities a written
request or requests that the Company effect a registration on Form S-3 (or any
successor to Form S-3) or any similar short-form registration statement, or, if
such short-form registration statement is not available for use by the Company,
on Form S-1 (or any successor to Form S-1) and any related qualification or
compliance with respect to all or a part of the Registrable Securities owned by
such Holder or Holders, the Company will:

               (a) promptly give written notice of the proposed registration,
and any

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related qualification or compliance, to all other Holders of Registrable
Securities; and

               (b) as soon as practicable, but in any event within thirty (30)
days of receipt of such request, file such registration statement and all such
qualifications and compliances as may be so requested and as would permit or
facilitate the sale and distribution of all or such portion of such Holder's or
Holders' Registrable Securities as are specified in such request, together with
all or such portion of the Registrable Securities of any other Holder or Holders
joining in such request as are specified in a written request given within
fifteen (15) days after receipt of such written notice from the Company;
provided, however, that the Company shall not be obligated to effect any such
registration, qualification or compliance pursuant to this Section 1.4:

               (i) if the Holders, together with the holders of any other
     securities of the Company entitled to inclusion in such registration,
     propose to sell Registrable Securities and such other securities (if any)
     at an aggregate price to the public of less than one million dollars
     ($1,000,000);

               (ii) if the Company shall furnish to the Holders a certificate
     signed by the Chairman of the Board of Directors of the Company stating
     either (A) that in the good faith judgment of the Board of Directors of the
     Company, it would be seriously detrimental to the Company and its
     stockholders for such registration to be effected at such time, or (B) that
     the Company intends to make a public offering within one hundred five (105)
     days of the receipt of the request of such Holder or Holders, the Company
     shall have the right to defer the filing of the registration statement for
     a period of not more than one hundred five (105) days after receipt of the
     request of the Holder or Holders under this Section 1.4; provided that such
     right to delay a request shall be exercised by the Company not more than
     once in any twelve (12) month period;

               (iii) if the Company has already effected a registration for the
     Holders pursuant to this Section 1.4, and such registration statement
     remains effective; or

               (iv) in any particular jurisdiction in which the Company would be
     required to qualify to do business or to execute a general consent to
     service of process in effecting such registration, qualification or
     compliance.

          1.5 Obligations of the Company. Whenever required under this Section 1
to effect the registration of any Registrable Securities, the Company shall, as
expeditiously as reasonably possible (and subject to the foregoing):

               (a) Prepare and file with the SEC a registration statement with
respect to such Registrable Securities and use its reasonable best efforts to
cause such registration statement to become effective as soon as possible, and
keep such registration statement effective until all shares registered
thereunder cease to be Registrable Securities; provided, however, that at any
time upon written notice to the participating Holders and for a period not to
exceed ninety (90) days thereafter (exclusive of any deferral under Section 1.4)
(the "SUSPENSION PERIOD"), the Company may suspend the use or effectiveness of
any registration statement (and the participating Holders hereby agree not to
offer or sell any Registrable Securities pursuant to such

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registration statement during the Suspension Period) if the Company reasonably
concludes that there is or may be in existence material nonpublic information or
events involving the Company, the failure of which to be disclosed in the
prospectus included in the registration statement could result in a Violation
(as defined below), or the Company intends to complete a public offering within
ninety (90) days, other than pursuant to a Special Registration Statement. In no
event shall any Suspension Period, when taken together with all prior Suspension
Periods, exceed ninety (90) days in the aggregate in any twelve (12) month
period. If so directed by the Company, all Holders registering shares under such
registration statement shall (i) not offer to sell any Registrable Securities
pursuant to the registration statement during the period in which the delay or
suspension is in effect after receiving notice of such delay or suspension; and
(ii) use their best efforts to deliver to the Company (at the Company's expense)
all copies, other than permanent file copies then in such Holders' possession,
of the prospectus relating to such Registrable Securities current at the time of
receipt of such notice.

               (b) Prepare and file with the SEC such amendments and supplements
to such registration statement and the prospectus used in connection with such
registration statement as may be necessary to comply with the provisions of the
Act with respect to the disposition of all securities covered by such
registration statement;

               (c) Furnish to the Holders such numbers of copies of a
prospectus, including a preliminary prospectus, in conformity with the
requirements of the Act, and such other documents as they may reasonably request
in order to facilitate the disposition of Registrable Securities owned by them;

               (d) Use its reasonable best efforts to register and qualify the
securities covered by such registration statement under such other securities or
Blue Sky laws of such jurisdictions as shall be reasonably requested by the
Holders; provided that the Company shall not be required in connection therewith
or as a condition thereto to qualify to do business or to file a general consent
to service of process in any such states or jurisdictions, unless the Company is
already subject to service in such jurisdiction and except as may be required by
the Act;

               (e) In the event of any underwritten public offering, enter into
and perform its obligations under an underwriting agreement, in usual and
customary form, with the managing underwriter of such offering. Each Holder
participating in such underwriting shall also enter into and perform its
obligations under such an agreement, and such agreement shall specify that, and
the Company shall cause, the same opinions of counsel of the Company and
"comfort letters" of the auditors of the Company as are delivered to the
managing underwriter of such offering to also be addressed and delivered to each
Holder;

               (f) Promptly notify each Holder of Registrable Securities covered
by such registration statement at any time when a prospectus relating thereto is
required to be delivered under the Act as a result of the happening of any event
as a result of which the prospectus included in such registration statement, as
then in effect, includes an untrue statement of a material fact or omits to
state a material fact required to be stated therein or necessary to make the
statements therein not misleading in the light of the circumstances then
existing and

