Method for replicating an array of nucleic acid probes

• US 5,795,714 A
• Filed: 08/23/1993
• Issued: 08/18/1998
• Est. Priority Date: 11/06/1992
• Status: Expired due to Term

• Current Assignee: Trustees of Boston University
• Original Assignee: Trustees of Boston University
• Inventors: Przetakiewicz, Marek, Sano, Takeshi, Cantor, Charles R., Smith, Cassandra L.
• Primary Examiner(s): Houtteman, Scott W.
• Application Number:
  US08/110,691
• Time in Patent Office: 1,821 Days
• Field of Search: 435/6, 435/91.1, 536/24.3, 536/24.33, 536/25.3
• US Class Current: 435/6.15
• 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 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• 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: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/204 specific length of the oligonucleotides
• CPC Class Codes: C12Q 2565/515 characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C12Q 2565/537 : characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 80/00 : Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers

Abstract

The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'"'"'- and/or 3'"'"'-overhangs.

Claims

1. A method for replicating an array of single-stranded probes on a solid support comprising the steps of:

a) synthesizing an array of nucleic acids each comprising a non-variant sequence of length C at a 3'"'"'-terminus and a variable sequence of length R at a 5'"'"'-terminus;

b) fixing the array to a first solid support;

c) synthesizing a set of nucleic acids each comprising a sequence complementary to the non-variant sequence;

d) hybridizing the nucleic acids of the set to the array;

e) enzymatically extending the nucleic acids of the set using the variable sequences of the array as templates;

f) denaturing the set of extended nucleic acids; and

g) fixing the denatured nucleic acids of the set to a second solid support to create the replicated array of single-stranded probes.

2. The method of claim 1 wherein the nucleic acids of the set are conjugated with biotin and the second solid support comprises streptavidin.

3. The method of claim 1 wherein the nucleic acids of the array are between about 15-30 nucleotides in length and the nucleic acids of the set are between about 10-25 nucleotides in length.

4. The method of claim 1 wherein C is between about 7-20 nucleotides and R is between about 3-5 nucleotides.

5. The method of claim 1 wherein the solid supports are selected from the group consisting of plastics, ceramics, metals, resins, gels, membranes and chips.

6. The method of claim 1 wherein the nucleic acids of the set are enzymatically extended with a DNA polymerase and one or more deoxynucleotide triphosphates.

7. The method of claim 1 wherein denaturing is performed with heat, alkali, organic solvents, binding proteins, enzymes, salts or combinations thereof.

8. The method of claim 1 further comprising the step of hybridizing the replicated array with a second set of nucleic acids complementary to the non-variant sequence of the replicated array to create a double-stranded replicated array.

9. The method of claim 1 wherein the solid supports are two-dimensional or three-dimensional matrixes.

10. The method of claim 8 wherein a double-stranded portion of the partially double-stranded replicated array comprise a restriction endonuclease site.

11. The method of claim 8 wherein the partially double-stranded replicated array have 5'"'"'- or 3'"'"'-overhangs.

12. The method of claim 8 wherein the partially double-stranded replicated array comprises about 4^R different probes.

13. The method of claim 8 wherein the partially double-stranded replicated array comprise a detectable label.

14. The method of claim 13 wherein the detectable label is selected from the group consisting of radioisotopes, stable isotopes, enzymes, fluorescent and luminescent chemicals, chromatic chemicals, metals, electric charges, and spatial chemicals.

15. A method for replicating an array of single-stranded probes on a solid support comprising the steps of:

a) fixing a first array of nucleic acids each comprising a non-variant sequence of length C at a 3'"'"'-terminus and a variable sequence of length R at a 5'"'"'-terminus to a first solid support;

b) synthesizing a first set of nucleic acids each comprising a sequence complementary to the non-variant sequence;

c) hybridizing the nucleic acids of the first set to the first array;

d) enzymatically extending the nucleic acids of the first set using the variable sequences of the first array as templates;

e) denaturing the first set of extended nucleic acids;

f) fixing the denatured nucleic acids of the first set to a second solid support to create the replicated array of single-stranded probes; and

g) hybridizing the replicated array with a second set of nucleic acids complementary to the constant sequence of the replicated array to create a partially double-stranded replicated array.

16. The method of claim 15 wherein the nucleic acids of the first set are conjugated with biotin and the second solid support comprises streptavidin.

17. The method of claim 15 wherein the nucleic acids of the first array are between about 15-30 nucleotides in length and the nucleic acids of the first set are between about 10-25 nucleotides in length.

18. The method of claim 15 wherein C is between about 7-20 nucleotides and R is between about 3-5 nucleotides.

19. The method of claim 15 wherein the partially double-stranded replicated array comprises about 4^R different probes.

20. The method of claim 15 wherein the solid supports are selected from the group consisting of plastics, ceramics, metals, resins, gels, membranes and chips.

21. The method of claim 15 wherein the solid supports are two-dimensional or three-dimensional matrixes.

22. A method for replicating an array of single-stranded probes on a solid support comprising the steps of:

a) fixing an array of nucleic acids each comprising a non-variant sequence of length C at a 3'"'"'-terminus and a variable sequence of length R at a 5'"'"'-terminus to a first solid support;

b) synthesizing a set of nucleic acids each comprising a sequence complementary to the non-variant sequence;

c) hybridizing the nucleic acids of the set to the array;

d) enzymatically extending the nucleic acids of the set using the variable sequences of the array as templates;

e) denaturing the set of extended nucleic acids; and

f) fixing the denatured nucleic acids of the set to a second solid support with a streptavidin-biotin or an avidin-biotin bond to create the replicated array of single-stranded probes.

23. The method of claim 22 wherein the nucleic acids of the array are between about 15-30 nucleotides in length and the nucleic acids of the set are between about 10-25 nucleotides in length.

24. The method of claim 22 wherein C is between about 7-20 nucleotides and R is between about 3-5 nucleotides.

25. The method of claim 22 wherein the solid supports are selected from the group consisting of plastics, ceramics, metals, resins, gels, membranes and chips.

26. The method of claim 22 wherein the nucleic acids of the set are enzymatically extended with a DNA polymerase and one or more deoxynucleotide triphosphates.

27. The method of claim 22 wherein denaturing is performed with heat, alkali, organic solvents, binding proteins, enzymes, salts or combinations thereof.

28. The method of claim 22 wherein the solid supports are two-dimensional or three-dimensional matrixes.

29. The method of claim 22 wherein the replicated array comprises about 4^R different probes.