AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                             LYNX THERAPEUTICS, INC.
 
 
     LYNX THERAPEUTICS, INC., a corporation organized and existing under the
General Corporation Law of the State of Delaware, DOES HEREBY CERTIFY:
 
     FIRST: The original Certificate of Incorporation of Lynx Therapeutics, Inc.
(the "Corporation") was filed with the Secretary of State of the State of
Delaware on February 18, 1992 under the name of Applied Genomics Incorporated.
 
     SECOND: The Amended and Restated Certificate of Incorporation in the form
attached hereto as Exhibit A has been duly adopted in accordance with the
provisions of Sections 141, 242 and 245 of the General Corporation Law of the
State of Delaware by the Board of Directors of the Corporation.
 
     THIRD: The Amended and Restated Certificate of Incorporation in the form
attached hereto as Exhibit A has been duly adopted in accordance with the
provisions of Sections 212, 242 and 245 of the General Corporation Law of the
State of Delaware by the stockholders of the Corporation, and notice was
provided in accordance with said Section 222. The total number of outstanding
shares entitled to vote was 11,349,865 shares of Common Stock. A majority of the
outstanding shares of Common Stock voted in favor of this Amended and Restated
Certificate of Incorporation.
 
     FOURTH: The Amended and Restated Certificate of Incorporation so adopted
reads in full as set forth in Exhibit A attached hereto and is hereby
incorporated by reference.
 
     IN WITNESS WHEREOF, Lynx Therapeutics, Inc. has caused this Certificate to
be signed by the Chief Financial Officer in Hayward, California this 20th day of
June, 2000.
 
                                     LYNX THERAPEUTICS, INC.
 
 
 
                                     By \s\  Edward C. Albini
                                       -----------------------------------------
                                       Edward C. Albini, Chief Financial Officer
 
 
ATTEST:
 
 
By \s\ James C. Kitch
  ----------------------------------
  James C. Kitch, Secretary
 
 
                                       1.
 
<PAGE>   2
 
                                    EXHIBIT A
 
                AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                             LYNX THERAPEUTICS, INC.
 
 
                                       I.
 
     The name of this corporation is Lynx Therapeutics, Inc.
 
                                      II.
 
     The address of the registered office of this corporation in the State of
Delaware is 1013 Centre Road, City of Wilmington, County of New Castle. The name
of this corporation's registered agent at said address is The Prentice-Hall
Corporation System, Inc.
 
                                      III.
 
     The purpose of this corporation is to engage in any lawful act or activity
for which a corporation may be organized under the General Corporation Law of
Delaware.
 
                                      IV.
 
     A.   This Corporation is authorized to issue two classes of stock to be
designated, respectively, "Preferred Stock" and "Common Stock." The total number
of shares which the corporation is authorized to issue is Sixty-two million
(62,000,000) shares. Sixty million (60,000,000) shares shall be Common Stock,
par value one cent ($.01) per share (the "Common Stock") and Two million
(2,000,000) shares shall be Preferred Stock, par value one cent ($.01) per share
(the "Preferred Stock").
 
     B.   The shares of Preferred Stock may be issued from time to time in one
or more series. The Board of Directors of the corporation is expressly
authorized to provide for the issue of all or any of the shares of Preferred
Stock in one or more series, and to fix the number of shares and to determine or
alter for each such series, such voting powers, full or limited, or no voting
powers, and such designations, preferences, and relative, participating,
optional, or other rights and such qualifications, limitations or restrictions
thereof, as shall be stated and expressed in the resolution or resolutions
adopted by the Board of Directors providing for the issue of such shares and as
may be permitted by the General Corporation Law of the State of Delaware. The
Board of Directors is also expressly authorized to increase or decrease (but not
below the number of shares of such series then outstanding) the number of shares
of any series subsequent to the issue of shares of that series. In case the
number of shares of any such series shall be so decreased, the shares
constituting such decrease shall resume the status that they had prior to the
adoption of the resolution originally fixing the number of shares of such
series.
 
 
                                       1.
 
<PAGE>   3
 
                                       V.
 
     For the management of the business and for the conduct of the affairs of
the corporation, and in further definition, limitation and regulation of the
powers of the corporation, of its directors and of its stockholders or any class
thereof, as the case may be, it is further provided that:
 
     (a)  The management of the business and the conduct of the affairs of the
corporation shall be vested in its Board of Directors. The number of directors
which shall constitute the whole Board of Directors shall be fixed by the Board
of Directors in the manner provided in the Bylaws.
 
     (b)  The Board of Directors may from time to time make, amend, supplement
or repeal the Bylaws.
 
     (c)  The directors of the corporation need not be elected by written ballot
unless the Bylaws so provide.
 
                                      VI.
 
     To the fullest extent permitted by the General Corporation Law of Delaware,
as the same exists or may hereafter be amended, a director of this corporation
shall not be liable to the corporation or its stockholders for monetary damages
for breach of fiduciary duty as a director.
 
                                      VII.
 
     The corporation is to have perpetual existence.
 
                                     VIII.
 
     The corporation reserves the right to amend, alter, change or repeal any
provision contained in this Certificate of Incorporation, in the manner now or
hereafter prescribed by statute, and all rights conferred upon the stockholders
herein are granted subject to this right.
 
 
                                       2.