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promptly prepare and distribute any amendment, prospectus or supplement
necessary to render the registration statement not deficient or misleading;

               (g) Cause all such Registrable Securities registered hereunder to
be listed on each securities exchange on which similar securities issued by the
Company are then listed (or the Nasdaq Global Market, if applicable);

               (h) Provide a transfer agent and registrar for all Registrable
Securities registered hereunder and a CUSIP number for all such Registrable
Securities, in each case not later than the effective date of such registration;

               (i) Otherwise use its best efforts to comply with the securities
laws of the United States and other applicable jurisdictions and all applicable
rules and regulations of the SEC and comparable governmental agencies in other
applicable jurisdictions and make generally available to its holders, in each
case as soon as practicable, an earnings statement of the Company which will
satisfy the provisions of Section 11(a) of the Act; and

               (j) Otherwise cooperate with the underwriter or underwriters, the
SEC and other regulatory agencies and take all actions and execute and deliver
or cause to be executed and delivered all documents necessary to effect the
registration of any Registrable Securities hereunder.

          1.6 Furnish Information. It shall be a condition precedent to the
obligations of the Company to take any action pursuant to this Section 1 with
respect to the Registrable Securities of any selling Holder that such Holder
shall furnish to the Company such information regarding itself, the Registrable
Securities held by it, and the intended method of disposition of such securities
as shall be required to effect the registration of such Holder's Registrable
Securities.

          1.7 Expenses of Registration. The Company shall bear and pay all
expenses incurred in connection with any registration, filing or qualification
of Registrable Securities with respect to the registrations pursuant to this
Section 1 for each Holder, including (without limitation) all registration,
filing, and qualification fees, printers and accounting fees relating or
apportionable thereto and the fees and disbursements of one counsel for the
Holders registering their shares thereunder, but excluding underwriting
discounts and commissions relating to the Registrable Securities.

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          1.8 Indemnification. In the event any Registrable Securities are
included in a registration statement under this Section 1:

               (a) To the extent permitted by law, the Company will indemnify,
defend and hold harmless each Holder, its officers, directors, employees, agents
and representatives, any underwriter (as defined in the Act) for such Holder and
each person, if any, who controls such Holder or underwriter within the meaning
of the Act or the 1934 Act (each, a "COMPANY INDEMNIFIED PERSON"), against any
losses, claims, damages, or liabilities (joint or several) to which they may
become subject under the Act, the 1934 Act or other federal or state law,
insofar as such losses, claims, damages, or liabilities (or actions in respect
thereof) (the "COMPANY INDEMNIFIED AMOUNT") arise out of or are based upon any
of the following (collectively, a "VIOLATION"): (i) any untrue statement of a
material fact contained in such registration statement, including any
preliminary prospectus or final prospectus contained therein or any amendments
or supplements thereto, (ii) the omission to state therein a material fact
required to be stated therein, or necessary to make the statements therein not
misleading, or (iii) any violation or alleged violation by the Company of the
Act, the 1934 Act, any state securities law or any rule or regulation
promulgated under the Act, the 1934 Act or any state securities or Blue Sky laws
or any rule or regulation thereunder in connection with such registration; and
the Company will pay to each such Company Indemnified Person, as incurred, any
legal or other expenses reasonably incurred by them in connection with
investigating or defending any Company Indemnified Amount; provided, however,
that the indemnity agreement contained in this subsection 1.8(a) shall not apply
to amounts paid in settlement of any such loss, claim, damage, liability, or
action if such settlement is effected without the consent of the Company (which
consent shall not be unreasonably withheld), nor shall the Company be liable in
any such case for any such Company Indemnified Amount as to any Company
Indemnified Person to the extent such liability arises out of or is based upon a
Violation (i) which occurs in reliance upon and in conformity with written
information relating to such Company Indemnified Person and furnished expressly
for use in connection with such registration by such Company Indemnified Person
or (ii) contained in a preliminary prospectus and corrected in a final or
amended prospectus if such seller, underwriter or controlling person received
notice of such final or amended prospectus prior to the effective date of the
registration statement but failed to deliver a copy of the final or amended
prospectus at or prior to the confirmation of the sale of the Registrable
Securities to the person asserting any such loss, claim, damage or liability
resulting from a Violation contained in such preliminary prospectus, in any case
where such delivery is required by the Act.

               (b) To the extent permitted by law, each selling Holder will
indemnify and hold harmless the Company, each of its directors, each of its
officers who has signed the registration statement, each person, if any, who
controls the Company within the meaning of the Act, any underwriter, any other
Holder selling securities in such registration statement and any controlling
person of any such underwriter or other Holder, against any losses, claims,
damages, or liabilities (joint or several) to which any of the foregoing persons
may become subject, under the Act, the 1934 Act or other federal or state law,
insofar as such losses, claims, damages, or liabilities (or actions in respect
thereto) (the "HOLDER INDEMNIFIED AMOUNT") arise out of or are based upon any
Violation, in each case to the extent (and only to the extent) that such
Violation occurs in reliance upon and in conformity with written information
relating to such Holder and

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furnished by such Holder expressly for use in connection with such registration;
and each such Holder will pay, as incurred, any legal or other expenses
reasonably incurred by any person intended to be indemnified pursuant to this
subsection 1.8(b), in connection with investigating or defending any Holder
Indemnified Amount; provided, however, that the indemnity agreement contained in
this subsection 1.8(b) shall not apply to amounts paid in settlement of any such
loss, claim, damage, liability or action if such settlement is effected without
the consent of the Holder, which consent shall not be unreasonably withheld; and
provided, that, in no event shall any indemnity under this subsection 1.8(b)
exceed the net proceeds from the offering received by such Holder.

