Exhibit 4.1


 


NEITHER
THESE SECURITIES NOR THE SECURITIES ISSUABLE UPON EXERCISE OF THESE SECURITIES
HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES
ACT”), OR APPLICABLE STATE SECURITIES LAWS. 
THE SECURITIES MAY NOT BE OFFERED FOR SALE, SOLD, TRANSFERRED OR
ASSIGNED (I) IN THE ABSENCE OF (A) AN EFFECTIVE REGISTRATION
STATEMENT FOR THE SECURITIES UNDER THE SECURITIES ACT OR (B) AN AVAILABLE
EXEMPTION FROM, OR IN A TRANSACTION NOT SUBJECT TO, THE REGISTRATION
REQUIREMENTS OF THE SECURITIES ACT AND IN ACCORDANCE WITH APPLICABLE STATE
SECURITIES LAWS OR BLUE SKY LAWS AS EVIDENCED BY A LEGAL OPINION OF COUNSEL
REASONABLY SATISFACTORY TO THE COMPANY AND ITS TRANSFER AGENT OR (II) UNLESS
SOLD PURSUANT TO RULE 144 UNDER SAID ACT. 
NO REPRESENTATION IS MADE BY THE ISSUER AS TO THE AVAILABILITY OF THE
EXEMPTION PROVIDED BY RULE 144 UNDER THE SECURITIES ACT FOR RESALES OF THESE
SECURITIES.


 


HELICOS BIOSCIENCES CORPORATION


 


WARRANT TO PURCHASE COMMON STOCK


 




	
   

  	
   

  	
   

  
	
  Warrant
  No.     

  	
   

  	
  Original Issue Date:
  December       , 2008

  






 


Helicos BioSciences Corporation, a Delaware
corporation (the “Company”),
hereby certifies that, for value received,
                              
or its permitted registered assigns (the “Holder”),
is entitled to purchase from the Company up to a total of
                
shares of common stock, $0.001 par value per share (the “Common Stock”), of the Company (each such
share, a “Warrant Share” and all
such shares, the “Warrant Shares”)
at an exercise price per share equal to $0.45 per share (as adjusted from time
to time as provided in Section 9 herein, the “Exercise Price”), at any time and from time to time on or
after the date hereof (the “Trigger Date”)
and through and including 5:30 P.M., New York City time, on December       ,
2013 (the “Expiration Date”), and
subject to the following terms and conditions:


 


This Warrant (this “Warrant”) is one of a series of similar warrants issued
pursuant to that certain Securities Purchase Agreement, dated December 19,
2008, by and among the Company and the Purchasers identified therein (the “Purchase Agreement”).  All such warrants are referred to herein,
collectively, as the “Warrants.”


 


1.             Definitions.
In addition to the terms defined elsewhere in this Warrant, capitalized terms
that are not otherwise defined herein have the meanings given to such terms in
the Purchase Agreement.


 


2.             Registration
of Warrants.  The Company shall register this Warrant, upon
records to be maintained by the Company for that purpose (the “Warrant Register”), in the name of the
record Holder (which shall include the initial Holder or, as the case may be,
any registered assignee to which this Warrant is permissibly assigned
hereunder) from time to time.  The
Company may deem and treat the registered Holder of this Warrant as the
absolute owner hereof for the purpose of any exercise hereof or any
distribution to the Holder, and for all other purposes, absent actual notice to
the contrary.


 

















 


3.             Registration
of Transfers. Subject to
the restrictions on transfer set forth in Section 4.1 of the Purchase
Agreement and compliance with all applicable securities laws, the Company shall
register the transfer of all or any portion of this Warrant in the Warrant
Register, upon surrender of this Warrant, with the Form of Assignment
attached as Schedule 2 hereto duly completed and signed, to the Company’s
transfer agent or to the Company at its address specified in the Purchase
Agreement and (x) delivery, at the request of the Company, of an opinion
of counsel reasonably satisfactory to the Company to the effect that the
transfer of such portion of this Warrant may be made pursuant to an available
exemption from the registration requirements of the Securities Act and all
applicable state securities or blue sky laws and (y) delivery by the
transferee of a written statement to the Company certifying that the transferee
is an “accredited investor” as defined in Rule 501(a) under the
Securities Act, to the Company at its address specified in the Purchase
Agreement. Upon any such registration or transfer, a new warrant to purchase
Common Stock in substantially the form of this Warrant (any such new warrant, a
“New Warrant”) evidencing the
portion of this Warrant so transferred shall be issued to the transferee, and a
New Warrant evidencing the remaining portion of this Warrant not so
transferred, if any, shall be issued to the transferring Holder.  Any New Warrant issued pursuant to a partial
exercise of this Warrant or as a result of a transfer of this Warrant shall be
deemed to have the Original Issue Date of December     ,
2008 which is the date that this Warrant was initially issued to such Holder or
its predecessor.  The acceptance of the
New Warrant by the transferee thereof shall be deemed the acceptance by such
transferee of all of the rights and obligations in respect
of the New Warrant that the Holder has in respect of this Warrant. The Company
shall prepare, issue and deliver at its own expense any New Warrant under this Section 3.


