Exhibit 4.1


 


SECOND AMENDMENT TO RIGHTS AGREEMENT


 


This
SECOND AMENDMENT (“Amendment”), effective as of June 11, 2008
(subject to Section 3 of this Amendment), to the Stockholder Protection
Rights Agreement, dated as of April 28, 1999, as amended by the Amendment
to Rights Agreement, dated as of April 17, 2002, (the “Rights Agreement”),
by and between Applera Corporation, f/k/a PE Corporation, a Delaware
corporation (the “Company”) and Computershare Trust Company, N.A., f/k/a
EquiServe Trust Company, N.A (as successor rights agent to BankBoston, N.A.) (the
“Rights Agent”).


 


W I T N E S S E T H


 


WHEREAS,
the Board of Directors of the Company has determined it advisable and in the
best interest of the Company and its stockholders to amend the Rights Agreement
as set forth herein immediately prior to and in connection with the execution
and delivery of that certain Agreement and Plan of Merger to be entered into
among Invitrogen Corporation, a Delaware corporation, Atom Acquisition, LLC, a
Delaware limited liability company and the Company (the “Merger Agreement”);
and


 


WHEREAS,
capitalized terms used but not otherwise defined herein shall have the
respective meanings ascribed to such terms in the Rights Agreement; and


 


WHEREAS,
pursuant to Section 27 (Supplements and Amendments) of the Rights
Agreement, for so long as rights are then redeemable, the Company may in its
sole and absolute discretion, and the Rights Agent shall if the Company so
directs, supplement or amend any provision of the Rights Agreement in any
respect, whether or not such supplement or amendment is adverse to any holder
of the Rights, without the approval of any holders of the Rights, and the
Company has so directed the Rights Agent to execute this Amendment; and


 


WHEREAS,
an officer of the Company has delivered to the Rights Agent a certificate as to
the compliance of this Amendment with the terms of Section 27  (Supplements and Amendments) of the Rights
Agreement.


 


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


 

















 


Section 1.           Amendments to Rights
Agreement. The Rights Agreement is hereby amended as set
forth in this Section 1.


 


(a)           Section 1 of the Rights
Agreement is hereby amended to add the following definitions of “Effective Time”,
“Merger” and “Merger Agreement” in the appropriate alphabetical order:


 


“‘Effective
Time’ shall have the meaning set forth in the Merger Agreement.”


 


“‘Merger’
shall have the meaning set forth in the Merger Agreement.”


 


“‘Merger
Agreement’ shall mean that certain Agreement and Plan of Merger, to be entered
into among Invitrogen Corporation, a Delaware corporation, Atom Acquisition,
LLC, a Delaware limited liability company and the Company, as amended from time
to time.”


 


(b)           Section 1 of the Rights
Agreement is hereby amended to add the following sentence immediately prior to
the last sentence of the definition of “Acquiring Person”:


 


“Notwithstanding anything in this Agreement to the contrary, none of Invitrogen
Corporation, a Delaware corporation, Atom Acquisition, LLC, a Delaware limited
liability company, nor any of their respective Affiliates or Associates shall
be deemed to be an Acquiring Person solely as a result of the approval,
execution, delivery or adoption of the Merger Agreement or the approval,
adoption or consummation of the Merger or any other transaction contemplated by
the Merger Agreement, or the public announcement of any thereof.”


 


(c)           Section 1(j) of
the Rights Agreement is hereby amended to add the following sentence at the end
of the definition of “Distribution Date”:


 


“Notwithstanding anything in this Agreement to the contrary, a
Distribution Date shall not be deemed to have occurred solely as a result of
the approval, execution, delivery or adoption of the Merger Agreement or the
approval, adoption or consummation of the Merger or any other transaction contemplated
by the Merger Agreement, or the public announcement of any thereof.”


 


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(d)           The definition of “Exempt Person”
set forth in Section 1(m) of the Rights Agreement is hereby amended
to read in its entirety as follows:


 


“(m) ‘Exempt Person’ shall mean (i) the Company, (ii) any
Subsidiary of the Company, (iii) any employee benefit plan of the Company
or of any Subsidiary of the Company, (iv) any entity or trustee holding Common
Stock for or pursuant to the terms of any such plan or for the purpose of
funding any such plan or funding other employee benefits for employees of the Company
or of any Subsidiary of the Company, (v) Invitrogen Corporation, a
Delaware corporation and/or (vi) any Affiliate or Associate of Invitrogen Corporation
solely as a result of the approval, execution, delivery or adoption of the
Merger Agreement or the approval, adoption or consummation of the Merger or any
other transaction contemplated by the Merger Agreement, or the public
announcement of any thereof.”


 


(e)           Section 1(ii) of
the Rights Agreement is hereby amended to add the following sentence at the end
of the definition of “Stock Acquisition Date”:


 


“Notwithstanding anything in this Agreement to the contrary, a Stock
Acquisition Date shall not be deemed to have occurred solely as a result of the
approval, execution, delivery or adoption of the Merger Agreement or the
approval, adoption or consummation of the Merger or any other transaction
contemplated by the Merger Agreement, or the public announcement of any
thereof.”