               (c) Promptly after receipt by an indemnified party under this
Section 1.8 of notice of the commencement of any action (including any
governmental action), such indemnified party will, if a claim in respect thereof
is to be made against any indemnifying party under this Section 1.8, deliver to
the indemnifying party a written notice of the commencement thereof and the
indemnifying party shall have the right to participate in, and, to the extent
the indemnifying party so desires, jointly with any other indemnifying party
similarly noticed, to assume the defense thereof with counsel mutually
satisfactory to the parties; provided, however, that an indemnified party
(together with all other indemnified parties which may be represented without
conflict by one counsel) shall have the right to retain one separate counsel,
with the fees and expenses to be paid by the indemnifying party, if
representation of such indemnified party by the counsel retained by the
indemnifying party would be inappropriate due to actual or potential differing
interests between such indemnified party and any other party represented by such
counsel in such proceeding. The failure to deliver written notice to the
indemnifying party within a reasonable time of the commencement of any such
action, if prejudicial to its ability to defend such action, shall relieve such
indemnifying party of any liability to the indemnified party under this Section
1.8, but the omission so to deliver written notice to the indemnifying party
will not relieve it of any liability that it may have to any indemnified party
otherwise than under this Section 1.8.

               (d) If the indemnification provided for in this Section 1.8 is
held by a court of competent jurisdiction to be unavailable to an indemnified
party with respect to any loss, liability, claim, damage, or expense referred to
herein, then the indemnifying party, in lieu of indemnifying such indemnified
party hereunder, shall contribute to the amount paid or payable by such
indemnified party as a result of such loss, liability, claim, damage, or expense
in such proportion as is appropriate to reflect the relative fault of the
indemnifying party on the one hand and of the indemnified party on the other in
connection with the Violation that resulted in such loss, liability, claim,
damage, or expense as well as any other relevant equitable considerations. The
relative fault of the indemnifying party and of the indemnified party shall be
determined by reference to, among other things, whether the untrue or alleged
untrue statement of a material fact or the omission to state a material fact
relates to information supplied by the indemnifying party or by the indemnified
party and the parties' relative intent, knowledge, access to information, and
opportunity to correct or prevent such statement or omission; and provided,
that, in no event shall any contribution under this subsection 1.8(d) exceed the
net proceeds from the offering received by such Holder.

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               (e) Notwithstanding the foregoing, to the extent that the
provisions on indemnification and contribution contained in the underwriting
agreement entered into in connection with the underwritten public offering are
in conflict with the foregoing provisions, the provisions in the underwriting
agreement shall control.

               (f) The obligations of the Company and Holders under this Section
1.8 shall survive the completion of any offering of Registrable Securities in a
registration statement under this Section 1, and otherwise.

          1.9 Reports Under 1934 Act. With a view to making available to the
Holders the benefits of Rule 144 promulgated under the Act and any other rule or
regulation of the SEC that may at any time permit a Holder to sell securities of
the Company to the public without registration or pursuant to a registration on
Form S-3, the Company agrees to use its reasonable best efforts to:

               (a) make and keep public information available, as those terms
are understood and defined in SEC Rule 144, at all times after ninety (90) days
after the effective date of the first registration statement filed by the
Company for the offering of its securities to the general public;

               (b) take such action, including the voluntary registration of its
Common Stock under Section 12 of the 1934 Act, as is necessary to enable the
Holders to utilize Form S-3 for the sale of their Registrable Securities, such
action to be taken as soon as practicable after the end of the fiscal year in
which the first registration statement filed by the Company for the offering of
its securities to the general public is declared effective;

               (c) file with the SEC in a timely manner all reports and other
documents required of the Company under the Act and the 1934 Act; and

               (d) furnish to any Holder, so long as the Holder owns any
Registrable Securities, forthwith upon request (i) a written statement by the
Company that it has complied with the reporting requirements of SEC Rule 144 (at
any time after ninety (90) days after the effective date of the first
registration statement filed by the Company), the Act and the 1934 Act (at any
time after it has become subject to such reporting requirements), or that it
qualifies as a registrant whose securities may be resold pursuant to Form S-3
(at any time after it so qualifies), (ii) a copy of the most recent annual or
quarterly report of the Company and such other reports and documents so filed by
the Company, and (iii) such other information as may be reasonably requested in
availing any Holder of any rule or regulation of the SEC which permits the
selling of any such securities without registration or pursuant to such form.

          1.10 Assignment of Registration Rights. The rights to cause the
Company to register Registrable Securities pursuant to this Section 1 may be
assigned (but only with all related obligations) by a Holder to a Permitted
Assignee (as defined below), provided that: (a) the Company is, within a
reasonable time after such transfer, furnished with written notice of the name
and address of such transferee or assignee and the securities with respect to
which such registration rights are being assigned; (b) such transferee or
assignee agrees in writing to be bound by and subject to the terms and
conditions of this Agreement; and (c) such assignment

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shall be effective only if immediately following such transfer the further
disposition of such securities by the transferee or assignee is restricted under
the Act. For purposes of this Section 1.10 a "PERMITTED ASSIGNEE" shall mean an
entity that acquires all or substantially all of the ownership interests of a
Holder.

