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EXHIBIT 10.52

                                 THIRD AMENDMENT
                                       TO
                  COLLABORATION RESEARCH AND LICENSE AGREEMENT

This Third Amendment ("Third Amendment") is entered into by and between ELI
LILLY AND COMPANY, an Indiana corporation, having offices at Lilly Corporate
Center, Indianapolis, Indiana 46285 ("Lilly"), and between AURORA BIOSCIENCES
CORPORATION, a Delaware corporation having offices at 11010 Torreyana Road, San
Diego, California 92121 ("Aurora") and is effective as of the last date that
this Third Amendment is executed below.

WHEREAS, effective December 18, 1996, Lilly and Aurora entered into a
Collaborative Research and License Agreement, a First Amendment thereto on July
2, 1997, and a Second Amendment thereto on December 12, 1997 (the "Agreement");
and

WHEREAS, Lilly and Aurora are obligated to develop in collaboration with one
another the LILLYUHTSS under the Agreement;

WHEREAS, Lilly and Aurora desire to amend their obligations and rights under the
Agreement with respect to the LILLYUHTSS;

WHEREAS, Lilly desires to license certain intellectual property rights
Controlled by Aurora; and

NOW, THEREFORE, in consideration of the foregoing premises and of faithful
performance of the covenants herein contained, the parties hereto agree as
follows:

1.       All definitions not specifically defined herein are defined in the
         Agreement.

2.       Within *** days of the effective date of this Third Amendment, Lilly
         will pay to Aurora a nonrefundable, noncreditable payment of ***
         Dollars ($***), for designing, developing and manufacturing Module ***.

3.       Lilly shall have no obligation to make further payments of any kind to
         Aurora with respect to the LILLYUHTSS or any portion thereof, except as
         provided in Section 2 of this Third Amendment. Lilly shall *** under
         Section 5.1.1 (iii) of the Agreement to use *** and *** the LILLYUHTSS
         for *** and ***.

4.       Aurora shall have no further obligations whatsoever related to design,
         development, manufacture, support, validation or completion related to
         *** or any portion thereof. Aurora shall not have any obligations under
         Section *** of the Agreement to pay any payment related to the
         completion of the LILLYUHTSS. Aurora's obligations under Section *** of
         the Agreement are abrogated as of the effective date of this Third
         Amendment.


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5.       Lilly and Aurora may elect, by specific written agreement by both
         parties, to re-initiate the LILLYUHTSS development and delivery on
         conditions, terms and scheduling to be agreed upon at such time, in
         writing.

6.       Sections 2.1 (including 2.1.1 (Project Management), 2.1.2 (Development
         and Delivery), 2.1.3 (Validation and Completion), 2.1.5 (Penalty),
         2.1.4 (Payments), and 2.1.6 (Most Favored Nations and Syndicate
         Limitations), 2.1.7 (Supply of Aurora Reporters), 2.1.8 (terms for
         Aurora Reporters), 4.1 (Service and Support), 11.3 (Termination Without
         Cause by Lilly), 11.4 (Partial Performance) and Exhibits 1.1 and 4.1 of
         the Agreement are hereby removed and shall have no force or effect.

7.       Aurora will deliver to Lilly the VIPR in accordance with the terms set
         forth in Aurora invoice number ***, attached hereto as Exhibit ***.

8.       Lilly will pay Aurora the following payments in consideration of the
         use of Aurora Reporter System Technology and Aurora Reporter System
         Patent Rights from December 18, *** through December 17, ***:

                  a) *** Dollars ($***) payable by ***;

                  b) ***  Dollars  ($***)  payable as follows  *** (i) *** or
                  (ii) *** of *** ($***) *** to be paid by *** and ***; and

                  c) *** Dollars  ($***)  payable as follows  *** (i) *** or
                  (ii) *** of *** Dollars  ($***) *** to be paid by *** and ***.