 


4.             Exercise
and Duration of Warrants.


 


(a)           All
or any part of this Warrant shall be exercisable by the registered Holder in
any manner permitted by Section 10 of this Warrant at any time and from
time to time on or after the Trigger Date and through and including 5:30 P.M.
New York City time, on the Expiration Date. At 5:30 P.M., New York City
time, on the Expiration Date, the portion of this Warrant not exercised prior
thereto shall be and become void and of no value and this Warrant shall be
terminated and no longer outstanding.


 


(b)           The
Holder may exercise this Warrant by delivering to the Company (i) an
exercise notice, in the form attached as Schedule 1 hereto (the “Exercise Notice”), completed and duly
signed,  and (ii) payment of the
Exercise Price for the number of Warrant Shares as to which this Warrant is
being exercised (which may take the form of a “cashless exercise” if so
indicated in the Exercise Notice and if a “cashless exercise” may occur at such
time pursuant to Section 10 below), and the date on which the last of such
items is delivered to the Company (as determined in accordance with the notice
provisions hereof) is an “Exercise Date.”  The Holder shall not be required to deliver
the original Warrant in order to effect an exercise hereunder.  Execution and delivery of the Exercise Notice
shall have the same effect as cancellation of the original Warrant and issuance
of a New Warrant evidencing the right to purchase the remaining number of
Warrant Shares.


 


2

















 


 5.            Delivery
of Warrant Shares.


 


(a)           Upon
exercise of this Warrant, the Company shall promptly (but in no event later
than three Trading Days after the Exercise Date) issue or cause to be issued
and cause to be delivered to or upon the written order of the Holder and in such
name or names as the Holder may designate (provided that, if the Registration
Statement is not effective and the Holder directs the Company to deliver a
certificate for the Warrant Shares in a name other than that of the Holder or
an Affiliate of the Holder, it shall deliver to the Company on the Exercise
Date an opinion of counsel reasonably satisfactory to the Company to the effect
that the issuance of such Warrant Shares in such other name may be made
pursuant to an available exemption from the registration requirements of the
Securities Act and all applicable state securities or blue sky laws), (i) a
certificate for the Warrant Shares issuable upon such exercise, free of
restrictive legends, or (ii) an electronic delivery of the Warrant Shares
to the Holder’s account at the Depository Trust Company (“DTC”) or a similar organization, unless in
the case of clause (i) and (ii) a registration statement covering the
resale of the Warrant Shares and naming the Holder as a selling stockholder
thereunder is not then effective or the Warrant Shares are not freely
transferable without volume and manner of sale restrictions pursuant to Rule 144
under the Securities Act, in which case such Holder shall receive a certificate
for the Warrant Shares issuable upon such exercise with appropriate restrictive
legends.  The Holder, or any Person
permissibly so designated by the Holder to receive Warrant Shares, shall be
deemed to have become the holder of record of such Warrant Shares as of the
Exercise Date.  If the Warrant Shares are
to be issued free of all restrictive legends, the Company shall, upon the
written request of the Holder, use its reasonable best efforts to deliver, or
cause to be delivered, Warrant Shares hereunder electronically through DTC or
another established clearing corporation performing similar functions, if
available; provided, that, the Company may, but will not be required to, change
its transfer agent if its current transfer agent cannot deliver Warrant Shares
electronically through such a clearing corporation.


 


(b)           In addition
to any other rights available to the Holder, if by the close of the third
Trading Day after delivery of an Exercise Notice and the payment of the
aggregate exercise price in any manner permitted by Section 10 of this
Warrant, the Company fails to deliver to the Holder a certificate representing
the required number of Warrant Shares in the manner required pursuant to Section 5(a),
and if after such third Trading Day and prior to the receipt of such Warrant
Shares, the Holder purchases (in an open market transaction or otherwise)
shares of Common Stock to deliver in satisfaction of a sale by the Holder of
the Warrant Shares which the Holder anticipated receiving upon such exercise (a
“Buy-In”), then the Company
shall, within three (3) Trading Days after the Holder’s request and in the
Holder’s sole discretion, either (1) pay in cash to the Holder an amount
equal to the Holder’s total purchase price (including brokerage commissions, if
any) for the shares of Common Stock so purchased (the “Buy-In Price”), at which point the Company’s
obligation to deliver such certificate (and to issue such Warrant Shares) shall
terminate or (2) promptly honor its obligation to deliver to the Holder a
certificate or certificates representing such Warrant Shares and pay cash to
the Holder in an amount equal to the excess (if any) of Holder’s
total purchase price (including brokerage commissions, if any) for the shares
of Common Stock so purchased in the Buy-In over the product of (A) the
number of shares of Common Stock purchased in the Buy-In, times (B) the
closing bid price of a share of Common Stock on the Exercise Date.