          1.11 "Market Stand-Off" Agreement. The Investor hereby agrees that,
during the one hundred eighty (180) day period following the effective date of
the registration statement for the Qualified Public Offering or such other
period as requested of all Company executive officers required to file Forms 3
and 4 and directors of the Company by the underwriters in the Qualified Public
Offering in order to comply with Rule 2711 of the National Association of
Securities Dealers or otherwise, the Investor shall not, to the extent requested
by the Company and such underwriter, directly or indirectly sell, offer to sell,
contract to sell (including, without limitation, any short sale), grant any
option to purchase or otherwise transfer or dispose of (other than to donees who
agree to be similarly bound) any securities of the Company held by it at any
time during such period except Common Stock included in such registration;
provided, however, that all executive officers and directors of the Company
enter into similar agreements. In addition to the obligations under this
Section, the Investor agrees to execute a separate agreement on form
satisfactory to such underwriter containing such covenant and obligation.

     In order to enforce the foregoing covenant, the Company may impose
stop-transfer instructions with respect to the Registrable Securities of the
Investor (and the shares or securities of every other person subject to the
foregoing restriction) until the end of such period.

     Notwithstanding the foregoing, the obligations described in this Section
1.11 shall not apply to a registration relating solely to employee benefit plans
on Form S-1 or Form S-8 or similar forms which may be promulgated in the future,
or a registration relating solely to SEC Rule 145, or a transaction on Form S-4
or similar forms which may be promulgated in the future.

          1.12 Termination of Registration Rights.

          The right of any Holder to request registration or inclusion in any
registration pursuant to Section 1 shall terminate once all Company securities
held by such Holder cease to be Registrable Securities, and this Agreement shall
terminate once all of the securities covered hereby cease to be Registrable
Securities.

     2. Miscellaneous.

          2.1 Successors and Assigns. Except as otherwise provided herein, the
terms and conditions of this Agreement shall inure to the benefit of and be
binding upon the respective successors and permitted assigns of the parties
(including transferees of any shares of Registrable Securities). Nothing in this
Agreement, express or implied, is intended to confer upon any party other than
the parties hereto or their respective successors and assigns any rights,
remedies, obligations, or liabilities under or by reason of this Agreement,
except as expressly provided in this Agreement. Subject to the terms of this
Agreement, no party hereby may assign its rights or obligations hereunder
(whether by operation of law or otherwise, including by merger, asset sale, sale
of stock or otherwise) without the prior written consent of the other parties
hereto.

                                       11

<PAGE>

          2.2 Governing Law. This Agreement shall be governed in all respects by
the laws of the State of Delaware without giving effect to principles of
conflicts of law thereunder.

          2.3 Counterparts. This Agreement 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. One or more counterparts
of this Agreement may be delivered via telecopier with the intention that they
shall each have the same effect as an original counterpart hereof.

          2.4 Titles and Subtitles. The titles and subtitles used in this
Agreement are used for convenience only and are not to be considered in
construing or interpreting this Agreement.

          2.5 Notices. Unless otherwise provided, all notices, requests,
consents and other communications hereunder shall be in writing, shall be
addressed to the receiving party's address set forth below or to such other
address as a party may designate by notice hereunder, and shall be either (i)
delivered by hand, (ii) made by telecopy or facsimile transmission, (iii) sent
by overnight courier, or (iv) sent by registered or certified mail, return
receipt requested, postage prepaid.

If to the Company:    Archemix Corp.
                      300 Third Street
                      Cambridge, MA 02142
                      Attn: Chief Executive Officer
                      Facsimile: (617) 621-9300

With a copy to:       Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
                      One Financial Center
                      Boston, MA 02111
                      Attn: Jeffrey M. Wiesen, Esquire
                      Facsimile: (617) 542-2241

If to the Investor:   Nuvelo, Inc.
                      201 Industrial Road, Suite 310
                      San Carlos, CA 94070
                      Attn: Chief Executive Officer
                      Facsimile: (650) 517-8058

With a copy to:       Cooley Godward LLP
                      Five Palo Alto Square
                      3000 El Camino Real
                      Palo Alto, CA 94306-2155
                      Attn: John Geschke, Esquire
                      Facsimile: (650) 849-7400

                                       12

<PAGE>

     All notices, requests, consents and other communications hereunder shall be
deemed to have been given either (i) if by hand, at the time of the delivery
thereof to the receiving party at the address of such party set forth above,
(ii) if made by telecopy or facsimile transmission, at the time that receipt
thereof has been acknowledged by electronic confirmation or otherwise, (iii) if
sent by overnight courier, on the next business day following the day such
notice is delivered to the courier service, or (iv) if sent by registered or
certified mail, on the fifth business day following the day such mailing is
made.

          2.6 Expenses. If any action at law or in equity is necessary to
enforce or interpret the terms of this Agreement, the prevailing party shall be
entitled to reasonable attorneys' fees, costs and necessary disbursements in
addition to any other relief to which such party may be entitled.

