COMBIMATRIX CORP
S-1, EX-3.1, 2000-11-22
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                                                                     EXHIBIT 3.1

                      RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                             COMBIMATRIX CORPORATION



I.      The present name of the Corporation is CombiMatrix Corporation. The
        original certificate of incorporation of the Corporation was filed with
        the Secretary of State of the State of Delaware on July 11, 2000

II.     This Restated Certificate of Incorporation restates and amends the
        Certificate of Incorporation of the Corporation filed with the Secretary
        of State of the State of Delaware on July 11, 2000, was duly adopted in
        accordance with the provisions of Sections 242 and 245 of the General
        Corporation Law, and was approved by written consent of the stockholders
        of the Corporation given in accordance with the provisions of Section
        228 of the General Corporation Law, prompt notice of such action will be
        given to those stockholders who did not consent in writing.

III.    The text of the Certificate of Incorporation of the Corporation is
        hereby amended and restated to read in its entirety as follows:

                                    Article I

        The name of the corporation is CombiMatrix Corporation (the
"Corporation").

                                   Article II

        The address of the registered office of the Corporation in the State of
Delaware is 9 East Loockerman Street in the City of Dover, County of Kent. The
name of its registered agent at such address is National Registered Agents, Inc.

                                   Article III

        The purpose of the Corporation is to engage in any lawful act or
activity for which corporations may be organized under the General Corporation
Law of Delaware.

                                   Article IV

        A. The total number of shares of all classes that this Corporation shall
have the authority to issue shall be three hundred fifty million (350,000,000),
which shall be divided into two classes, one to be designated "Common Stock,"
which shall consist of three hundred million (300,000,000) authorized shares,
$0.001 par value per share, and a second class to be designated as "Preferred
Stock," which shall consist of fifty million (50,000,000) authorized shares,
$0.001 par value per share.


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        B. The Preferred Stock may be issued from time to time in one or more
series, each series to be appropriately designated by a distinguishing number,
letter or title prior to the issue of any shares thereof.

        C. Each series of Preferred Stock shall consist of such number of shares
and have such voting powers, full or limited, or no voting powers, and such
designations, preferences and relative, participating, optional or other special
rights, and the qualifications, limitations or restrictions thereof, as shall be
stated in the resolution or resolutions providing for the issuance of such
series adopted by the Board of Directors of the Corporation (the "Board of
Directors"), and the Board of Directors is hereby expressly vested with
authority, to the full extent now or hereafter provided by law, to adopt any
such resolution or resolutions.

        The authority of the Board of Directors with respect to each series
shall include, but not be limited to, determination of the following:

                (i) the number of shares constituting that series and the
        distinctive designation of that series;

                (ii) the dividend rate on the shares of that series, whether
        dividends shall be cumulative, and, if so, from which date or dates, and
        the relative rights of priority, if any, of payment of dividends on
        shares of that series;

                (iii) whether that series shall have voting rights, in addition
        to the voting rights provided by law, and if so, the terms of such
        voting rights;

                (iv) whether that series shall have conversion privileges and,
        if so, the terms and conditions of such conversion, including provision
        for adjustment of the conversion rate in such events as the Board of
        Directors shall determine;

                (v) whether the shares of that series shall be redeemable, and,
        if so, the terms and conditions of such redemption, including the date
        or date upon or after which they shall be redeemable, and the amount per
        share payable in case of redemption, which amount may vary under
        different conditions and at different redemption dates;

                (vi) whether the series shall have a sinking fund for the
        redemption or purchase of shares of that series and, if so, the terms
        and amount of such sinking fund;

                (vii) the rights of the shares of that series in the event of
        voluntary or involuntary liquidation, dissolution or winding-up of the
        Corporation, and the relative rights of priority, if any, of payment of
        shares of that series; and

                (viii) any other relative rights, preferences and limitations of
        that series.

                                    Article V

        In furtherance and not in limitation of the powers conferred by the laws
of the State of Delaware, the Board of Directors is expressly authorized to
adopt, alter, amend and repeal the Bylaws of the Corporation.