 


(f)            The first paragraph of Section 3(a) of
the Rights Agreement is hereby amended to add the following sentence at the end
thereof:


 


“Notwithstanding anything in this Agreement to the contrary, no
Distribution Date shall be deemed to have occurred solely as a result of the
approval, execution, delivery or adoption of the Merger Agreement or the
approval, adoption or consummation of the Merger or any other transaction
contemplated by the Merger Agreement, or the public announcement of any
thereof.”


 


(g)           Section 11(a)(ii) of
the Rights Agreement is hereby amended to add the following sentence at the end
thereof:


 


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“Notwithstanding anything in this Agreement to the contrary, no event described
in this Section 11(a)(ii) shall be deemed to have occurred solely as
a result of the approval, execution, delivery or adoption of the Merger
Agreement or the approval, adoption or consummation of the Merger or any other
transaction contemplated by the Merger Agreement, or the public announcement of
any thereof.”


 


(h)           Section 13(a) of
the Rights Agreement is hereby amended to add the following sentence at the end
thereof:


 


“Notwithstanding anything in this Agreement to the contrary, no event
described in this Section 13 shall be deemed to have occurred solely as a
result of the approval, execution, delivery or adoption of the Merger Agreement
or the approval, adoption or consummation of the Merger or any other
transaction contemplated by the Merger Agreement, or the public announcement of
any thereof.”


 


(i)            Section 25 of the
Rights Agreement is hereby amended to delete the Rights Agent address
information in its entirety and replace it with the following:


 


“Computershare
Trust Company, N.A.


250
Royall Street


Canton,
MA  02021


Attn:
Client Services”


 


(j)            Section 25 of the
Rights Agreement is hereby further amended to add the following subsection at
the end thereof:


 


“(c)         Notwithstanding
anything in this Agreement to the contrary, the Company shall not be required
to give notice under this Section 25 solely as a result of the approval,
execution, delivery or adoption of the Merger Agreement or the approval,
adoption or consummation of the Merger or any other transaction contemplated by
the Merger Agreement, or the public announcement of any thereof.”


 


(k)           The Rights Agreement is
hereby amended to add the following new Section 35 at the end thereof:


 


“Section 35.  Force Majeure.  Notwithstanding anything to the contrary
contained herein, the Rights Agent shall not be liable for any delays or
failures in performance resulting from acts beyond its reasonable control
including, without limitation, acts of God, terrorist acts, shortage of supply,
breakdowns or malfunctions, interruptions or malfunction of computer 


 


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facilities, or loss of data due to power
failures or mechanical difficulties with information storage or retrieval
systems, labor difficulties, war, or civil unrest.”


 


Section 2.           Termination of
Merger Agreement.  If for any
reason the Merger Agreement is terminated, then this Amendment shall be of no
further force and effect and the Rights Agreement shall remain exactly the same
as it existed immediately prior to the effectiveness of this Amendment.  If for any reason the Merger Agreement is
terminated, the Company shall notify the Rights Agent in accordance with Section 26
of the Rights Agreement.


 


Section 3.           Effectiveness.  This Amendment shall be deemed effective as
of, and immediately prior to, the execution and delivery of the Merger
Agreement.  Except as amended by this
Amendment, the Rights Agreement shall remain in full force and effect and shall
be otherwise unaffected by this Amendment.


 


Section 4.           Severability.  If any provision of this Amendment, or the
application of such provision to any person or circumstance, shall be held by a
court of competent jurisdiction or other authority to be invalid, illegal or
unenforceable, the remainder of the provisions of this Amendment shall remain
in full force and effect and shall in no way be affected, impaired or
invalidated.


 


Section 5.           Counterparts.  This Amendment may be executed in any number
of counterparts, and each of such counterparts shall for all purposes be deemed
an original, but all such counterparts shall together constitute but one and
the same instrument.


 


Section 6.           Governing Law.  This Amendment shall be deemed to be a
contract made under the laws of the State of Delaware and for all purposes
shall be governed by and construed in accordance with the laws of such state
applicable to contracts made and to be performed entirely within such state.


 


Section 7.           Descriptive
Headings.  Descriptive
headings of the several sections of this Amendment are inserted for convenience
only and shall not control or affect the meaning or construction of any of the
provisions of this Amendment.


 


Section 8.           Further
Assurances.  Each of the
parties to this Amendment shall cooperate and take such action as may be
reasonably requested by the other party in order to carry out the provisions
and purposes of this Amendment, the Rights Agreement and the transactions
contemplated hereunder and/or thereunder.


 


[SIGNATURE PAGE FOLLOWS]


 


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IN
WITNESS WHEREOF, the parties hereto have caused this Second Amendment to be
duly executed as of the day and year first written above.


 


 


	
   

  	
  APPLERA CORPORATION  

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
  By:

  	
  /s/
  Thomas P. Livingston

  
	
   

  	
   

  	
  Name:
  Thomas P. Livingston 

  
	
   

  	
   

  	
  Title:
  Vice President and Secretary

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
  COMPUTERSHARE TRUST COMPANY, 

  N.A  

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
  By:

  	
  /s/
  Tyler Haynes

  
	
   

  	
   

  	
  Name:
  Tyler Haynes 

  
	
   

  	
   

  	
  Title:
  Managing Director