          2.7 Entire Agreement; Amendments and Waivers. This Agreement
constitutes the full and complete agreement of the parties hereto, and
supersedes all prior agreements, whether written or oral, with respect to the
subject matter hereof. Any term of this Agreement may be amended and the
observance of any term of this Agreement may be waived (either generally or in a
particular instance and either retroactively or prospectively), only with the
written consent (i) of the Company, (ii) the Investor (so long as the Investor
holds Registrable Securities) and (iii) any transferee or assignee of
Registrable Securities pursuant to Section 1.10 of this Agreement who holds not
less than 250,000 shares of Registrable Securities. Any amendment or waiver
effected in accordance with this paragraph shall be binding upon each holder of
any Registrable Securities then outstanding, each future holder of all such
Registrable Securities, and the Company.

          2.8 Severability. If one or more provisions of this Agreement are held
to be unenforceable under applicable law, such provision shall be excluded from
this Agreement and the balance of the Agreement shall be interpreted as if such
provision were so excluded and shall be enforceable in accordance with its
terms.

          2.9 Interpretation. The parties hereby acknowledge and agree that: (i)
each party and its counsel reviewed and negotiated the terms and provisions of
this Agreement and have contributed to its revision; (ii) the rule of
construction to the effect that any ambiguities are resolved against the
drafting party shall not be employed in the interpretation of this Agreement;
and (iii) the terms and provisions of this Agreement shall be construed fairly
as to all parties hereto and not in a favor of or against any party, regardless
of which party was generally responsible for the preparation of this Agreement.

          2.10 Remedies. It is specifically understood and agreed that any
breach of the provisions of this Agreement by any person subject hereto will
result in irreparable injury to the other parties hereto, that the remedy at law
alone will be an inadequate remedy for such breach, and that, in addition to any
other remedies which they may have, such other parties may enforce their
respective rights by actions for specific performance (to the extent permitted
by law).

             [THE REMAINDER OF THE PAGE IS LEFT INTENTIONALLY BLANK]

                                       13

<PAGE>

     IN WITNESS WHEREOF, the parties hereto have executed this REGISTRATION
RIGHTS AGREEMENT or caused this Agreement to be executed by their duly
authorized representatives, as of the date first written above.

                                        COMPANY:

                                        ARCHEMIX CORP.

                                        By:
                                            ------------------------------------
                                        Name:
                                              ----------------------------------
                                        Title:
                                               ---------------------------------

                                        INVESTOR:

                                        NUVELO, INC.

                                        By:
                                            ------------------------------------
                                        Name:
                                              ----------------------------------
                                        Title:
                                               ---------------------------------

                                       14

<PAGE>

                                TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                                                            PAGE
                                                                            ----
<S>                                                                         <C>
1. Registration Rights...................................................      1
   1.1  Definitions......................................................      1
   1.2  Sale or Transfer of Shares; Legend...............................      2
   1.3  "Piggyback" Registration.........................................      3
   1.4  Demand Registration..............................................      4
   1.5  Obligations of the Company.......................................      5
   1.6  Furnish Information..............................................      7
   1.7  Expenses of Registration.........................................      7
   1.8  Indemnification..................................................      8
   1.9  Reports Under 1934 Act...........................................     10
   1.10 Assignment of Registration Rights................................     10
   1.11 "Market Stand-Off" Agreement.....................................     11
   1.12 Termination of Registration Rights...............................     11
2. Miscellaneous.........................................................     11
   2.1  Successors and Assigns...........................................     11
   2.2  Governing Law....................................................     12
   2.3  Counterparts.....................................................     12
   2.4  Titles and Subtitles.............................................     12
   2.5  Notices..........................................................     12
   2.6  Expenses.........................................................     13
   2.7  Entire Agreement; Amendments and Waivers.........................     13
   2.8  Severability.....................................................     13
   2.9  Interpretation...................................................     13
   2.10 Remedies.........................................................     13
</TABLE>

                                       -i-<PAGE>
                                                                    Exhibit 4.5

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE SOLD, PLEDGED OR
OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT
OR PURSUANT TO AN EXEMPTION FROM THE REGISTRATION REQUIREMENTS THEREOF.

                            WARRANT TO PURCHASE STOCK

Corporation:                             ARCHEMIX CORP., a Delaware corporation
Number of Shares:                        80,000
Class of Stock:                          Series A Convertible Preferred Stock
Initial Exercise Price:                  $1.00 per share
Issue Date:                              October 3, 2001
Expiration Date:                         October 3, 2008

     THIS WARRANT CERTIFIES THAT, in consideration of the payment of $1.00 and
for other good and valuable consideration, COMERICA BANK-CALIFORNIA or its
permitted assignee ("Holder") is entitled to purchase the number of fully paid
and nonassessable shares of the class of securities (the "Shares") of the
corporation (the "Company") at the initial exercise price per Share (the
"Warrant Price") all as set forth above and as adjusted pursuant to Article 2 of
this warrant, subject to the provisions and upon the terms and conditions set
forth in this warrant.

ARTICLE 1. EXERCISE.

     1.1   Method of Exercise. Holder may exercise this warrant by delivering
this warrant and a duly executed Notice of Exercise in substantially the form
attached as Appendix 1 to the principal office of the Company. Unless Holder is
exercising the conversion right set forth in Section 1.2, Holder shall also
deliver to the Company a check for the aggregate Warrant Price for the Shares
being purchased.

     1.2   Conversion Right. In lieu of exercising this warrant as specified in
Section 1.1, Holder may from time to time after the earlier of an Acquisition
(as defined herein) or the closing of a registered public offering of the
Company's common stock convert this warrant, in whole or in part, into a number
of Shares determined by dividing (a) the aggregate fair market value of the
Shares or other securities otherwise issuable upon exercise of this warrant
minus the aggregate Warrant Price of such Shares by (b) the fair market value of
one Share. The fair market value of the Shares shall be determined pursuant to
Section 1.3.

