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

• US 6,030,782 A
• Filed: 11/21/1997
• Issued: 02/29/2000
• Est. Priority Date: 03/05/1997
• Status: Expired due to Term

• Current Assignee: Beckman Coulter Incorporated (Danaher Corporation)
• Original Assignee: Orchid Bio Computer Incorporated
• Inventors: Anderson, Steve, Rogers, Yu-Hui
• Primary Examiner(s): Houtteman, Scott W.
• Application Number:
  US08/975,862
• Time in Patent Office: 830 Days
• Field of Search: 435/6, 536/24.3
• 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 hilgh specificity and high efficiency.

Claims

1. A method for attaching a modified nucleic acid molecule to a coated solid-phase via a disulfide bond, said modified nucleic acid molecule being modified such that a 3'"'"' carbon atom or a 5'"'"' carbon atom of a sugar moiety of a nucleotide of said nucleic acid molecule possesses a sulfhydryl group or a disulfide group, said method comprising coupling said modified nucleic acid molecule to said coated solid-phase, wherein where said modified nucleic acid molecule is a modified nucleic acid molecule having a sulfhydryl group, said coated solid-phase is coated with a disulfidesilane, and where said modified nucleic acid molecule is a modified nucleic acid molecule having a disulfide group said coated solid-phase is coated with a mercaptosilane and wherein said disulfide bond is formed between a sulfur atom of either said sulfhydryl group or said disulfide group and a sulfur atom of either said disulfidesilane or said mercaptosilane.

3. 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.

4. 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.

5. The method according to claim 1 wherein said nucleic acid molecule is an oligonucleotide.

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

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

8. The method according to claim 1 wherein the disulfide group of said disulfide modified nucleic acid molecule is reduced by means of a reducing agent.

9. The method according to claim 8 wherein the coupling step is by means of a disulfide formation reaction between the sulfhydryl group of said mercaptosilane coated solid-phase and the reduced disulfide modified nucleic acid molecule.

10. The method according to claim 8 wherein said reducing agent is selected from the group consisting of mercaptoethanol and dithiothreitol.

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

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

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

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

15. 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.

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

20. The method of claim 14 wherein said polystyrene support is a 96-well microtiter plate containing hydrophilic groups.

21. The method of claim 14 wherein said polystyrene support is a 96-pin array designed to fit into a 96-well microtiter plate.

22. The method of claim 12 wherein said glass is selected from a group consisting of a microscope slide, glasss plate, quart wafer or silicon wafer.

24. 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.

25. The method according to claim 16 wherein the array is assembled by means of a robotic liquid dispenser on a piezoelectric ink jet deposition.

26. The method according to claim 25 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.

27. The method according to claim 1 wherein said mercaptosilane has the structure ##STR4## 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.

28. The method according to claim 1 wherein said disulfidesilane has the structure ##STR5## wherein X is alkoxy, acyloxy or halogen group;

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

R is a non-hydrolizable group; and

L is a linker arm.

29. The method accoding to claim 27 or 28 wherein said linker arm is (CH₂)_n, (CH₂)_n -aromatic-(CH₂)_n or an aromatic group, and wherein n is at least 1.

30. The method according to claim 28, wherein said non-hydrolyzable group is selected from the group consisting of an alkyl, alkene, alkane, cycloalkyl, and aromatic group.

2. A method for attaching a nucleic acid molecule to a solid-phase via a disulfide bond, said nucleic acid molecule being modified such that a 3'"'"' carbon atom or a 5'"'"' carbon atom of a sugar moiety of a nucleotide of said nucleic acid molecule possesses a sulthydryl group or a disulfide group, said method comprising the steps of:

(A) coating the surface of the solid-phase with a mercaptosilane or a disulfidesilane, wherein said mercaptosilane comprises a sulfliydryl group and said disulfidesilane comprise a disulfide group; and

(B) (i) coupling a sulfhydryl modified nucleic acid molecule to the disulfide group of said disulfidesilane by means of a covalent disulfide bond;

or

(ii) coupling a disulfide modified nucleic acid molecule to the sulfhydryl groups of said mercaptosilane by means of a covalent disulfide bond;

wherein said disulfide bond is formed between a sulfur atom of either said sulfhydryl group or said disulfide group and a sulfur atom of either said disulfidesilane or said mercaptosilane.

17. The method of claim 2 wherein said immobilized nucleic acid is a polynucleotide and wherein said method additionally comprises the steps:

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

(D) detecting the presence of the captured analyte.

18. The method of claim 2 wherein said immobilized nucleic acid is a polynucleotide and wherein said method additionally comprises the steps of:

(C'"'"') (i) amplifying a specific region of a specific genome using a polymerase chain reaction, said region having a sequence complementary to said immobilized polynutcleotide;

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

(D'"'"') detecting the presence of the captured amplification product.

19. The method of claim 2 wherein said immobilized nucleic acid is a polynucleotide and wherein said method additionally comprises the steps:

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

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

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

23. The method according to claim 2 wherein said coating step is by means of an aerosol, a vaporization means or any other mechanical means.

31. A modified nucleic acid molecule coupled via a disulfide bond to a coated solid-phase, said modified nucleic acid molecule being modified such that a 3'"'"' carbon atom or a 5'"'"' carbon atom of a sugar moiety of a nucleotide of said nucleic acid molecule possesses a sulfhydryl group or a disulfide group, wherein where said modified nucleic acid molecule is a modified nucleic acid molecule having a sulfhydryl group, said coated solid-phase is coated with a disulfidesilane, and where said modified nucleic acid molecule is a modified nucleic acid molecule having a disulfide group said coated solid-phase is coated with a mercaptosilane, and wherein said disulfide bond is formed between a sulfur atom of either said sulfhydryl group or said disulfide group and a sulfur atom of either said disulfidesilane or said mercaptosilane.