Methods for screening factorial chemical libraries

• US 5,541,061 A
• Filed: 04/29/1992
• Issued: 07/30/1996
• Est. Priority Date: 04/29/1992
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymax Incorporated
• Inventors: Fodor, Stephen P. A., Stryer, Lubert
• Primary Examiner(s): Parr, Margaret
• Assistant Examiner(s): Green, Lora M.
• Application Number:
  US07/876,792
• Time in Patent Office: 1,553 Days
• Field of Search: 435/5, 435/7.1, 435/6, 436/501, 436/518, 550/333, 550/334
• US Class Current: 506/9
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00592 Split-and-pool, mix-and-divide processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: C07K 1/047 Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C07K 1/06 using protecting groups or activating agents C07K1/003, C07K1/006 take precedence
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures

Abstract

A method and library for determining the sequence of monomers in a polymer which is complementary to a receptor. The method provides for formation of pooled (6) and separate (10, 12) products. Separate products are subjected only to subsequent pooled coupling steps. Each pooled product is subsequently divided for formation of pooled and separate products. The resulting polymer library includes groups of polymer products. A first group of products (42) is used to identify the monomer at a first location in a polymer that is complementary to a receptor. A second group of products (44) is used to identify the monomer at a second location in a polymer that is complementary to a receptor.

Claims

1. A method of identifying first and second monomers in a polymer that specifically binds to a receptor of interest, said polymer selected from the group consisting of oligonucleotides and peptides, comprising the steps of:

coupling first and second monomers in a first basis set to individual solid substrates and mixing substrates to form first pooled products;

coupling said first and second monomers from said first basis set to individual substrates, and not mixing said substrates to form at least first and second separate products;

separately coupling first and second monomers from a second basis set to substrates from said first pooled products and not mixing said substrates to form at least third and fourth separate products;

coupling said first and second monomers from said second basis set to individual substrates from said first separate products and mixing said substrates to form second pooled products;

coupling said first and second monomers from said second basis set to individual substrates from said second separate products to form third pooled products; and

exposing a receptor to said third and fourth separate products to identify a second monomer in a polymer which is complementary to a receptor, and exposing said second and third pooled products to said receptor to identify a first monomer in a polymer which specifically binds to said receptor.

2. The method as recited in claim 1 wherein said step of exposing to a receptor is preceded by the step of performing additional steps of coupling and mixing to said second pooled products and said third pooled products.

3. The method as recited in claim 1 further comprising the step of mixing a portion of said third and fourth separate products to form fourth pooled products.

4. The method as recited in claim 3 further comprising the step of separately coupling monomers from a third basis set to said fourth pooled products.

5. The method as recited in claim 1 wherein said monomers are amino acids.

6. The method as recited in claim 1 wherein said monomers are nucleotides.

7. The method as recited in claim 1 wherein said steps are repeated to screen polymers having at least three monomers therein.

8. The method as recited in claim 1 wherein at least one of said first and second monomers cannot be determined unambiguously, further comprising the steps of:

synthesizing an array of potentially specifically binding polymers using a light-directed synthesis technique; and

detecting binding of said receptor to said potentially specifically binding polymers.