     1.3   Fair Market Value. If the Shares are traded regularly in a public
market, the fair market value of the Shares shall be the closing price of the
Shares (or the closing price of the Company's stock into which the Shares are
convertible) reported for the business day immediately before Holder delivers
its Notice of Exercise to the Company. If the Shares are not regularly traded in
a public market, the Board of Directors of the Company shall determine fair
market value in its reasonable good faith judgment. The foregoing
notwithstanding, if Holder advises the Board of Directors in writing that Holder
disagrees with such determination, then the Company and Holder shall promptly
agree upon a reputable investment banking firm to

                                        1
<PAGE>

undertake such valuation. If the valuation of such investment banking firm is
more than 10% greater than that determined by the Board of Directors, then all
fees and expenses of such investment banking firm shall be paid by the Company.
In all other circumstances, such fees and expenses shall be paid by Holder.

     1.4   Delivery of Certificate and New Warrant. Promptly after Holder
exercises or converts this warrant, the Company shall deliver to Holder
certificates for the Shares acquired and, if this warrant has not been fully
exercised or converted and has not expired, a new warrant representing the
Shares not so acquired.

     1.5   Replacement of Warrants. On receipt of evidence reasonably
satisfactory to the Company of the loss, theft, destruction or mutilation of
this warrant and, in the case of loss, theft or destruction, on delivery of an
indemnity agreement reasonably satisfactory in form and amount to the Company
or, in the case of mutilation, on surrender and cancellation of this warrant,
the Company at its expense shall execute and deliver, in lieu of this warrant, a
new warrant of like tenor.

     1.6   Repurchase on Sale, Merger, or Consolidation of the Company.

           1.6.1 "Acquisition." For the purpose of this warrant, "Acquisition"
means any sale, license, or other disposition of all or substantially all of the
assets (including intellectual property) of the Company, or any reorganization,
consolidation, or merger of the Company where the holders of the Company's
securities before the transaction beneficially own less than 50% of the
outstanding voting securities of the surviving entity after the transaction.

           1.6.2 Assumption of Warrant. Upon the closing of any Acquisition the
successor entity shall assume the obligations of this warrant, and this warrant
shall then be exercisable for the same securities, cash, and property as would
be payable for the Shares issuable upon exercise of the unexercised portion of
this warrant as if such Shares were outstanding on the record date for the
Acquisition and subsequent closing. The Warrant Price shall be adjusted
accordingly.

ARTICLE 2. ADJUSTMENTS TO THE SHARES.

     2.1   Stock Dividends, Splits, Etc. If the Company declares or pays a
dividend on its common stock payable in common stock, or other securities,
subdivides the outstanding common stock into a greater amount of common stock,
then upon exercise of this warrant, for each Share acquired, Holder shall
receive, without cost to Holder, the total number and kind of securities to
which Holder would have been entitled had Holder owned the Shares of record as
of the date the dividend or subdivision occurred.

     2.2   Reclassification, Exchange or Substitution. Upon any
reclassification, exchange, substitution, or other event that results in a
change of the number and/or class of the securities issuable upon exercise or
conversion of this warrant, Holder shall be entitled to receive, upon exercise
or conversion of this warrant, the number and kind of securities and property
that Holder would have received for the Shares if this warrant had been
exercised immediately before such reclassification, exchange, substitution, or
other event. Such an event shall include any automatic conversion of the
outstanding or issuable securities of the Company of the same class

                                       2
<PAGE>

or series as the Shares to common stock pursuant to the terms of the Company's
Certificate of Incorporation upon the closing of a registered public offering of
the Company's common stock. The Company or its successor shall promptly issue to
Holder a new warrant for such new securities or other property. The new warrant
shall provide for adjustments which shall be as nearly equivalent as may be
practicable to the adjustments provided for in this Article 2 including, without
limitation, adjustments to the Warrant Price and to the number of securities or
property issuable upon exercise of the new warrant. The provisions of this
Section 2.2 shall similarly apply to successive reclassifications, exchanges,
substitutions, or other events.

     2.3   Adjustments for Combinations, Etc. If the outstanding Shares are
combined or consolidated, by reclassification or otherwise, into a lesser number
of shares, the Warrant Price shall be proportionately increased.

     2.4   Adjustments for Diluting Issuances. The number of Shares issuable
upon the conversion of the Shares into common stock shall be subject to
adjustment, from time to time, in the manner set forth in the Certificate of
Incorporation of Company in the form existent on the Issue Date.

     2.5   No Impairment. The Company shall not, by amendment of its Certificate
of Incorporation or through a reorganization, transfer of assets, consolidation,
merger, dissolution, issue, or sale of securities or any other voluntary action,
avoid or seek to avoid the observance or performance of any of the terms to be
observed or performed under this warrant by the Company, but shall at all times
in good faith assist in carrying out all the provisions of this Article 2 and in
taking all such action as may be necessary or appropriate to protect Holder's
rights under this Article against impairment. If the Company takes any action
affecting the Shares or its common stock other than as described above that
adversely affects Holder's rights under this warrant, the Warrant Price shall be
adjusted downward and the number of Shares issuable upon exercise of this
warrant shall be adjusted upward in such a manner that the aggregate Warrant
Price of this warrant is unchanged.