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                                   Article VI

        A. Subject to the rights of the holders of any series of Preferred
Stock, the number of directors of the Corporation shall be fixed from time to
time by a Bylaw of the Corporation or amendment thereof duly adopted by the
Board of Directors.

        B. The directors, other than those who may be elected by the holders of
Preferred Stock or any other class or series of stock having a preference over
the Common Stock as to dividends or upon liquidation pursuant to the terms of
this Restated Certificate of Incorporation or any resolution or resolutions
providing for the issuance of such class or series of stock adopted by the Board
of Directors, shall be divided into three classes, Class I, Class II and Class
III, as nearly equal in number as possible. The term of office for the Class I
directors shall expire at the annual meeting of the stockholders in 2001; the
term of office for the Class II directors shall expire at the annual meeting of
the stockholders in 2002; and the term of office for the Class III directors
shall expire at the annual meeting of the stockholders in 2003. At each annual
meeting of the stockholders commencing in 2001, the successors to the directors
whose terms are expiring shall be elected to a term expiring at the third
succeeding annual meeting of the stockholders. If the number of directors is
changed, any increase or decrease shall be apportioned among the classes so as
to maintain the number of directors in each class as nearly equal as possible,
and any additional directors of any class elected to fill a vacancy resulting
from an increase in such class shall hold office for a term that shall coincide
with the remaining term of that class, but in no case will a decrease in the
number of directors shorten the term of any incumbent director. A director shall
hold office until the annual meeting for the year in which his or her term
expires and until his or her successor shall be elected and shall qualify,
subject, however, to prior death, resignation, retirement, disqualification or
removal from office.

        C. Notwithstanding any other provisions of this Restated Certificate of
Incorporation, and notwithstanding that a lesser percentage may be permitted
from time to time by applicable law, no provision of this Article VI may be
altered, amended or repealed in any respect, nor may any provision inconsistent
therewith be adopted, unless such alteration, amendment, repeal or adoption is
approved by the affirmative vote of the holders of at least 80 percent of the
combined voting power of the then outstanding shares of the Corporation's stock
entitled to vote generally in the election of directors ("Voting Stock"), voting
together as a single class.

                                   Article VII

        Unless and except to the extent that the Bylaws of the Corporation shall
so require, election of directors need not be by written ballot.

                                  Article VIII

        A. 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 (subject to any provision contained in the laws of the
State of Delaware) outside of the State of Delaware at such place or places as
may be designated from time to time by the Board of Directors or in the Bylaws
of the Corporation.


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        B. Special meetings of stockholders may be called only by the Board of
Directors, the Chairman of the Board of Directors, the Chief Executive Officer,
or Acacia (as defined below in Article IX) and may not be called by any other
person or persons; provided that the right of Acacia to call a special meeting
of stockholders shall cease at such time as Acacia and any person controlling,
controlled by or under common control with Acacia shall first cease to be the
owner, in the aggregate, of at least 25 percent of the Voting Stock.

                                   Article IX

        A. Certain Acknowledgments. The provisions of this Article IX shall (a)
regulate and define the conduct of certain affairs of the Corporation in
relation to business transactions between the Corporation and the Acacia
Affiliated Companies (as defined below in this Article IX) and (b) set forth and
define the powers, rights, duties and liabilities of the Corporation and its
directors, officers, and stockholders in connection with such transactions, in
recognition and anticipation that: Acacia will remain for the foreseeable future
a significant stockholder of the Corporation; that directors, officers and/or
employees of an Acacia Affiliated Company may serve as directors, officers
and/or employees of the Corporation; that Acacia Affiliated Companies, directly
or indirectly, engage and may engage in the same, similar or related lines of
business as those in which the Corporation, directly or indirectly, engages or
may engage and/or other business activities that overlap with or compete with
those in which the Corporation, directly or indirectly, engages or may engage;
and that the Corporation engages and may engage in business transactions with
the Acacia Affiliated Companies.

