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                                                                     EXHIBIT 3.1

                           SECOND AMENDED AND RESTATED

                          CERTIFICATE OF INCORPORATION

                                       OF

                             STRATAGENE CORPORATION

      Stratagene Corporation, a corporation organized and existing under the
General Corporation Law of the State of Delaware (the "General Corporation
Law"), hereby certifies as follows:

      1. The name of this Corporation is Stratagene Corporation. This
Corporation was originally incorporated under the name Stratagene Holding
Corporation, and the original Certificate of Incorporation of the Corporation
was filed with the Secretary of State of the State of Delaware on November 2,
1995.

      2. Pursuant to Sections 242 and 245 of the General Corporation Law, this
Second Amended and Restated Certificate of Incorporation restates and integrates
and amends the provisions of the Certificate of Incorporation of this
Corporation.

      3. The text of the Certificate of Incorporation as heretofore amended or
supplemented is hereby restated and amended to read in its entirety as follows:

            "FIRST: The name of the corporation (hereinafter the "Corporation")
is

                             STRATAGENE CORPORATION

            SECOND: The address, including street, number, city and county, of
the registered office of the Corporation in the State of Delaware is 2711
Centerville Road, Suite 400, City of Wilmington, County of New Castle; and the
name of the registered agent of the Corporation in the State of Delaware is The
Prentice-Hall Corporation System, Inc.

            THIRD: The nature of the business and of the purposes to be
conducted and promoted by the Corporation shall be to engage in any lawful act
or activity for which corporations may be organized under the General
Corporation Law of the State of Delaware.

            FOURTH: The Corporation is authorized to issue two classes of stock.
The total number of shares of both classes which the Corporation is authorized
to issue is 54,000,000, of which (i) 50,000,000 shares shall be designated
common stock ("Common Stock") and (ii) 4,000,000 shares shall be designated
preferred stock ("Preferred Stock"). The par value of each share of Common Stock
and of each share of Preferred Stock is
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$0.0001. The Preferred Stock may be issued from time to time in one or more
series, each series to be appropriately designated by a distinguishing letter or
title, prior to the issue of any shares thereof. The Board of Directors is
hereby authorized, by filing a certificate pursuant to the General Corporation
Law, to fix or alter from time to time the designation, powers, preferences,
privileges and rights of the shares of each such series, including, without
limitation, the dividend rights, dividend rate, conversion rights, voting
rights, rights and terms of redemption (including sinking fund provisions, if
any), the redemption price or prices, the liquidation preferences, any other
designations, preferences and relative, participating, optional or other special
rights, and any qualifications, limitations or restrictions thereof, of any
wholly unissued series of Preferred Stock, and the number of shares constituting
any such unissued series and the designation thereof, or any of the foregoing;
and to increase (but not above the total number of authorized shares of the
class) or decrease (but not below the number of shares of such series then
outstanding) the number of shares of any series of Preferred Stock subsequent to
the issue of shares of that series. In case the number of shares of any series
shall be so decreased, the shares constituting such decrease shall resume the
status which they had prior to the adoption of the resolution originally fixing
the number of shares of such series.

      The express terms and provisions of the Common Stock are as follows:

            1. Dividend Rights. Subject to the prior rights of holders of all
classes of stock at the time outstanding having prior rights as to dividends,
the holders of the Common Stock shall be entitled to receive, when, as and if
declared by the Board of Directors, out of any assets of the Corporation legally
available therefor, such dividends as may be declared from time to time by the
Board of Directors. Dividends may be in the form of cash, property or Common
Stock.

            2. Liquidation, Dissolution or Winding Up. Subject to the rights of
holders of any outstanding shares of Preferred Stock, in the event of any
liquidation, dissolution or winding up of the Corporation, whether voluntary or
involuntary, after payment or provision for payment of the debts and liabilities
of the Corporation, the holders of shares of Common Stock shall be entitled, on
a pari passu basis, to all remaining assets of the Corporation available for
distribution to its stockholders.

            3. Voting Rights. The holder of each share of Common Stock shall
have the right to one vote, and shall be entitled to notice of any stockholders'
meeting in accordance with the bylaws of this Corporation, and shall be entitled
to vote upon such matters and in such manner as is provided by law.

