Parallel selex

• US 5,789,160 A
• Filed: 06/05/1995
• Issued: 08/04/1998
• Est. Priority Date: 06/11/1990
• Status: Expired due to Term

• Current Assignee: Medallion Biomedical, LLC
• Original Assignee: NeXstar Pharmaceuticals, Inc. (Gilead Sciences Inc.)
• Inventors: Gold, Larry, Eaton, Bruce E.
• Primary Examiner(s): Elliott, George C.
• Assistant Examiner(s): SCHWARTZMAN, ROBERT A
• Application Number:
  US08/463,101
• Time in Patent Office: 1,156 Days
• Field of Search: 435/6, 435/91.2, 536/23.1
• US Class Current: 506/9
• CPC Class Codes: A61K 47/547 Chelates, e.g. Gd-DOTA or Zinc-amino acid chelates; Chelate-forming compounds, e.g. DOTA or ethylenediamine being covalently linked or complexed to the pharmacologically- or therapeutically-active agent
• CPC Class Codes: A61K 47/549 Sugars, nucleosides, nucleotides or nucleic acids
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07K 14/001 by chemical synthesis
• CPC Class Codes: C12N 15/1048 SELEX
• CPC Class Codes: C12N 15/115 Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
• CPC Class Codes: C12N 2310/13 Decoys
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/53 partially self-complementary or closed
• CPC Class Codes: C12N 9/1276 RNA-directed DNA polymerase (2.7.7.49), i.e. reverse transcriptase or telomerase
• CPC Class Codes: C12Q 1/37 involving peptidase or proteinase
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/113 incorporating modified backbone
• CPC Class Codes: C12Q 2525/205 Aptamer
• CPC Class Codes: C12Q 2541/101 Selex
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: F02B 2075/027 : four
• CPC Class Codes: G01N 2333/16 : HIV-1, HIV-2
• CPC Class Codes: G01N 2333/163 : Regulatory proteins, e.g. tat, nef, rev, vif, vpu, vpr, vpt, vpx
• CPC Class Codes: G01N 2333/503 : basic FGF [bFGF]
• CPC Class Codes: G01N 2333/575 : Hormones
• CPC Class Codes: G01N 2333/62 : Insulins
• CPC Class Codes: G01N 2333/8125 : Alpha-1-antitrypsin
• CPC Class Codes: G01N 2333/96433 : Serine endopeptidases (3.4.21)
• CPC Class Codes: G01N 2333/96436 : Granzymes
• CPC Class Codes: G01N 2333/96455 : Kallikrein (3.4.21.34; 3.4.21.35)
• CPC Class Codes: G01N 2333/96486 : Metalloendopeptidases (3.4.24)
• CPC Class Codes: G01N 2333/966 : Elastase
• CPC Class Codes: G01N 2333/9726 : Tissue plasminogen activator
• CPC Class Codes: G01N 2333/974 : Thrombin
• CPC Class Codes: G01N 2333/976 : Trypsin; Chymotrypsin
• CPC Class Codes: G01N 33/531 : Production of immunochemical test materials
• CPC Class Codes: G01N 33/532 : Production of labelled immunochemicals
• CPC Class Codes: G01N 33/535 : with enzyme label or co-enzymes, co-factors, enzyme inhibitors or enzyme substrates
• CPC Class Codes: G01N 33/56988 : HIV or HTLV
• CPC Class Codes: G01N 33/68 : involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: G01N 33/6842 : Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
• CPC Class Codes: G01N 33/76 : Human chorionic gonadotropin including luteinising hormone, follicle stimulating hormone, thyroid stimulating hormone or their receptors

Abstract

This invention disclosures a method for coevolving products from two or more reactants, along with the nucleic acid that can facilitate the reaction for making the products. The invention further discloses the products and facilitating nucleic acids produced by said method.

Claims

1. A method for identifying a product from a product library, wherein said product binds to a target, said method comprising:

(a) preparing a nucleic acid-first reactant test mixture comprised of nucleic acids each having a region of randomized sequence and each being coupled to a first reactant consisting of a small organic molecule with a molecular weight in the range of 2 to 1000;

(b) reacting said nucleic acid-first reactant test mixture with a free reactant consisting of a small organic molecule with a molecular weight in the range of 2 to 1000 to form a product library comprised of products formed by the reaction of said first reactant and said free reactant, wherein said reaction is facilitated by the nucleic acid coupled to said first reactant;

(c) partitioning between members of said product library based on their ability to bind to said target; and

(d) identifying said products which bind to said target.