 


(c)           To
the extent permitted by law, the Company’s obligations to issue and deliver
Warrant Shares in accordance with and subject to the terms hereof (including
the limitations set forth in Section 11 below) are absolute and
unconditional, irrespective of any action or inaction by the Holder to enforce
the same, any waiver or consent with respect to any provision hereof, the 


 


3

















 


recovery of any judgment against any Person or
any action to enforce the same, or any setoff, counterclaim, recoupment,
limitation or termination, or any breach or alleged breach by the Holder or any
other Person of any obligation to the Company or any violation or alleged
violation of law by the Holder or any other Person, and irrespective of any
other circumstance that might otherwise limit such obligation of the Company to
the Holder in connection with the issuance of Warrant Shares. Nothing herein
shall limit the Holder’s right to pursue any other remedies available to it
hereunder, at law or in equity including, without limitation, a decree of
specific performance and/or injunctive relief with respect to the Company’s
failure to timely deliver certificates representing shares of Common Stock upon
exercise of the Warrant as required pursuant to the terms hereof.


 


6.             Charges,
Taxes and Expenses. Issuance and
delivery of certificates for shares of Common Stock upon exercise of this
Warrant shall be made without charge to the Holder for any issue or transfer
tax, transfer agent fee or other incidental tax or expense in respect of the
issuance of such certificates, all of which taxes and expenses shall be paid by
the Company; provided, however,
that the Company shall not be required to pay any tax that may be payable in
respect of any transfer involved in the registration of any certificates for
Warrant Shares or the Warrants in a name other than that of the Holder or an
Affiliate thereof. The Holder shall be responsible for all other tax liability
that may arise as a result of holding or transferring this Warrant or receiving
Warrant Shares upon exercise hereof.


 


7.             Replacement
of Warrant.  If this Warrant is mutilated, lost, stolen or
destroyed, the Company shall issue or cause to be issued in exchange and
substitution for and upon cancellation hereof, or in lieu of and substitution
for this Warrant, a New Warrant, but only upon receipt of evidence reasonably satisfactory
to the Company of such loss, theft or destruction (in such case) and, in each
case, a customary and reasonable indemnity and surety bond, if requested by the
Company. Applicants for a New Warrant under such circumstances shall also
comply with such other reasonable regulations and procedures and pay such other
reasonable third-party costs as the Company may prescribe. If a New Warrant is
requested as a result of a mutilation of this Warrant, then the Holder shall
deliver such mutilated Warrant to the Company as a condition precedent to the
Company’s obligation to issue the New Warrant.


 


8.             Reservation
of Warrant Shares. The Company
represents, warrants, covenants and agrees that it will at all times reserve
and keep available out of the aggregate of its authorized but unissued and
otherwise unreserved Common Stock, solely for the purpose of enabling it to
issue Warrant Shares upon exercise of this Warrant as herein provided, the
number of Warrant Shares that are issuable and deliverable upon the exercise of
this entire Warrant, free from preemptive rights or any other contingent
purchase rights of persons other than the Holder (taking into account the
adjustments and restrictions of Section 9). The Company covenants that all
Warrant Shares so issuable and deliverable shall, upon issuance and the payment
of the applicable Exercise Price in accordance with the terms hereof, be duly
and validly authorized, issued and fully paid and nonassessable. The Company
will take all such action as may be reasonably necessary to assure that such
shares of Common Stock may be issued as provided herein without violation of
any applicable law or regulation, or of any requirements of any securities
exchange or automated quotation system upon which the Common Stock may be
listed.


 


9.             Certain
Adjustments. The Exercise
Price and number of Warrant Shares issuable upon exercise of this Warrant are
subject to adjustment from time to time as set forth in this Section 9.


 


(a)           Stock
Dividends and Splits. If the
Company, at any time while this Warrant is outstanding, (i) pays a stock
dividend on its Common Stock or otherwise makes a distribution on 


 


4

















 


any class of capital stock that is payable in
shares of Common Stock, (ii) subdivides its outstanding shares of Common
Stock into a larger number of shares, (iii) combines its outstanding
shares of Common Stock into a smaller number of shares or (iv) issues by
reclassification of shares of Common Stock any shares of capital of the Company,
then in each such case the Exercise Price shall be multiplied by a fraction,
the numerator of which shall be the number of shares of Common Stock
outstanding immediately before such event and the denominator of which shall be
the number of shares of Common Stock outstanding immediately after such event.
Any adjustment made pursuant to clause (i) of this paragraph shall become
effective immediately after the record date for the determination of
stockholders entitled to receive such dividend or distribution, and any
adjustment pursuant to clause (ii) or (iii) of this paragraph shall
become effective immediately after the effective date of such subdivision or
combination.


