ARCA BIOPHARMA , I NC. WARRANT TO PURCHASE COMMON STOCK

Exhibit 4.9

THIS WARRANT AND THE UNDERLYING SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO SUCH SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE CORPORATION THAT SUCH REGISTRATION IS NOT REQUIRED.

ARCA BIOPHARMA , I NC .

WARRANT TO PURCHASE COMMON STOCK

Void After October 10, 2013

This certifies that, for value received, Boulder Ventures IV (Annex), L.P., with its principal office at 1900 Ninth Street, Suite 200, Boulder, CO 80302, or its assigns (the “ Holder ” or “ Purchaser ”), is entitled to subscribe for and purchase at the Exercise Price (as defined below) from ARCA biopharma, Inc., a Delaware corporation, with its principal office at 8001 Arista Place, Suite 200, Broomfield, Colorado 80021 (the “ Corporation ”), up to a number of Exercise Shares (as defined below), upon the terms and subject to the adjustments as provided herein.

This Warrant is being issued pursuant to the terms of the Note and Warrant Purchase Agreement, dated September 24, 2008, as amended by the First Amendment thereto, dated as of the date hereof, (as amended, the “ Note and Warrant Purchase Agreement ”) by and among the Corporation and the Purchasers listed on the Schedule of Purchasers thereto, as the same may be further amended from time to time (the “ Schedule of Purchasers ”). Capitalized terms used herein but not otherwise defined shall have the meanings given to them in the Note and Warrant Purchase Agreement.

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

(a) “ Exercise Period ” shall mean the time period commencing with the date of this Warrant and ending five (5) years from date of this Warrant, unless sooner terminated as provided below.

(b) “ Exercise Price ” shall mean the lesser of (i) $3.253 or (ii) the product of (x) the Parent Trading Price (as defined in the Merger Agreement) and (y) the Exchange Ratio (as defined in the Merger Agreement and determined in accordance with the methodology reflected in the Spreadsheet (as defined in the Merger Agreement)); provided, however that in no event shall the Exercise Price be less than $1.6265; and provided, further that the Exercise Price shall be subject to adjustment pursuant to the terms herein, including Section 5 below. Notwithstanding the forgoing, if the Merger (as defined below) does not close on or before March 31, 2009, the Exercise Price shall be $1.6265, subject to adjustment pursuant to the terms herein, including Section 5 below.

(c) “ Exercise Shares ” shall mean a number of shares of common stock of the Corporation (the “ Common Stock ”) issuable upon exercise of this Warrant equal to (i) one-fifth (1/5 ^th ) of such Purchaser’s Total Purchase Price (as defined in the Note and Warrant Purchase Agreement) divided by (b) the Exercise Price, rounded up to the nearest share and subject to adjustment pursuant to the terms herein, including Section 5 below.

(d) “ Merger Agreement ” shall mean that certain Agreement and Plan of Merger and Reorganization dated September 24, 2008, by and among the Corporation, Nuvelo, Inc., a Delaware corporation (the “ Parent ”) and Dawn Acquisition Sub, Inc., a Delaware corporation (the “ Merger Sub ”), pursuant to which Merger Sub will merge with and into the Corporation and the stockholders of the Corporation will receive shares of the capital stock of Parent in exchange for their capital stock of the Corporation (the “ Merger ”).

2. E XERCISE OF W ARRANT .

2.1 I N G ENERAL . The rights represented by this Warrant may be exercised in whole or in part at any time during the Exercise Period, by delivery of the following to the Corporation at its address set forth above (or at such other address as it may designate by notice in writing to the Holder):

(a) an executed Notice of Exercise in the form attached hereto;

(b) payment of the Exercise Price either (i) in cash or by check, or (ii) by cancellation of indebtedness, or (iii) pursuant to Section 2.1 below; and

(c) this Warrant.

Upon the exercise of the rights represented by this Warrant, a certificate or certificates for the Exercise Shares so purchased, registered in the name of the Holder or persons affiliated with the Holder, if the Holder so designates, shall be issued and delivered to the Holder as soon as practicable after the rights represented by this Warrant shall have been so exercised.

The person in whose name any certificate or certificates for Exercise Shares are to be issued upon exercise of this Warrant shall be deemed to have become the holder of record of such shares on the date on which this Warrant was surrendered and payment of the Exercise Price was made, irrespective of the date of delivery of such certificate or certificates, except that, if the date of such surrender and payment is a date when the stock transfer books of the Corporation are closed, such person shall be deemed to have become the holder of such shares at the close of business on the next succeeding date on which the stock transfer books are open.

2.2 Net Exercise . Notwithstanding any provisions herein to the contrary, if the fair market value of one share of the Corporation’s Common Stock is greater than the Exercise Price (at the date of calculation as set forth below), in lieu of exercising this Warrant by payment of cash, the Holder may elect (the “ Conversion Right ”) to receive shares equal to the value (as

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determined below) of this Warrant (or the portion thereof being canceled) by surrender of this Warrant at the principal office of the Corporation together with the properly endorsed Notice of Exercise, in which event the Corporation shall issue to the Holder a number of shares of Common Stock computed using the following formula:

For purposes of the above calculation, the fair market value of one share of Common Stock shall be determined by the Corporation’s Board of Directors in good faith; provided, however, that in the event that this Warrant is exercised when the Corporation’s Common Stock is traded in a public market, the fair market value of each share of Common Stock shall be the closing price of a share of Common Stock for the business day immediately before the day the Holder delivers its Notice of Exercise to the Company.

3. C OVENANTS OF THE C ORPORATION .

3.1 Covenants as to Exercise Shares . The Corporation covenants and agrees that all Exercise Shares that may be issued upon the exercise of the rights represented by this Warrant will, upon issuance, be validly issued and outstanding, fully paid and nonassessable, and free from all taxes, liens and charges with respect to the issuance thereof. The Corporation further covenants and agrees that the Corporation shall at all times during the Exercise Period have authorized and reserved, free from preemptive rights, a sufficient number of shares of its Common Stock to provide for the exercise of the rights represented by this Warrant. If at any time during the Exercise Period the number of authorized but unissued shares of Common Stock shall not be sufficient to permit exercise of this Warrant, the Corporation will take such corporate action as may, in the opinion of its counsel, be necessary to increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purposes.

3.2 No Impairment . Except and to the extent as waived or consented to by the Holder, the Corporation will not, by amendment of its Certificate of Incorporation or through any 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 hereunder by the Corporation, but will at all times in good faith assist in the carrying out of all the provisions of this Warrant and in the taking of all such action as may be necessary or appropriate in order to protect the exercise rights of the Holder against impairment.

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3.3 Notices of Record Date . In the event of any taking by the Corporation of a record of the holders of any class of securities for the purpose of determining the holders thereof who are entitled to receive any dividend (other than a cash dividend which is the same as cash dividends paid in previous quarters) or other distribution, the Corporation shall mail to the Holder, at least ten (10) days prior to the date specified herein, a notice specifying the date on which any such record is to be taken for the purpose of such dividend or distribution.

3.4 Notice of Expiration. If this Warrant has not been fully exercised on or before the date thirty (30) days prior to the end of the Exercise Period, the Corporation shall thereafter provide Holder with at least twenty (20) days advance written notice of the date on which this Warrant is to expire. If the Corporation fails to provide such notice, the Exercise Period shall be extended until the date thirty (30) days after the date said notice is provided to Holder. I