Replicable probe array

• US 6,514,768 B1
• Filed: 01/29/1999
• Issued: 02/04/2003
• Est. Priority Date: 01/29/1999
• Status: Expired due to Fees

• Current Assignee: Surmodics IVD, Inc. (Surmodics Incorporated)
• Original Assignee: Surmodics Incorporated
• Inventors: Swanson, Melvin J., Guire, Patrick E.
• Primary Examiner(s): Ponnaluri, Padmashri
• Application Number:
  US09/240,466
• Time in Patent Office: 1,467 Days
• Field of Search: 536/22.1, 536/24.3, 536/25.3, 536/25.32, 536/23.1, 435/6, 435/7.1, 435/7.92, 435/7.94, 435/7.95, 435/DIG.45, 436/518, 436/527, 436/807, 436/809
• US Class Current: 436/518
• 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 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel 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 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: Y10S 436/807 Apparatus included in process claim, e.g. physical support structures
• CPC Class Codes: Y10S 436/809 Multifield plates or multicontainer arrays
• CPC Class Codes: Y10S 977/849 with scanning probe

Abstract

A system for producing substantially identical specific binding ligand (e.g., nucleic acid) probe arrays, for instance, by preparing and replicating an original master array and/or by providing a reusable assay array that is capable of being regenerated. In one embodiment the system includes the preparation and use of a) a master array surface having address sequences immobilized in the form of a patterned, and optionally random, array, b) a multi-ligand conjugate having a binding domain complementary to an address sequence, a binding domain complementary to a target sequence, and a third ligand for use in forming (e.g., by binding or polymerization) the conjugates into or onto the surface of assay array, which can be used with or upon disassociation of the address and its complementary sequences.

Claims

1. An apparatus for producing an assay array, the apparatus comprising:

a) a master array comprising a support surface having a plurality of address ligands immobilized thereon in the form of a patterned array, wherein each address ligand comprises a nucleic acid sequence;

b) a plurality of multi-ligand conjugates, each multi-ligand conjugate comprising a core having attached thereto;

(i) at least one molecule of a first ligand binding domain, comprising a nucleic acid sequence selected to bind in a complementary manner with a specific address ligand of the master array but not with target nucleic acid sequences that may be present in a biological sample, (ii) at least one molecule of a second ligand binding domain, comprising a nucleic acid sequence selected to bind in a complementary manner with a specific target nucleic acid sequence that may be present in the biological sample, and (iii) at least one molecule of a third ligand, the third ligand comprising a binding ligand configured to bind the multi-ligand conjugate to a binding partner; and

c) an assay array support comprising a support surface and a plurality of binding partners selected to bind the third ligand for attachment of the multi-ligand conjugates to the assay array support to form the assay array.

2. An apparatus according to claim 1, wherein the nucleic acids of the master array and the multi-ligand conjugates each comprise a synthetic oligonucleotide.

3. An apparatus according to claim 1 further comprising a linking agent, the linking agent providing attachment of the address ligand with the master array support surface.

4. An apparatus according to claim 3 wherein the linking agent comprises a micro-bead.

5. An apparatus according to claim 1 wherein the first ligand binding domain, second ligand binding domain and third ligand are independently attached to the core of the multi-ligand conjugate.

6. An apparatus according to claim 1 wherein the binding ligand comprises biotin.

7. An apparatus according to claim 1 wherein the assay array support is coated with attachment sites for the third ligand.

8. An apparatus according to claim 7 wherein the third ligand comprises a binding ligand, and the attachment sites comprise molecules of a binding partner specific for the third ligand.

9. An apparatus of claim 1, wherein the third ligand is a biotin-poly(alkyleneoxide) amine derivative and the binding partner is avidin.

10. An apparatus of claim 9, wherein the third ligand is a biotin-poly(ethyleneoxide) amine derivative formed by reacting an N-oxysuccinimide ester of biotin with a poly(ethyleneoxide) diamine.

11. An apparatus of claim 9, wherein the avidin is attached to the assay support through a photoreactive siloxane reagent.

12. An apparatus of claim 11, wherein the photoreactive siloxane reagent is formed by reacting aminopropyldimethylmethoxy siloxane with the acid chloride of benzoylbenzoic acid.

13. An apparatus comprising a transitory structure formed in a process of producing an assay array, the transitory structure comprising:

a) a master array support;

b) a plurality of address ligands attached to the master array support, wherein each address ligand comprises a nucleic acid sequence;

c) an assay array support comprising a support surface and avidin attached to the support surface;

d) a plurality of multi-ligand conjugates attached to the assay array support, each multi-ligand conjugate comprising a core having attached thereto;

(i) a first ligand comprising a nucleic acid sequence bound in a complementary manner with a specific address ligand attached to the master array support but not with target nucleic acid sequences that may be present in a biological sample;

(ii) a second ligand comprising a nucleic acid sequence selected to bind in a complementary manner with a specific target nucleic acid sequence that may be present in a biological sample;

(iii) a third ligand comprising a biotin-poly(alkyleneoxide) amine derivative bound to the avidin attached to the assay support.

14. An apparatus of claim 13, wherein the third ligand is a biotin-poly(ethyleneoxide) amine derivative formed by reacting an N-oxysuccinimide ester of biotin with a poly(ethyleneoxide) diamine.

15. An apparatus of claim 13, wherein the avidin is attached to the support surface through a photoreactive siloxane reagent.