 


(b)           Pro Rata
Distributions. 
If the Company, at any time while this Warrant is outstanding,
distributes to all holders of Common Stock for no consideration (i) evidences
of its indebtedness, (ii) any security (other than a distribution of
Common Stock covered by the preceding paragraph) or (iii) rights or
warrants to subscribe for or purchase any security, or (iv) any other
asset (in each case, “Distributed Property”),
then, upon any exercise of this Warrant that occurs after the record date fixed
for determination of stockholders entitled to receive such distribution, the
Holder shall be entitled to receive, in addition to the Warrant Shares
otherwise issuable upon such exercise (if applicable), the Distributed Property
that such Holder would have been entitled to receive in respect of such number
of Warrant Shares had the Holder been the record holder of such Warrant Shares
immediately prior to such record date without regard to any limitation on
exercise contained therein.


 


(c)           Fundamental Transactions. If, at any time while this Warrant is
outstanding  (i) the Company effects
any merger or consolidation of the Company with or into another Person, in
which the Company is not the survivor or the stockholders of the Company
immediately prior to such merger or consolidation do not own, directly or
indirectly, at least 50% of the voting securities of the surviving entity, (ii) the
Company effects any sale of all or substantially all of its assets or a
majority of its Common Stock is acquired by a third party, in each case,  in one or a series of related transactions, (iii) any
tender offer or exchange offer (whether by the Company or another Person) is
completed pursuant to which all or substantially all of the holders of Common
Stock are permitted to tender or exchange their shares for other securities,
cash or property, or (iv) the Company effects any reclassification of the
Common Stock or any compulsory share exchange pursuant to which the Common
Stock is effectively converted into or exchanged for other securities, cash or
property (other than as a result of a subdivision or combination of shares of
Common Stock covered by Section 9(a) above) (in any such case, a “Fundamental Transaction”), then the Holder
shall have the right thereafter to receive, upon exercise of this Warrant, the
same amount and kind of securities, cash or property as it would have been
entitled to receive upon the occurrence of such Fundamental Transaction if it
had been, immediately prior to such Fundamental Transaction, the holder of the
number of Warrant Shares then issuable upon exercise in full of this Warrant
without regard to any limitations on exercise contained herein (the “Alternate Consideration”).  The Company shall not effect any such
Fundamental Transaction unless prior to or simultaneously with the consummation
thereof, any successor to the Company, surviving entity or the corporation
purchasing or otherwise acquiring such assets or other appropriate corporation
or Person shall assume the obligation to deliver to the Holder, such Alternate
Consideration as, in accordance with the foregoing provisions, the Holder may
be entitled to receive, and the other obligations under this Warrant.  The provisions of this paragraph (c) shall
similarly apply to subsequent transactions analogous of a Fundamental
Transaction type.


 


5

















 


(d)           Number
of Warrant Shares.
Simultaneously with any adjustment to the Exercise Price pursuant to paragraph (a) of
this Section 9, the number of Warrant Shares that may be purchased upon
exercise of this Warrant shall be increased or decreased proportionately, so
that after such adjustment the aggregate Exercise Price payable hereunder for
the increased or decreased number of Warrant Shares shall be the same as the
aggregate Exercise Price in effect immediately prior to such adjustment.


 


(e)           Calculations.
All calculations under this Section 9 shall be made to the nearest cent or
the nearest share, as applicable.


 


(f)            Notice
of Adjustments. Upon the
occurrence of each adjustment pursuant to this Section 9, the Company at
its expense will promptly notify the Holders of the applicable adjustment,
compute such adjustment, in good faith, in accordance with the terms of this
Warrant and prepare a certificate setting forth such adjustment, including a
statement of the adjusted Exercise Price and adjusted number or type of Warrant
Shares or other securities issuable upon exercise of this Warrant (as
applicable), describing the transactions giving rise to such adjustments and
showing in detail the facts upon which such adjustment is based. Upon written
request, the Company will promptly deliver a copy of each such certificate to
the Holder and to the Company’s transfer agent.


 


(g)           Notice
of Corporate Events. If, while
this Warrant is outstanding, the Company (i) declares a dividend or any
other distribution of cash, securities or other property in respect of its
Common Stock, including, without limitation, any granting of rights or warrants
to subscribe for or purchase any capital stock of the Company or any
subsidiary, (ii) authorizes or approves, enters into any agreement
contemplating or solicits stockholder approval for any Fundamental Transaction
or (iii) authorizes the voluntary dissolution, liquidation or winding up
of the affairs of the Company, then, except if such notice and the contents
thereof shall be deemed to constitute material non-public information, the
Company shall deliver to the Holder a notice of such transaction at least ten (10) business
days prior to the applicable record or effective date on which a Person would
need to hold Common Stock in order to participate in or vote with respect to
such transaction; provided, however,
that the failure to deliver such notice or any defect therein shall not affect
the validity of the corporate action required to be described in such notice. To the extent that any notice
provided hereunder constitutes, or contains, material, non-public information
regarding the Company or any of its subsidiaries, the Company shall
simultaneously file such notice with the Commission (as defined in the Purchase
Agreement) pursuant to a Current Report on Form 8-K.