2. The method of claim 1 wherein said nucleic acid-first reactant test mixture comprises nucleic acids having a region of conserved sequences and a region of randomized sequences.

3. The method of claim 1 wherein said nucleic acid is selected from the group of single-stranded RNA, single-stranded DNA and double-stranded DNA.

4. The method of claim 1 wherein said nucleic acid first reactant test mixture comprises modified nucleotides.

5. The method of claim 1 further comprising an organometallic catalyst covalently linked to said nucleic acids of said nucleic acid-first reactant test mixture.

6. The method of claim 1 which further comprises a linker group coupled between said first reactant and said nucleic acid.

7. The method of claim 1 wherein said first reactant is a dienophile, said free reactant is a diene, and said product is a cyclohexene derivative.

8. The method of claim 1 wherein said nucleic acid-first reactant test mixture comprises an organometallic catalyst in solution with said nucleic acids coupled to said first reactant.

9. The method of claim 4 wherein said modified nucleotides have been chemically modified at the ribose and/or phosphate and/or base positions.

10. The method of claim 4 wherein said modified mucleotides are pyrimidines modified at the 2'"'"'- or 5- positions.

11. The method of claim 6 wherein said modified nucleotides are purines modified at the 8- position.

12. The method of claim 6 wherein said modified nucleotides are modified with a chemical group which increases charge, polarizability, hydrogen bonding, electrostatic interaction or fluxionality of the nucleotide.

13. The method of claim 6 wherein said linker group has a size in the range of 10 to 1000 Å

.

14. The method of claim 12 wherein said chemical group is selected from the group consisting of hydrophobic moieties, hydrophilic moieties, metal atoms in various oxidation states, rigid structures, imidazoles, primary alcohols, carboxylates, guanidium groups, amino groups, thiols and organometallic catalysts.

15. The method of claim 12 wherein said chemical group comprises an amino acid side chain or analogs thereof.

16. The method of claim 13 wherein said linker group is selected from the group consisting of polyethylene glycol, polyvinyl alcohol, polyacrylates and polypeptides.

17. A method for identifying a product from a product library, wherein said product binds to a target molecule, said method comprising:

(a) preparing a nucleic acid-first reactant test mixture comprises of nucleic acids each having a region of randomized sequence and each being coupled to a first reactant consisting of a small organic molecule with a molecular weight in the range of 2 to 1000;

(b) reacting said nucleic acid-first reactant test mixture with a free reactant consisting of a small organic molecule with a molecular weight in the range of 2 to 1000 to form a product library comprised of nucleic acids coupled to a product formed by the reaction of said first reactant and said free reactant;

(c) partitioning said products having increased affinity to the target from the remainder of the product library; and

(d) identifying said product from said library.

18. The method of claim 17 which further comprises between steps b and c, contacting the product library with a non-target and partitioning away products which bind to said non-target.

19. A method for identifying a facilitating nucleic acid, wherein said nucleic acid is selected for its ability to facilitate a reaction between a first reactant coupled to said nucleic acid and a free reactant, wherein each reactant is consisting of a small organic molecule with a molecular weight in the range of 2 to 1000, to form a product which binds to a target, said method comprising:

(a) preparing a nucleic acid-first reactant test mixture comprised of nucleic acids each having a region of randomized sequence and each being coupled to a first reactant;

(b) mixing said nucleic acid-first reactant test mixture with a plurality of free reactants under conditions favorable for a nucleic acid facilitated reaction between said first reactant and said free reactant to form said product;

(c) isolating members of said nucleic acid-first reactant test mixture which formed said products; and

(d) identifying said facilitating nucleic acid.

20. A method for simultaneously identifying facilitating nucleic acids and producing a product library, wherein said facilitating nucleic acids facilitate the reaction between a first reactant and at least one free reactant, wherein each reactant is consisting of a small organic molecule with a molecular weight in the range of 2 to 1000, to form said product library, said method comprising:

(a) preparing a nucleic acid-first reactant test mixture comprised of nucleic acids each having a region of randomized sequence and each being coupled to said first reactant;

(b) reacting said nucleic acid-first reactant test mixture with said free reactant to form a product library; and

(c) identifying said facilitating nucleic acids.