Covalent attachment of nucleic acid molecules onto solid-phases via disulfide bonds

• US 5,837,860 A
• Filed: 03/05/1997
• Issued: 11/17/1998
• Est. Priority Date: 03/05/1997
• Status: Expired due to Term

• Current Assignee: Beckman Coulter Incorporated (Danaher Corporation)
• Original Assignee: Molecular Tool, Inc. (Laboratory Corporation Of America Holdings)
• Inventors: Anderson, Stephen, Rogers, Yu-Hui
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/812,010
• Time in Patent Office: 622 Days
• Field of Search: 435/6, 435/810, 436/501, 536/23.1, 536/25.3, 935/77, 935/78
• US Class Current: 506/32
• 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 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• 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: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

Methods for the covalent, specific and reversible immobilization of nucleic acid molecules onto solid-phases by means of a reversible disulfide bond for nucleic acid molecule array preparation are described. These methods can be used to prepare reusable nucleic acid molecule arrays with high specificity and high efficiency.

Claims

1. A method for the covalent attachment of nucleic acid molecules to a solid-phase, which comprises the steps of:

A) coating a solid-phase surface with a mercaptosilane wherein said mercaptosilane comprises sulfhydryl groups; and

B) coupling a sulfhydryl or disulfide modified nucleic acid molecule to the sulfhydryl groups of said mercaptosilane by means of a covalent disulfide bond.

2. The method according to claim 1 wherein said nucleic acid molecule is modified at a 5'"'"' carbon of a sugar moiety of the nucleic acid molecule.

3. The method according to claim 1 wherein said nucleic acid molecule is modified at a 3'"'"' carbon of a sugar moiety of the nucleic acid molecule.

4. The method according to claim 1 wherein said nucleic acid molecules are oligonucleotides.

5. The method according to claim 1 wherein the coupling step is by means of a disulfide exchange reaction between said disulfide modified nucleic acid molecules and the sulfhydryl groups of said mercaptosilane coated surface.

6. The method according to claim 1 wherein the disulfide groups of said disulfide modified nucleic acid molecules are reduced by means of a reducing agent.

7. The method according to claim 6 wherein the coupling step is by means of a disulfide formation reaction between the sulfhydryl groups of said mercaptosilane coated solid-phase and the reduced disulfide modified nucleic acid molecules.

8. The method according to claim 6 wherein said reducing agent is mercaptoethanol.

9. The method according to claim 6 wherein said reducing agent is dithiothreitol.

10. The method according to claim 1 wherein said coupling reaction forms a disulfide bond wherein said disulfide bond is reversible.

11. The method according to claim 1 wherein said solid-phase is glass.

12. The method according to claim 1 wherein said solid-phase is plastic.

13. The method according to claim 12 wherein said plastic is polystyrene plastic.

14. The method according to claim 1 wherein said solid-phase is selected from the group consisting of a bead, a plate, a column, a pin and a dipstick.

15. The method according to claim 1 wherein the coupling reaction creates an array of more than one distinct immobilized nucleic acid molecule.

16. The method of claim 1 wherein said immobilized nucleic acid is a polynucleotide and wherein said method additionally comprises the steps of:

(A'"'"') capturing from a solution at least one strand of a specific polynucleotide analyte by hybridization to said immobilized polynucleotide; and

(B'"'"') detecting the presence of the captured analyte.

17. The method of claim 1 wherein said immobilized nucleic acid is a polynucleotide and wherein said method additionally comprises the steps of:

(A") amplifying a specific region of a specific genome using a polymerase chain reaction, said region having a sequence complementary to said immobilized polynucleotide; and

(B") capturing from solution at least one strand of said amplification product by hybridization to said immobilized polynucleotide; and

(C") detecting the presence of the captured amplification product.

18. The method of claim 1 wherein said immobilized nucleic acid is a polynucleotide and wherein said method additionally comprises the steps of:

(A'"'"'") incubating a sample of nucleic acid of a target organism, containing a single nucleotide polymorphism in the presence of said immobilized polynucleotide primer and at least one dideoxynucleotide derivative, under conditions sufficient to permit a polymerase mediated, template-dependent extension of said primer, said extension causing the incorporation of a single dideoxynucleotide to the 3'"'"'-terminus of said primer, said single dideoxynucleotide being complementary to the single nucleotide of the polymorphic site of said polymorphism;

(B'"'"'") permitting said template-dependent extension of said primer molecule, and said incorporation of said single dideoxynucleotide; and

(C'"'"'") determining the identity of the nucleotide incorporated into said polymorphic site, said identified nucleotide being complementary to said nucleotide of said polymorphic site.

19. The method of claim 13 wherein said polystyrene support is a 96-well microtiter plate containing hydrophilic groups.

20. The method of claim 13 wherein said polystyrene support is a 96-pin array designed to fit into a 96-well microtiter plate.

21. The method of claim 11 wherein said glass is selected from a group consisting of a microscope slide, glasss plate, quart wafer or silicon wafer.

22. The method according to claim 1 wherein said coating step is by means of an aerosol, a vaporization means or any other mechanical means.

23. The method according to claim 1 wherein the mercaptosilane comprises at least one hydrolizable group and a sulfydryl group wherein said sulfhydyl group is attached to the mercaptosilane via a linker arm.

24. The method according to claim 15 wherein the array is assembled by means of a robotic liquid dispenser on a piezoelectric ink jet deposition.

25. The method according to claim 24 wherein each nucleic acid molecule occupies a spot of at least 10 microns in diameter and each nucleic acid spot is spaced no closer, center to center, than the average spot diameter.

26. The method according to claim 1 wherein said mercaptosilane has the structure ##STR2## wherein X is alkoxy, acyloxy or halogen group;

Y and Z are alkoxy, acyloxy, halogen group or a non-hydrolizable inert group; and

L is a linker arm.

27. The method accoding to claim 26 wherein said linker arm is (CH₂)_n, (CH₂)_n -aromatic-(CH₂)_n or an aromatic group, and wherein n is at least 1.