        B. Corporate Opportunities.

        1. Business Entity Level. Subject to Section B.2 of this Article IX, if
an Acacia Affiliated Company acquires knowledge of a potential transaction or
matter which may be a corporate opportunity for both an Acacia Affiliated
Company and the Corporation, the Acacia Affiliated Company shall be under no
obligation to communicate or present such corporate opportunity to the Joint
Business Development Committee (as defined below in this Article IX) and shall
not be liable to the Corporation or its stockholders by reason of the fact that
such Acacia Affiliated Company pursues or acquires such corporate opportunity
for itself, directs such corporate opportunity to another person or entity
(including another Acacia Affiliated Company), or does not present such
corporate opportunity to the Joint Business Development Committee.

        2. Interlocking Director/Officer Level. If a director or officer of the
Corporation who is also a director or officer of an Acacia Affiliated Company
acquires knowledge of a potential transaction or matter which may be a corporate
opportunity for both the Corporation and any Acacia Affiliated Company, such
director or officer of the Corporation shall not be liable to the Corporation or
its stockholders by reason of the fact that such Acacia Affiliated Company
pursues or acquires such corporate opportunity for itself or directs such
corporate opportunity to another person or does not present such corporate
opportunity to the Joint Business Development Committee, if such director or
officer acts in a manner consistent with the following policy:

                (i) a corporate opportunity for both the Corporation and any
        Acacia Affiliated Company offered to any person who is a director but
        not an officer of the Corporation


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        and who is also a director or officer of an Acacia Affiliated Company
        shall first be offered to the Joint Business Development Committee only
        if such opportunity is expressly offered to such person solely in his
        capacity as a director of the Corporation, and otherwise shall first be
        offered to such Acacia Affiliated Company; and

                (ii) a corporate opportunity for both the Corporation and any
        Acacia Affiliated Company offered to any person who is an officer of the
        Corporation and who is also a director but not an officer of an Acacia
        Affiliated Company shall first be offered to the Joint Business
        Development Committee, unless such opportunity is expressly offered to
        such person solely in his capacity as a director of such Acacia
        Affiliated Company in which case such opportunity shall first be offered
        to such Acacia Affiliated Company.

For the purposes of this Article IX, "corporate opportunity of the Corporation"
shall be any business opportunity which the Corporation is financially able to
undertake, which is, from its nature, in the line of the Corporation's business,
of practical advantage to the Corporation and is one in which the Corporation
has an interest or a reasonable expectancy, and which, by having an Acacia
Affiliated Company embrace the opportunity, will result in a conflict between
the interest or reasonable expectancy of the Corporation and the interest or
reasonable expectancy of an Acacia Affiliated Company or its officers or
directors.

        C. Joint Business Development Committee. If a transaction between one or
more Acacia Affiliated Companies and the Corporation shall arise, or a corporate
opportunity is presented to the Joint Business Development Committee in
accordance with Section B of this Article IX, the Joint Business Development
Committee shall convene and examine the relevant facts, formulate a proposed
arrangement between the Corporation and the Acacia Affiliated Companies and
submit its written recommendation with respect thereto to the body referred to
in Section C of this Article IX that has been selected to consider the fairness
to the Corporation of the recommendation. A majority of the members of the Joint
Business Development Committee shall constitute a quorum, and the approval of
all members present and constituting a quorum shall be required to take action
by the Joint Business Development Committee. The notice and other procedural
requirements set forth in the Bylaws of the Corporation applicable to committees
of the Corporation's Board of Directors shall be applicable to the conduct of
the affairs of the Joint Business Development Committee. The Board of Directors
of the Corporation shall appoint such number of members of the Joint Business
Development Committee as shall be provided from time to time in the Bylaws of
the Corporation.

