Methods for producing ligand arrays

• US 7,534,563 B2
• Filed: 06/30/2003
• Issued: 05/19/2009
• Est. Priority Date: 06/30/2003
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Hargreaves, John S.
• Primary Examiner(s): Low; Christopher
• Assistant Examiner(s): Lundgren; Jeffrey S.
• Application Number:
  US10/610,829
• Publication Number:
  US 20040265476A1
• Time in Patent Office: 2,150 Days
• Field of Search: None
• US Class Current: 435/6.11
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00441 using lasers
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00664 Three-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00677 : Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00707 : separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01J 2219/00729 : Peptide nucleic acids [PNA]
• CPC Class Codes: B01J 2219/00731 : Saccharides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C03C 17/30 : with silicon-containing compounds
• CPC Class Codes: C03C 17/3405 : with at least two coatings of organic materials C03C17/36, C03C17/42 take precedence
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 33/54353 : with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393
• CPC Class Codes: Y10T 428/2995 : Silane, siloxane or silicone coating

Abstract

Methods for producing ligand substrates and arrays, e.g., peptide and nucleic acid arrays, as well as the arrays produced thereby, methods for use of the arrays and kits that include the same are provided. In the subject methods, a substrate having a surface displaying photocleavable functional groups that produce surface bound photocleavage produced functional groups upon irradiation is first provided, where the photocleavable groups are then cleaved to produce a surface that displays desired functional groups. The resultant substrates, optionally after an additional functionalization step, are then contacted with ligands or monomeric precursors thereof, e.g., via deposition of each different ligand onto a different region of the surface, resulting in covalent attachment of the contacted ligands to the surface. The subject methods find use in the preparation of a variety of different types of arrays, where the produced arrays find use in a variety of different applications, including both genomic and proteomic applications.

Claims

1. A method of producing an array of at least two different ligands covalently bonded to a surface of a substrate, said method comprising:

(a) providing a substrate having a surface displaying photocleavable functional groups by contacting a surface of a substrate with a first silanizing reagent comprising a terminal photocleavable functional group to produce a surface displaying photocleavable functional groups;

(b) cleaving said photocleavable functional groups on said surface to produce a patterned surface displaying feature regions of photocleavage produced functional groups; and

(c) producing by in situ synthesis at least two different polymeric ligands in at least two different feature regions to produce said array;

wherein said method includes a single photocleavage step that occurs prior to said producing step (c) and wherein said photocleavage produced functional groups are hydroxyl groups.

2. The method according to claim 1, wherein said in situ synthesis method comprises depositing drops of monomeric precursors of said ligands onto said feature regions.

3. The method according to claim 2, wherein said drops are deposited by pulse-jet deposition.

4. A method of producing an array of at least two different ligands covalently bonded to a surface of a substrate, said method comprising:

(a) contacting a surface of a substrate with at least a first silanizing reagent comprising a photocleavable functional group to produce a surface displaying photocleavable functional groups;

(b) cleaving said photocleavable functional groups on said surface to produce a patterned surface displaying feature regions of hydroxyl functional groups; and

(c) producing by in situ synthesis at least two different ligands in at least two different feature regions produced in step (b) to produce said array;

wherein said method includes a single photocleavage step that occurs prior to said producing step (c).

5. The method according to claim 4, wherein said silanizing reagent comprises terminal silyl and photocleavable groups separated by an alkyl chain.

6. The method according to claim 5, wherein said alkyl chain is from about 2 to about 20 carbon atoms in length.

7. The method according to claim 6, wherein said silanizing reagent has the formula:

Y-(L)_n-Si(R^LR^XR^Y)

wherein;

R^L is a leaving group;

R^X and R^Y are independently lower alkyl or a leaving group;

L is a C₂-C₂₀ alkyl chain;

n is 0 or 1; and

Y is a photocleavable group.

8. The method according to claim 7, wherein said photocleavable group is cleaved when irradiated at a wavelength ranging from about 230 nm to about 700 nm for a period of time ranging from about 0.1 s to about 12 hours.

9. The method according to claim 8, wherein said photocleavable group is chosen from amide, carbonyl, ester, peroxide and aromatic.

10. The method according to claim 9, wherein said photocleavable group is benzoyloxy.

11. The method according to claim 4, wherein said contacting comprises contacting said surface with a second silanizing reagent.

12. The method according to claim 11, wherein said second silanizing reagent has the formula:

R¹-(L)_n-Si(R^LR^xR^y)

wherein;

R^L is a leaving group;

R^x and R^Y are independently lower alkyl or a leaving group;

L is a C₂-C₂₀ alkyl chain;

n is 0 or 1; and

R¹ is a chemically inert moiety.

13. The method according to claim 4, wherein said method comprises converting said hydroxyl functional group to a reactive functional group.

14. The method according to claim 4, wherein said producing step (c) comprises depositing monomeric ligand precursors onto said surface.

15. The method according to claim 4, wherein said substrate is glass.

16. The method according to claim 4, wherein said ligands are selected from oligonucleotides, polynucleotides, peptide-nucleic acids and peptides.

17. The method according to claim 16, wherein said polynucleotides are deoxyribonucleic acids.

18. The method according to claim 4, wherein said contacting comprises contacting a fluid composition of said silanizing reagent with said substrate.

19. The method according to claim 4, wherein said cleaving step reduces the contact angle of said surface by 30°

or more.

20. A method of producing an array of at least two different ligands covalently bonded to a surface of a substrate, said method comprising:

(a) contacting a surface of a substrate with a mixture of a first silanizing reagent comprising a terminal photocleavable functional group and a second silanizing agent lacking said terminal photocleavable functional group to produce a surface displaying photocleavable functional groups;

(b) cleaving said photocleavable functional groups on said surface to produce a patterned surface displaying feature regions of hydroxyl functional groups; and

(c) producing at least two different ligands by in situ synthesis in at least two different feature regions produced in step (b) to produce said array;

wherein said method includes a single photocleavage step that occurs prior to said producing step (c).