     2.6   Certificate as to Adjustments. Upon each adjournment of the Warrant
Price, the Company at its expense shall promptly compute such adjustment, and
furnish Holder with a certificate of its Chief Financial Officer setting forth
such adjustment and the facts upon which such adjustment is based. The Company
shall, upon written request, furnish Holder a certificate setting forth the
Warrant Price in effect upon the date thereof and the series of adjustments
leading to such Warrant Price.

ARTICLE 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY.

     3.1   Representations and Warranties. The Company hereby represents and
warrants to the Holder as follows:

           (a) The initial Warrant Price referenced on the first page of this
warrant is not greater than the fair market value of the Shares as of the date
of this warrant.

           (b) All Shares which may be issued upon the exercise of the purchase
right represented by this warrant, and all securities, if any, issuable upon
conversion of the Shares, shall, upon issuance, be duly authorized, validly
issued, fully paid and nonassessable, and free of

                                       3

<PAGE>

any liens and encumbrances except for restrictions on transfer provided for
herein or under applicable federal and state securities laws.

           (c) The Company's capitalization table attached to this warrant is
true and complete as of the Issue Date.

     3.2   Notice of Certain Events. If the Company proposes at any time (a) to
declare any dividend or distribution upon its common stock, whether in cash,
property, stock, or other securities and whether or not a regular cash dividend;
(b) to offer for subscription pro rata to the holders of any class or series of
its stock any additional shares of stock of any class or series or other rights;
(c) to effect any reclassification or recapitalization of common stock; or (d)
to merge or consolidate wish or into any other corporation, or sell, lease,
license, or convey all or substantially all of its assets, or to liquidate,
dissolve or wind up, then, in connection with each such event, the Company shall
give Holder (1) at least 20 days prior written notice of the date on which a
record will be taken for such dividend, distribution, or subscription rights
(and specifying the date on which the holders of common stock will be entitled
thereto) or for determining rights to vote, if any, in respect of the matters
referred to in (a) and (b) above; and (2) in the case of the matters referred to
in (c) and (d) above at least 20 days prior written notice of the date when the
same will take place (and specifying the date on which the holders of common
stock will be entitled to exchange their common stock for securities or other
property deliverable upon the occurrence of such event).

     3.3   Information Rights. So long as the Holder holds this warrant and/or
any of the Shares, the Company shall deliver to the Holder (a) promptly after
mailing, copies of all communiques to the shareholders of the Company, (b)
within ninety (90) days after the end of each fiscal year of the Company, the
annual audited financial statements of the Company certified by independent
public accountants of recognized standing and (c) within forty-five (45) days
after the end of each of the first three quarters of each fiscal year, the
Company's quarterly, unaudited financial statements.

ARTICLE 4. MISCELLANEOUS.

     4.1   Term. This warrant is exercisable in whole or in part, at any time
and from time to time on or before the Expiration Date set forth above.

     4.2   Compliance with Securities Act.

           (a) The Holder acknowledges that this warrant and the Shares have not
been registered under the Securities Act of 1933, as amended, and the rules and
regulations thereunder, or any successor legislation (the "Securities Act") and,
subject to Section 4.3, agrees not to sell, pledge, distribute, offer for sale,
transfer or otherwise dispose of this warrant or any Shares in the absence of
(i) an effective registration statement under the Securities Act covering this
warrant or such Shares and registration or qualification of this warrant or such
Shares under any applicable "blue sky" or state securities law then in effect,
or (ii) an opinion of counsel, satisfactory to the Company, that such
registration and qualification are not required. The Company may delay issuance
of the Shares until completion of any action or obtaining of any consent, which
the Company deems necessary under any applicable law (including without

                                       4

<PAGE>

limitation state securities or "blue sky" laws).

           (b) Without limiting the generality of Section 4.2(a), unless the
offer and sale of any Shares shall have been effectively registered under the
Securities Act, the Company shall be under no obligation to issue the Shares
unless and until the Holder shall have executed the Notice of Exercise in
substantially the form attached as Appendix 1, including the warranty at the
time of such exercise that the Holder is acquiring such shares for its own
account, for investment and not with a view to, or for sale in connection with,
the distribution of any such shares.

           (c) Certificates delivered to the Holder pursuant to Section 1.2
shall bear the following legend or a legend in substantially similar form:

     "THE SHARES REPRESENTED BY THIS CERTIFICATE HAVE BEEN TAKEN FOR INVESTMENT
     AND THEY MAY NOT BE SOLD OR OTHERWISE TRANSFERRED BY ANY PERSON, INCLUDING
     A PLEDGEE, IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT FOR THE
     SHARES UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR AN OPINION OF
     COUNSEL, SATISFACTORY TO THE COMPANY, THAT AN EXEMPTION FROM REGISTRATION
     IS THEN AVAILABLE."

     4.3   Transfer Procedure. Subject to the provisions of Section 4.2, Holder
may transfer all or part of this warrant or the Shares issuable upon exercise of
this warrant (or the securities issuable, directly or indirectly, upon
conversion of the Shares, if any) by giving the Company notice of the portion of
the warrant being transferred setting forth the name, address and taxpayer
identification number of the transferee and surrendering this warrant to the
Company for reissuance to the transferee(s) (and Holder, if applicable);
provided, however, that Holder may transfer all or part of this warrant to its
affiliates, including, without limitation, Holder's parent company, at any time
without notice to the Company, and such affiliate shall then be entitled to all
the rights of Holder under this warrant and any related agreements, and the
Company shall cooperate fully in ensuring that any stock issued upon exercise of
this warrant is issued in the name of the affiliate that exercises the warrant.
The terms and conditions of this warrant shall inure to the benefit of, and be
binding upon, the Company and the holders hereof and their respective permitted
successors and assigns.