            FIFTH: The Corporation is to have perpetual existence.

            SIXTH: The number of directors which constitute the whole Board of
Directors of the Corporation shall be as specified in the Corporation's bylaws.
In


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furtherance and not in limitation of the power conferred by statute, the Board
of Directors is expressly authorized to make, alter or repeal the bylaws of the
Corporation.

            SEVENTH: Elections of directors need not be by written ballot unless
a stockholder demands election by written ballot at the meeting and before
voting begins or unless the bylaws of the Corporation shall so provide.

            EIGHTH: Meetings of stockholders may be held within or without the
State of Delaware, as the bylaws of the Corporation may provide. The books of
the Corporation may be kept outside of the State of Delaware at such place or
places as may be designated from time to time by the Board of Directors of the
Corporation or in the bylaws of the Corporation.

            NINTH: The personal liability of the directors of the Corporation is
hereby eliminated to the fullest extent permitted by paragraph (7) of subsection
(b) of Section 102 of the General Corporation Law, as the same may be amended
and supplemented.

            TENTH: The Corporation shall to the fullest extent permitted by
Section 145 of the General Corporation Law, as the same may be amended or
supplemented, indemnify all of its officers and directors against expenses,
losses and liabilities sought to be imposed on them for actions or omissions in
their capacity as such (including positions as officers and directors of other
corporations or similar positions in non-corporate entities which are
subsidiaries of the Corporation or other entities in which an officer or
director serves as an officer, director or in a comparable position at the
request of the Corporation); provided, however, that any obligation to provide a
defense shall extend only to the reasonable fees and expenses of a single
counsel, for all indemnitees as a group, selected and provided by the
Corporation and reasonably acceptable to the affected officer(s) and
director(s), unless the provision of separate counsel for individual officers
and directors is otherwise required by law or by a separate written agreement,
in which case the Corporation shall select and provide such separate counsel
reasonably acceptable to such officer(s) and director(s).

            ELEVENTH: Any action that may be taken at any annual or special
meeting of the stockholders of the Corporation may be taken without a meeting,
without prior notice and without a vote, if, and only if, a consent in writing,
setting forth the action so taken, shall be signed by holders of all of the
shares of capital stock of the Corporation having the right to vote with respect
to such action.

            TWELFTH: Notwithstanding any other provisions of this Certificate of
Incorporation or the bylaws of the Corporation (and notwithstanding the fact
that a lesser percentage may be specified by law, this Certificate of
Incorporation or the bylaws of the Corporation), the affirmative vote of the
holders of at least two-thirds (2/3) of the voting power of the shares of the
then outstanding Common Stock of the Corporation, excluding shares owned by
holders of ten percent (10%) or more of the Corporation's Common


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Stock, shall be required to amend or repeal, or adopt any provisions
inconsistent with, Article ELEVENTH of this Certificate of Incorporation, in
addition to any affirmative vote required by law or this Certificate of
Incorporation with respect to any other shares of the capital stock of the
Corporation.

            THIRTEENTH: From time to time any of the provisions of this
certificate of incorporation may be amended, altered or repealed, and other
provisions authorized by the laws of the State of Delaware at the time in force
may be added or inserted in the manner and at the time prescribed by said laws,
and all rights at any time conferred upon the stockholders of the Corporation by
this Certificate of Incorporation are granted subject to the provisions of this
Article THIRTEENTH."

      4. The foregoing Second Amended and Restated Certificate of Incorporation
has been duly approved by the Board of Directors of the Corporation.

      5. The foregoing Second Amended and Restated Certificate of Incorporation
has been approved by the outstanding shares of the Corporation in accordance
with Sections 228, 242 and 245 of the General Corporation Law. The number of
shares voting in favor of the foregoing Second Amended and Restated Certificate
of Incorporation equaled or exceeded the vote required.

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      IN WITNESS WHEREOF, the Corporation has caused this Second Amended and
Restated Certificate of Incorporation to be signed by Joseph A. Sorge, its
Chairman and Chief Executive Officer, this 2nd day of June, 2004.

                                         STRATAGENE CORPORATION


                                         By:    /s/ JOSEPH A. SORGE, M.D.
                                              ----------------------------------
                                         Name:  Joseph A. Sorge, M.D.
                                         Title: Chief Executive Officer


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