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                                                                   EXHIBIT 3.1.1

                           CERTIFICATE OF AMENDMENT TO
                              AMENDED AND RESTATED
                         CERTIFICATE OF INCORPORATION OF
                             LYNX THERAPEUTICS, INC.

         Lynx Therapeutics, Inc. (the "Corporation"), a corporation organized
and existing under the General Corporation Law of the State of Delaware, DOES
HEREBY CERTIFY:

         FIRST:   The name of the Corporation is Lynx Therapeutics, Inc.

         SECOND:  The Corporation's original Certificate of Incorporation was
filed with the Secretary of State of the State of Delaware on February 18, 1992
under the name of Applied Genomics Incorporated.

         THIRD:   The Board of Directors of the Corporation, acting in
accordance with the provision of Sections 141 and 242 of the General Corporation
Law of the State of Delaware adopted resolutions to amend the first paragraph of
Article IV of the Amended and Restated Certificate of Incorporation of the
Corporation to read in its entirety as follows:

         "This Corporation is authorized to issue two classes of stock to be
         designated, respectively, "Preferred Stock" and "Common Stock." The
         total number of shares that 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").
         Effective as of 5:00 p.m., Eastern time, on the date this Certificate
         of Amendment to Amended and Restated Certificate of Incorporation is
         filed with the Secretary of State of the State of Delaware, each seven
         (7) shares of the Corporation's Common Stock, par value one cent ($.01)
         per share, issued and outstanding shall, automatically and without any
         action on the part of the respective holders thereof, be combined and
         converted into one (1) share of Common Stock, par value one cent ($.01)
         per share, of the Corporation. No fractional shares shall be issued
         and, in lieu thereof, any holder of less than one share of Common Stock
         shall be entitled to receive cash for such holder's fractional share
         based upon the closing sales price of the Corporation's Common Stock as
         reported on The Nasdaq National Market as of the date this Certificate
         of Amendment is filed with the Secretary of State of the State of
         Delaware."

         FOURTH: This Certificate of Amendment to Amended and Restated
Certificate of Incorporation was submitted to the stockholders of the
Corporation and was duly approved by the required vote of the stockholders of
the Corporation in accordance with Sections 222 and 242 of the Delaware General
Corporation Law. The total number of outstanding shares entitled to vote or
consent to this Amendment was 30,491,073 shares of Common Stock. A majority of
the outstanding shares of Common Stock, voting together as a single class, voted
in favor of this Certificate of Amendment to Amended and Restated Certificate of
Incorporation. The vote required was a majority of the outstanding shares of
Common Stock, voting together as a single class.

         IN WITNESS WHEREOF, Lynx Therapeutics, Inc. has caused this Certificate
of Amendment to be signed by its Chief Executive Officer as of January 15, 2003.

                                                   LYNX THERAPEUTICS, INC.

                                                   /s/ Kevin P. Corcoran
                                                   -----------------------------
                                                   Kevin P. Corcoran
                                                   Chief Executive Officer