 


10.           Payment
of Exercise Price. The Holder
shall pay the Exercise Price in immediately available funds; provided, however, that if, on any
Exercise Date there is not an effective Registration Statement registering, or no
current prospectus available for, the resale of the Warrant Shares by the
Holder, then the Holder may, in its sole discretion, satisfy its obligation to
pay the Exercise Price through a “cashless exercise”, in which event the
Company shall issue to the Holder the number of Warrant Shares determined as
follows:


 


X
= Y [(A-B)/A]


 


where:


 


X
= the number of Warrant Shares to be issued to the Holder.


 


6

















 


Y
= the total number of Warrant Shares with respect to which this Warrant is
being exercised.


 


A = the average of the Closing Sale Prices of
the shares of Common Stock (as reported by Bloomberg Financial Markets) for the
five (5) consecutive Trading Days ending on
the date immediately preceding the Exercise Date.


 


B
= the Exercise Price then in effect for the applicable Warrant Shares at the
time of such exercise.


 


For
purposes of this Warrant, “Closing Sale Price”
means, for any security as of any date, the last trade price for such security
on the principal securities exchange or trading market for such security, as
reported by Bloomberg Financial Markets, or, if such exchange or trading market
begins to operate on an extended hours basis and does not designate the last
trade price, then the last trade price of such security prior to 4:00 P.M.,
New York City time, as reported by Bloomberg Financial Markets, or if the
foregoing do not apply, the last trade price of such security in the
over-the-counter market on the electronic bulletin board for such security as
reported by Bloomberg Financial Markets, or, if no last trade price is reported
for such security by Bloomberg Financial Markets, the average of the bid
prices, or the ask prices, respectively, of any market makers for such security
as reported in the “pink sheets” by Pink Sheets LLC.  If the Closing Sale Price cannot be
calculated for a security on a particular date on any of the foregoing bases,
the Closing Sale Price of such security on such date shall be the fair market
value as mutually determined by the Company and the Holder.  If the Company and the Holder are unable to
agree upon the fair market value of such security, then the Board of Directors
of the Company shall use its good faith judgment to determine the fair market
value.  The Board of Directors’
determination shall be binding upon all parties absent demonstrable error.  All such determinations shall be
appropriately adjusted for any stock dividend, stock split, stock combination
or other similar transaction during the applicable calculation period.


 


11.           Limitations
on Exercise.   Notwithstanding anything to the contrary
contained herein, in no event shall the Holder be entitled to exercise this
Warrant for a number of Warrant Shares in excess of that number of Warrant
Shares
which, upon giving effect to such exercise, would cause the aggregate number of
shares of Common Stock beneficially owned by the Holder and
its Affiliates and any other Persons whose beneficial ownership of Common Stock
would be aggregated with the Holder’s for purposes of Section 13(d) of
the Exchange Act to exceed 19.99% of the voting power of
the Company, following such exercise, unless the Company obtains the requisite
stockholder approval under NASDAQ Marketplace Rule 4350(i)(1)(B) (the
“Issuance Limitation”), in which case,
the Issuance Limitation under this Section 11 shall no longer apply to the
Holder.  For purposes of this Section 11,
the aggregate number of shares of Common Stock beneficially owned by the
Investor and its Affiliates and any other Persons
whose beneficial ownership of Common Stock would be aggregated with the Holder’s
for purposes of Section 13(d) of the Exchange Act shall
include the shares of Common Stock issuable upon the exercise of this Warrant,
subject in all cases to the Issuance Limitation.


 


Notwithstanding anything to the contrary
contained herein, if the exercise of this Warrant by the Holder would trigger
the Issuance Limitation, thus requiring the Company to obtain stockholder
approval of such exercise pursuant to NASDAQ
Marketplace Rule 4350(i)(1)(B) prior
to such issuance, and such stockholder approval has not been obtained, (i) the
number of Warrant Shares issuable upon exercise shall be reduced to the maximum
extent that would not require stockholder approval under such Rule, and (ii) the
Company shall use its commercially reasonable efforts to obtain such
stockholder approval as soon as reasonably practicable.


 


7

















 


12.           No
Fractional Shares. No fractional
Warrant Shares will be issued in connection with any exercise of this
Warrant.  In lieu of any fractional
shares that would, otherwise be issuable, the number of Warrant Shares to be
issued shall be rounded down to the next whole number and the Company shall pay
the Holder in cash the fair market value (based on the Closing Sale Price) for
any such fractional shares.