         Lilly *** licenses to Aurora Reporter System Technology and Aurora
         Reporter System Patent Rights on *** by providing Aurora with at least
         *** written notice of *** its *** for ***, and by payment of ***
         payment of *** Dollars ($***) to *** as a *** payment of *** Dollars
         ($***) and a *** payment of *** Dollars ($***).



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9.       So long as Lilly has made payments in accordance with Section 8 of this
         Third Amendment hereof, then, at Lilly's request, Aurora will use ***
         supply Aurora Reporters *** days after receipt of a written purchase
         order therefor, *** pertaining to the Aurora Reporter Systems as Lilly
         may require in order to use the Aurora Reporter Systems *** Lilly.
         Lilly will be charged for all supplies so delivered ***. Lilly will pay
         for all supplies so ordered within *** days after delivery to Lilly.

10.      So long as Lilly satisfies its payment obligations under Section 8 of
         this Third Amendment for Aurora Reporters, Aurora *** Lilly to ***
         Exhibit 1.2 of the Agreement and developed by Aurora, for ***
         comparable to those *** by ***.

11.      Exhibit 1.2 of the Agreement is replaced with the new Exhibit 1.2
         attached *** and ***.

12.      Exhibit 5.1 of the Agreement is replaced with new Exhibit 5.1 attached,
         ***.

13.      Each party hereby voluntarily and knowingly releases and forever
         discharges the other party, its Affiliates and their respective
         shareholders, officers, directors, employees, agents, successors and
         assigns, from any and all actions, causes of action, debts, sums of
         money, damages, judgments, obligations, claims and demands whatsoever,
         whether or not presently known, and whether or not presently capable of
         being known, *** of the Agreement.

14.      The parties and each of them represent, warrant and agree that they
         have been fully advised by their respective attorneys regarding the
         contents of Section 1542 of the Civil Code of the State of California.
         Such Section 1542 reads as follows: "A general release does not extend
         to claims which the creditor does not know or suspect to exist in his
         favor at the time of executing the release, which if known by him must
         have materially effected his settlement with the debtor." The parties
         *** and any similar *** claim *** herein.



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15.      Lilly and its Affiliates and Aurora and its Affiliates shall *** to
         ensure that their respective officers, directors, consultants and
         employees *** any *** Third Party *** party including, but not limited
         to, the *** other party.

16.      Lilly and Aurora shall make reasonable efforts to agree promptly to the
         text of an Aurora Press Release (together with a "Q&A" document)
         announcing the substance of this amendment, subject to the terms in
         Section 8 of the Agreement.

17.      The obligations of Lilly and Aurora set forth in Section *** of the
         Agreement shall no longer apply with respect to Aurora UHTSS
         Technology, Aurora UHTSS Patent Rights, Lilly UHTSS Technology, and
         Lilly UHTSS Patent Rights, but shall continue in all other respects.

18.      The obligations of Lilly set forth in Section *** of the Agreement
         shall no longer apply with respect to Aurora UHTSS and Aurora UHTSS
         Patent Rights, but shall continue in all other respects.

19.      The last sentence of Section 11.7.1 shall be deleted in its entirety
         and replaced with the following:

              "Except as otherwise expressly provided in this Agreement, the
         rights and obligations of the parties under Sections *** and ***
         shall *** further *** or *** upon *** except that the licenses
         granted under *** and *** of the LILLYUHTSS *** deemed ***."

20.      Except as hereby amended, the parties confirm and ratify that the terms
         and conditions of the Agreement remain in full force and effect.

IN WITNESS WHEREOF, the parties, by duly authorized representatives, execute
this Third Amendment to the Agreement

ELI LILLY AND COMPANY                            AURORA BIOSCIENCES CORPORATION



By: /s/ August M. Watanabe                      By: /s/ Stuart Collinson
   ------------------------------                  ---------------------------

Title: Executive Vice President                 Title: CEO & President
      ---------------------------                     ------------------------

Date: November 22, 1999                         Date: 11-17-99
     ----------------------------                    -------------------------


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                                   EXHIBIT 1.2

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                                   EXHIBIT 5.1





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                                  EXHIBIT TA-7





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