        D. Certain Agreements and Transactions Permitted; Certain Fiduciary
Duties of Certain Stockholders, Directors and Officers. Subject to Section F of
this Article IX, agreements (or modifications or supplements to pre-existing
agreements, or allocations of corporate opportunities of the Corporation)
between the Corporation and any Acacia Affiliated Company pursuant to which the
Corporation and such Acacia Affiliated Company agree to engage in transactions
of any kind or nature with each other, or the performance of such agreement by
the Corporation or Acacia Affiliated Company, shall not be considered contrary
to (a) any fiduciary duty that Acacia Affiliated Companies may owe to the
Corporation or to any stockholder or other owner of an equity interest in the
Corporation by reason of the Acacia Affiliated Companies being a controlling
stockholder of the Corporation or participating in the control of the
Corporation or (b) any fiduciary duty of any director or officer of the
Corporation who is also


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a director, officer or employee of an Acacia Affiliated Company may owe to the
Corporation, or to any stockholder thereof, if a recommendation in favor of such
agreement or transaction has been made by the Joint Business Development
Committee pursuant to Section C of this Article IX and any of the following
additional conditions shall have been satisfied:

                (i) such agreement or, in the case of any such transaction that
        was not entered into in the performance of an agreement, such
        transaction, shall have been approved or ratified as being fair to the
        Corporation by the Board of Directors of the Corporation by the
        affirmative vote of a majority of the members (even though less than a
        quorum) who are not Interested Persons (as defined below in this Article
        IX) in respect of such agreement; provided, however, that, before
        approval of such agreement, the material facts of the relationship
        between the Corporation and the Acacia Affiliated Company and the
        material terms and facts as to such agreement were disclosed to or were
        known by the members of the Board of Directors who acted on approval of
        such agreement; or

                (ii) such agreement or, in the case of any such transaction that
        was not entered into in the performance of an agreement, such
        transaction, was approved as being fair to the Corporation by the
        affirmative vote of the holders of a majority of the shares of Voting
        Stock entitled to vote thereon and who voted thereon, exclusive of any
        Acacia Affiliated Company, its officers, its directors and any
        Interested Person in respect of such agreement.

Subject to Section F of this Article IX, Acacia as a stockholder of the
Corporation or participant in control of the Corporation, shall not have or be
under any fiduciary duty to refrain from entering into any agreement or
participating in any transaction that meets the requirements of any of clauses
(i) or (ii) of the immediately preceding sentence and any director, officer or
employee of the Corporation who is also a director, officer or employee of an
Acacia Affiliated Company shall not have or be under any fiduciary duty to the
Corporation to refrain from acting on behalf of the Corporation in respect of
any agreement or transaction that meets the requirements of any of clauses (i)
or (ii) of the immediately preceding sentence. Any person purchasing or
otherwise acquiring any shares of capital stock of the Corporation, or any
interest therein, shall be deemed to have notice of and to have consented to the
provisions of this Article IX.

        E. For purposes of this Article IX, the following definitions shall
apply:

                (a) "Acacia" shall mean Acacia Research Corporation, a Delaware
        corporation, and any corporate successors thereof.

                (b) "Acacia Affiliated Company" shall mean Acacia and any
        Business Entity that is controlled by Acacia, controls Acacia or is
        under common control with Acacia (other than the Corporation).

                (c) "Business Entity" shall mean any corporation, partnership,
        limited partnership, limited liability company or other business entity.

                (d) "Corporation" shall mean the Corporation and any Business
        Entity that is controlled by the Corporation


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                (e) "Interested Person" in respect of an agreement or
        transaction referred to in Section C of this Article IX shall mean any
        director, officer or employee of any of the Acacia Affiliated Companies
        and any person who has a financial interest that is material to such
        person in any of the Acacia Affiliated Companies or otherwise has a
        personal financial interest that is material to such person in such
        agreement or transaction; provided, however, that no such financial
        interest shall be considered material by reason of a person's ownership
        of securities of any of the Acacia Affiliated Companies, if such
        ownership of securities has been determined in good faith not to be
        reasonably likely to influence such individual's decision on behalf of
        the Corporation in respect of the agreement or transaction either in the
        specific instance by, or pursuant to a policy adopted by, the Board of
        Directors of the Corporation by the affirmative vote of a majority of
        the members (even though less than a quorum) who are not directors,
        officers or employees of any of the Acacia Affiliated Companies by the
        affirmative vote of a majority of such committee.