 


13.           Notices.
Any and all notices or other communications or deliveries hereunder (including,
without limitation, any Exercise Notice) shall be in writing and shall be
deemed given and effective on the earliest of (i) the date of
transmission, if such notice or communication is delivered via facsimile at the
facsimile number specified in the Purchase Agreement prior to 5:30 P.M.,
New York City time, on a Trading Day, (ii) the next Trading Day after the
date of transmission, if such notice or communication is delivered via
facsimile at the facsimile number specified in the Purchase Agreement on a day
that is not a Trading Day or later than 5:30 P.M., New York City time, on
any Trading Day, (iii) the Trading Day following the date of mailing, if
sent by nationally recognized overnight courier service specifying next
business day delivery, or (iv) upon actual receipt by the party to whom
such notice is required to be given, if by hand delivery. The address and
facsimile number of a party for such notices or communications shall be as set
forth in the Purchase Agreement unless changed by such party by two (2) Trading
Days’ prior notice to the other party in accordance with this Section 13.


 


14.           Warrant
Agent. The Company shall serve as warrant
agent under this Warrant. Upon thirty (30) days’ notice to the Holder, the
Company may appoint a new warrant agent. Any corporation into which the Company
or any new warrant agent may be merged or any corporation resulting from any
consolidation to which the Company or any new warrant agent shall be a party or
any corporation to which the Company or any new warrant agent transfers
substantially all of its corporate trust or shareholders services business
shall be a successor warrant agent under this Warrant without any further act.
Any such successor warrant agent shall promptly cause notice of its succession
as warrant agent to be mailed (by first class mail, postage prepaid) to the
Holder at the Holder’s last address as shown on the Warrant Register.


 


15.           Registration
Rights. The Holder of this Warrant is entitled
to the benefit of certain registration rights with respect to the Warrant
Shares issuable upon the exercise of this Warrant pursuant to that certain
Registration Rights Agreement, dated December 19, 2008, and the
registration rights with respect to the Warrant Shares issuable upon the
exercise of this Warrant by any subsequent Holder may only be assigned in
accordance with the terms and provisions of the Registration Rights Agreement.


 


16.           Miscellaneous.


 


(a)           No
Rights as a Stockholder. Unless otherwise permitted in this Warrant, the Holder,
solely in such Person’s capacity as a holder of this Warrant, shall not be
entitled to vote or receive dividends or be deemed the holder of share capital
of the Company for any purpose, nor shall anything contained in this Warrant be
construed to confer upon the Holder, solely in such Person’s capacity as the
Holder of this Warrant, any of the rights of a stockholder of the Company or
any right to vote, give or withhold consent to any corporate action (whether
any reorganization, issue of stock, reclassification of stock, consolidation,
merger, amalgamation, conveyance or otherwise), receive notice of meetings,
receive dividends or subscription rights, or otherwise, prior to the issuance
to the Holder of the Warrant Shares which such Person is then entitled to
receive upon the due exercise of this Warrant. In addition, nothing contained
in this Warrant shall be construed as imposing any liabilities on the Holder to
purchase any securities 


 


8

















 


(upon exercise of this Warrant or otherwise)
or as a stockholder of the Company, whether such liabilities are asserted by the
Company or by creditors of the Company.


 


(b)           Authorized
Shares. (i) The Company covenants that during the period the
Warrant is outstanding, it will reserve from its authorized and unissued Common
Stock a sufficient number of shares to provide for the issuance of the Warrant
Shares upon the exercise of any purchase rights under this Warrant.  The Company further covenants that its
issuance of this Warrant shall constitute full authority to its officers who
are charged with the duty of executing stock certificates to execute and issue
the necessary certificates for the Warrant Shares upon the exercise of the
purchase rights under this Warrant.  The
Company will take all such reasonable action as may be necessary to assure that
such Warrant Shares may be issued as provided herein without violation of any
applicable law or regulation, or of any requirements of the Trading Market upon
which the Common Stock may be listed. 
The Company covenants that all Warrant Shares which may be issued upon
the exercise of the purchase rights represented by this Warrant will, upon
exercise of the purchase rights represented by this Warrant, be duly
authorized, validly issued, fully paid and nonassessable and free from all
taxes, liens and charges created by the Company in respect of the issue thereof
(other than taxes in respect of any transfer occurring contemporaneously with
such issue).


 


(ii)           Except and to the extent as waived or consented to by the Holder, the
Company shall not by any action, including, without limitation, amending 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 of this Warrant, but will at all times in good faith assist in the
carrying out of all such terms and in the taking of all such actions as may be
necessary or appropriate to protect the rights of Holder as set forth in this
Warrant against impairment.  Without
limiting the generality of the foregoing, the Company will (a) not
increase the par value of any Warrant Shares above the amount payable therefor
upon such exercise immediately prior to such increase in par value, (b) take
all such action as may be necessary or appropriate in order that the Company
may validly and legally issue fully paid and nonassessable Warrant Shares upon
the exercise of this Warrant, and (c) use commercially reasonable efforts
to obtain all such authorizations, exemptions or consents from any public
regulatory body having jurisdiction thereof as may be necessary to enable the
Company to perform its obligations under this Warrant.