     4.4   Notices. All notices and other communications from the Company to the
Holder, or vice versa, shall be deemed delivered and effective when given
personally or mailed by first-class registered or certified mail, postage
prepaid, at such address as may have been furnished to the Company or the
Holder, as the case may be, in writing by the Company or such Holder from time
to time, with a copy to Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C., One
Financial Center, Boston, MA 02111, Attn: Jeffrey M. Wiesen, Esq. (provided that
failure to deliver a copy to a person other than Company shall not invalidate a
notice or communication otherwise delivered to Company in accordance with this
Section). All notices to the Holder shall be addressed as follows:

                                       5
<PAGE>

                            Comerica Bank-California
                            Attn: Controllers Department
                            P.O. Box 92991
                            Los Angeles, CA 90009-2991

                            with a copy to:

                            Comerica Bank-California
                            Attn: Warrant Administrator Special Markets Division
                            P.O. Box 7279
                            San Francisco, CA 94120-7279

     4.5   Waiver. This warrant and any term hereof may be changed, waived,
discharged or terminated only by an instrument in writing signed by the party
against which enforcement of such change, waiver, discharge or termination is
sought.

     4.6   Attorneys' Fees. In the event of any dispute between the parties
concerning the terms and provisions of this warrant, the party prevailing in
such dispute shall be entitled to collect from the other party all costs
incurred in such dispute, including reasonable attorneys' fees.

     4.7   Governing Law. This warrant shall be governed by and construed in
accordance with the laws of the State of Delaware, without giving effect to its
principles regarding conflicts of law.

                                            ARCHEMIX CORP.

                                            By:    /s/ Martin Stanton
                                                   ---------------------------

                                            Name:  Martin Stanton
                                                   ---------------------------

                                            Title: President
                                                   ---------------------------

Authorized signatories under Corporate Resolutions to Borrow or an authorized
signer(s) under a resolution covering warrants must sign the warrant.

                                       6

<PAGE>

                                   APPENDIX I

                               NOTICE OF EXERCISE

     1.    The undersigned hereby elects to purchase _____________ shares (the
"Warrant Stock") of the _____________ stock of ARCHEMIX CORP. (the "Company")
pursuant to the terms of the attached warrant, and tenders herewith payment of
the purchase price of such shares in full.

     1.    The undersigned hereby elects to convert the attached warrant into
shares in the manner specified in the warrant. This conversion is exercised with
respect to __________ of the shares covered by the warrant.

     [STRIKE PARAGRAPH THAT DOES NOT APPLY.]

     2.    Please issue a certificate or certificates representing said shares
in the name of the undersigned or in such other name as is specified below:

                                       Comerica Bank-California
                                       Attn: Controllers Department
                                       P.O. Box 92991
                                       Los Angeles, CA 90009
                                       Or Registered Assignee

     3.    The undersigned is aware that the Warrant Stock has not been and will
not be registered under the Securities Act of 1933, as amended (the "Securities
Act") or any state securities laws. The undersigned understands that reliance by
the Company on exemptions under the Securities Act is predicated in part upon
the truth and accuracy of the statements of the undersigned in this Notice of
Exercise.

     The undersigned represents and warrants that (1) it has been furnished with
all information which it deems necessary to evaluate the merits and risks of the
purchase of the Warrant Stock, (2) it has had the opportunity to ask questions
concerning the Warrant Stock and the Company and all questions posed have been
answered to its satisfaction, (3) it has been given the opportunity to obtain
any additional information it deems necessary to verify the accuracy of any
information obtained concerning the Warrant Stock and the Company and (4) it has
such knowledge and experience in financial and business matters that it is able
to evaluate the merits and risks of purchasing the Warrant Stock and to make an
informed investment decision relating thereto.

     The undersigned hereby represents and warrants that it is purchasing the
Warrant Stock for its own account for investment and not with a view to the sale
or distribution of all or any part of the Warrant Stock.

     The undersigned understands that because the Warrant Stock has not been
registered under the Securities Act, it must continue to bear the economic risk
of the investment for an indefinite period of time and the Warrant Stock cannot
be sold unless it is subsequently

                                       1

<PAGE>

registered under applicable federal and state securities laws or an exemption
from such registration is available.

     The undersigned agrees that, subject to Section 4.3 of the Warrant, it will
in no event sell or distribute or otherwise dispose of all or any part of the
Warrant Stock unless (1) there is an effective registration statement under the
Securities Act and applicable state securities laws covering any such
transaction involving the Warrant Stock, or (2) the Company receives an opinion
satisfactory to the Company of the undersigned's legal counsel stating that such
transaction is exempt from registration. The undersigned consents to the placing
of a legend on its certificate for the Warrant Stock stating that the Warrant
Stock has not been registered and setting forth the restriction on transfer
contemplated hereby and to the placing of a stop transfer order on the books of
the Company and with any transfer agents against the Warrant Stock until the
Warrant Stock may be legally resold or distributed without restriction.

COMERICA BANK-CALIFORNIA or Registered Assignee

--------------------------------------------
(Signature)

--------------------------------------------
(Date)

                                       2

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