                (f) "Joint Business Development Committee" shall mean a
        committee so designated by the Board of Directors of the Corporation
        which shall consist of an equal number of designees of the Corporation
        and of Acacia.

        F. The provisions of this Article IX shall have no further force or
effect at such time as Acacia and any person controlling, controlled by or under
common control with Acacia shall first cease to be the owner, in the aggregate,
of at least 25 percent of the Voting Stock; provided, however, that such
termination shall not terminate the effect of such provisions with respect to
(a) any agreement between the Corporation and any Acacia Affiliated Companies
that was entered into before such time or any transaction entered into in the
performance of such agreement, whether entered into before or after such time,
or (b) any transaction entered into between the Corporation and any of the
Acacia Affiliated Companies or the allocation of any opportunity between them
before such time.

        G. Notwithstanding any other provisions of this Restated Certificate of
Incorporation, and notwithstanding that a lesser percentage may be permitted
from time to time by applicable law, no provision of this Article IX may be
altered, amended or repealed in any respect, nor may any provision inconsistent
therewith be adopted, unless such alteration, amendment, repeal or adoption is
approved by the affirmative vote of the holders of at least 80 percent of the
combined voting power of the then outstanding shares of Voting Stock, voting
together as a single class.

                                    Article X

        A director of the Corporation shall not be liable to the Corporation or
its stockholders for monetary damages for breach of fiduciary duty as a
director, except to the extent such exemption from liability or limitation
thereof is not permitted under the General Corporation Law of Delaware as the
same exists or may hereafter be amended. If the General Corporation Law of
Delaware is amended after the date of the filing of this Restated Certificate of
Incorporation to authorize corporate action further eliminating or limiting the
personal liability of directors, then the liability of a director of the
Corporation shall be eliminated or limited to the fullest extent permitted by
the General Corporation Law of Delaware as so amended. Any repeal or


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modification of this Article by the stockholders of the Corporation shall not
adversely affect any right or protection of a director of the Corporation
existing at the time, or increase the liability of any director of the
Corporation with respect to any acts or omissions of such director occurring
prior to, such repeal or modification.

                                   Article XI

        The Corporation may indemnify to the fullest extent permitted by law any
person made or threatened to be made a party to an action or proceeding, whether
criminal, civil, administrative or investigative, by reason of the fact that
such person, his or her testator or intestate is or was a director, officer or
employee of the Corporation or any predecessor of the Corporation or serves or
served at any other enterprise as a director, officer or employee at the request
of the Corporation or any predecessor to the Corporation. No repeal or
modification of this Article by the stockholders shall adversely affect any
right or protection of a director of the Corporation existing by virtue of this
Article at the time of such repeal or modification.

                                   Article XII

        The Corporation hereby reserves the right at any time and from time to
time to amend, alter, change, or repeal any provisions contained in this
Restated Certificate of Incorporation, 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 now or hereafter prescribed by law, and all rights, preferences, and
privileges of whatsoever nature conferred upon stockholders, directors, or any
other persons whomsoever by or pursuant to this Restated Certificate of
Incorporation in its present form or as hereafter amended are granted subject to
the right reserved in this Article.

                           [Signature Page to Follow]


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        IN WITNESS WHEREOF, the Corporation has caused this Restated Certificate
of Incorporation to be signed by Stephen G. Burke, its Executive Vice President
of Finance, and acknowledged by Patrick D. de Maynadier, its Secretary, on this
15th day of November 2000.



                                       By: /s/ Stephen G. Burke
                                           -------------------------------
                                           Stephen G. Burke
                                           Executive Vice President of Finance

ATTEST:


By: /s/ Patrick D. de Maynadier
    -------------------------------
    Patrick D. de Maynadier
    Secretary


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