 


(iii)          Before taking any action which would result in an adjustment in the
number of Warrant Shares for which this Warrant is exercisable or in the
Exercise Price, the Company shall obtain all such authorizations or exemptions
thereof, or consents thereto, as may be necessary from any public regulatory
body or bodies having jurisdiction thereof.


 


(c)           Successors and Assigns.  Subject to the restrictions on transfer set
forth in this Warrant and in Section 4.1 of the Purchase Agreement, and
compliance with applicable securities laws, this Warrant may be assigned by the
Holder. This Warrant may not be assigned by the Company without the written
consent of the Holder except to a successor in the event of a Fundamental
Transaction. This Warrant shall be binding on and inure to the benefit of
the parties hereto and their respective successors and assigns. Subject to the
preceding sentence, nothing in this Warrant shall be construed to give to any
Person other than the Company and the Holder any legal or equitable right,
remedy or cause of action under this Warrant. This Warrant may be amended only
in writing signed by the Company and the Holder, or their successors and
assigns.


 


(d)           Amendment
and Waiver.  Except as otherwise
provided herein, the provisions of the Warrants may be amended and the Company
may take any action herein prohibited, or omit to perform any act herein
required to be performed by it, only if the Company has obtained the 


 


9

















 


written
consent of the Holders of Warrants representing no less than a majority of the
Warrant Shares obtainable upon exercise of the Warrants then outstanding,
provided, however, that in the event any waiver or amendment to this Warrant
should alter the Exercise Price or number of Warrant Shares available to
Holders then all Holders shall be treated equally and the Company shall be
required to obtain consent from all Holders to effect such waiver or amendment.


 


(e)           Acceptance.  Receipt of this Warrant by the Holder shall
constitute acceptance of and agreement to all of the terms and conditions
contained herein.


 


(f)            Governing Law; Jurisdiction.  ALL QUESTIONS CONCERNING THE CONSTRUCTION,
VALIDITY, ENFORCEMENT AND INTERPRETATION OF THIS WARRANT SHALL BE GOVERNED BY
AND CONSTRUED AND ENFORCED IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK
WITHOUT REGARD TO THE PRINCIPLES OF CONFLICTS OF LAW THEREOF. EACH PARTY HEREBY
IRREVOCABLY SUBMITS TO THE EXCLUSIVE JURISDICTION OF THE STATE AND FEDERAL
COURTS SITTING IN THE CITY OF NEW YORK, BOROUGH OF MANHATTAN, FOR THE
ADJUDICATION OF ANY DISPUTE HEREUNDER OR IN CONNECTION HEREWITH OR WITH ANY
TRANSACTION CONTEMPLATED HEREBY OR DISCUSSED HEREIN (INCLUDING WITH RESPECT TO
THE ENFORCEMENT OF ANY OF THE TRANSACTION DOCUMENTS), AND HEREBY IRREVOCABLY
WAIVES, AND AGREES NOT TO ASSERT IN ANY SUIT, ACTION OR PROCEEDING, ANY CLAIM
THAT IT IS NOT PERSONALLY SUBJECT TO THE JURISDICTION OF ANY SUCH COURT. EACH
PARTY HEREBY IRREVOCABLY WAIVES PERSONAL SERVICE OF PROCESS AND CONSENTS TO
PROCESS BEING SERVED IN ANY SUCH SUIT, ACTION OR PROCEEDING BY MAILING A COPY
THEREOF VIA REGISTERED OR CERTIFIED MAIL OR OVERNIGHT DELIVERY (WITH EVIDENCE
OF DELIVERY) TO SUCH PARTY AT THE ADDRESS IN EFFECT FOR NOTICES TO IT UNDER THE
PURCHASE AGREEMENT AND AGREES THAT SUCH SERVICE SHALL CONSTITUTE GOOD AND
SUFFICIENT SERVICE OF PROCESS AND NOTICE THEREOF. NOTHING CONTAINED HEREIN
SHALL BE DEEMED TO LIMIT IN ANY WAY ANY RIGHT TO SERVE PROCESS IN ANY MANNER
PERMITTED BY LAW. EACH PARTY HEREBY WAIVES ALL RIGHTS TO A TRIAL BY JURY.


 


(g)           Headings.  The headings herein are for convenience only,
do not constitute a part of this Warrant and shall not be deemed to limit or
affect any of the provisions hereof.


 


(h)           Severability.  In case any one or more of the provisions of
this Warrant shall be invalid or unenforceable in any respect, the validity and
enforceability of the remaining terms and provisions of this Warrant shall not
in any way be affected or impaired thereby, and the parties will attempt in
good faith to agree upon a valid and enforceable provision which shall be a
commercially reasonable substitute therefor, and upon so agreeing, shall
incorporate such substitute provision in this Warrant.


 


(i)            Remedies.  The Company stipulates that the remedies at
law of the Holder of this Warrant in the event of any default or threatened
default by the Company in the performance of or compliance with any of the
terms of this Warrant are not and will not be adequate and that, to the fullest
extent permitted by law, such terms may be specifically enforced by a decree
for the specific performance of any agreement contained herein or by an
injunction against a violation of any of the terms hereof or otherwise.


 


10
















 


IN WITNESS WHEREOF, the Company has caused this
Warrant to be duly executed by its authorized officer as of the date first
indicated above.


 


 


	
   

  	
  HELICOS BIOSCIENCES CORPORATION

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  By:

  	
   

  
	
   

  	
  Name:

  	
   

  
	
   

  	
  Title:

  	
   

  



 

















 


SCHEDULE
1


 


FORM OF
EXERCISE NOTICE


 


(To be executed
by the Holder to purchase shares of Common Stock under the foregoing Warrant)


 


Ladies and Gentlemen:


 


(1)           The
undersigned is the Holder of Warrant No.                     
(the “Warrant”) issued by Helicos BioSciences Corporation, a Delaware corporation
(the “Company”).  Capitalized terms used
herein and not otherwise defined herein have the respective meanings set forth
in the Warrant.


 


(2)           The
undersigned hereby exercises its right to purchase
                    
Warrant Shares pursuant to the Warrant.


 


(3)           The
Holder intends that payment of the Exercise Price shall be made as (check one):


 


Cash
Exercise


 


“Cashless
Exercise” under Section 10


 


(4)           If
the Holder has elected a Cash Exercise, the Holder shall pay the sum of
$              
in immediately available funds to the Company in accordance with the terms of
the Warrant.


 


(5)           Pursuant
to this Exercise Notice, the Company shall deliver to the Holder Warrant Shares
determined in accordance with the terms of the Warrant.


 


(6)           By
its delivery of this Exercise Notice, the undersigned represents and warrants
to the Company that in giving effect to the exercise evidenced hereby the
Holder will not beneficially own in excess of the number of shares of Common
Stock (as determined in accordance with Section 13(d) of the
Securities Exchange Act of 1934) permitted to be owned under Section 11 of
the Warrant to which this notice relates.


 


 


	
  Dated:

  	
                              

  	
  ,

  	
   

  	
   

  
	
   

  	
   

  
	
  Name of Holder:

  	
   

  	
   

  
	
   

  	
   

  
	
  By:

  	
   

  	
   

  
	
  Name:

  	
   

  	
   

  
	
  Title:

  	
   

  	
   

  
								



(Signature
must conform in all respects to name of Holder as specified on the face of the
Warrant)


 

















 


SCHEDULE
2


 


FORM OF
ASSIGNMENT


 


[To be
completed and signed only upon transfer of Warrant]


 


FOR VALUE RECEIVED, the undersigned hereby
sells, assigns and transfers unto                             
(the “Transferee”) the right represented by the within Warrant to purchase                 
shares of Common Stock of
                          
(the “Company”) to which the within Warrant relates and appoints
                            
attorney to transfer said right on the books of the Company with full power of
substitution in the premises. In
connection therewith, the undersigned represents, warrants, covenants and
agrees to and with the Company that:


 


(a)                                  the offer and sale of the Warrant
contemplated hereby is being made in compliance with Section 4(1) of
the United States Securities Act of 1933, as amended (the “Securities Act”) or
another valid exemption from the registration requirements of Section 5 of
the Securities Act and in compliance with all applicable securities laws of the
states of the United States;


 


(b)                                 the undersigned has not offered to
sell the Warrant by any form of general solicitation or general advertising,
including, but not limited to, any advertisement, article, notice or other
communication published in any newspaper, magazine or similar media or
broadcast over television or radio, and any seminar or meeting whose attendees
have been invited by any general solicitation or general advertising;


 


(c)                                  the undersigned has read the
Transferee’s investment letter included herewith, and to its actual knowledge,
the statements made therein are true and correct; and


 


(d)                                 the undersigned understands that the
Company may condition the transfer of the Warrant contemplated hereby upon the
delivery to the Company by the undersigned or the Transferee, as the case may
be, of a written opinion of counsel (which opinion shall be in form, substance
and scope customary for opinions of counsel in comparable transactions) to the
effect that such transfer may be made without registration under the Securities
Act and under applicable securities laws of the states of the United States.


 


	
  Dated:
  

  	
              

  	
  ,

  	
   

  	
   

  	
   

  	
   

  
	
   

  	
   

  	
  (Signature
  must conform in all respects to name of holder as specified on the face of
  the Warrant)

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
  Address
  of Transferee

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  In
  the presence of: