Method for fragmenting and labeling DNA involving abasic sites and phosphate labeling

• US 7,060,441 B2
• Filed: 05/03/2002
• Issued: 06/13/2006
• Est. Priority Date: 05/04/2001
• Status: Expired due to Fees

• Current Assignee: Bio Merieux, Centre National De La Recherche Scientifique, Universite Joseph Fourier
• Original Assignee: Centre National De La Recherche Scientifique, Biomerieux B.V. (Compagnie Merieux Alliance SAS), Universite Joseph Fourier
• Inventors: Tora, Christelle, Sothier, Isabelle, Laayoun, Ali, Kotera, Mitsuharu, Trevisiol, Emmanuelle, Lhomme, Jean, Bourget, Cecile
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US10/137,460
• Publication Number:
  US 20030143555A1
• Time in Patent Office: 1,502 Days
• Field of Search: 435/6, 435/91.2, 436/94
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/119 incorporating abasic sites
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

A single- or double-stranded deoxyribonucleic acid (DNA) is fragmented and labeled by chemically fragmenting the DNA by creating at least one abasic site on the DNA, and attaching a marker to at least one of the fragments by means of a labeling reagent, the reagent covalently and predominantly coupling to at least one phosphate of the fragment. This method can be applied in the field of diagnosis.

Claims

1. A method for fragmenting and labeling a single- or double-stranded deoxyribonucleic acid (DNA) comprising the following steps:

fragmenting the DNA by creating at least one abasic site on said DNA,

attaching a marker to at least one of the fragments by means of a labeling reagent, said reagent covalently and predominantly coupling to at least one phosphate of said fragment.

2. The method as claimed by claim 1, wherein the fragmentation and labeling are carried out in two steps.

3. The method as claimed in claim 1, wherein the fragmentation and labeling are carried out in one step.

4. The method as claimed in claim 1, wherein the abasic site is generated by the action of an acidic aqueous medium.

5. The method as claimed in claim 4, wherein the pH of the acidic medium is less than 5.

6. The method as claimed in claim 5, wherein the acidic aqueous medium is a sodium formate buffer at a pH of about 3.

7. The method as claimed in claim 1, wherein the DNA contains at least one modified base capable of generating an abasic site.

8. The method as claimed in claim 7, wherein the modified base capable of generating an abasic site is chosen from 8-bromopurine derivatives.

9. The method as claimed in claim 1, wherein the abasic site is generated by an alkylating agent or an oxidizing agent.

10. The method for labeling and fragmenting as claimed in claim 1, wherein the labeling reagent comprises, as reactive functional group, a motif chosen from the following compounds:

diazomethyl;

alkyl halide;

nitrosourea;

spirocyclopropane;

aziridine;

epoxide; and

trifluoromethanesulfonates.

11. The method as claimed in claim 10, wherein said labeling reagent is 5-(bromomethyl)fluorescein.

12. The method as claimed in claim 10, wherein the labeling reagent is chosen from the compounds of formula (I):

13. The method as claimed in claim 12, wherein Z is:

14. The method as claimed in claim 12, wherein the labeling reagent is chosen from the compounds of formula (2):

15. The method as claimed in claim 14, wherein the labeling reagent has the formula (3):

16. The method as claimed in claim 14, wherein R² is a fluorescent compound or a hapten.

17. The method as claimed in claim 10, wherein said labeling reagent is soluble in a water-miscible solvent.

18. A method for detecting a single- or double-stranded target deoxyribonucleic acid (DNA) comprising the following steps:

fragmenting and labeling said DNAs according to a method as claimed in claim 1,

under hybridization conditions, contacting the labeled fragments to at least one nucleic acid probe which is sufficiently specific for the target nucleic acid, and

detecting any hybrid formed using the marker.

19. The method for detecting a double-stranded target deoxyribonucleic acid (DNA) as claimed in claim 18, comprising, in addition, a denaturation step after the fragmentation and the labeling.

20. The method as claimed in claim 19, wherein the fragmentation, labeling and denaturation are carried out in a single step.

21. A method for detecting a target nucleic acid comprising the following steps:

enzymatically amplifying the target nucleic acid in order to generate a multitude of double-stranded DNA amplicons,

fragmenting and labeling said DNA amplicons according to a method as claimed in claim 1,

under hybridization conditions, contacting the labeled fragments to at least one nucleic acid probe which is sufficiently specific for the target nucleic acid, and

detecting any hybrid formed using the marker.

22. The method as claimed in claim 21, comprising, in addition, a denaturation step after the fragmentation and labeling step.

23. A method as claimed in claim 22, wherein the fragmentation, labeling and denaturation are carried out in a single step.

24. A method for detecting a polymorphism distributed in predetermined or nonpredetermined positions of a target nucleic acid by the presence of a plurality of deletions and/or insertions and/or mutations in the sequence of said target nucleic acid relative to a so-called reference sequence, comprising the following steps:

having a target DNA containing the entire polymorphism to be studied, said DNA being optionally generated by an enzymatic amplification technique,

fragmenting and labeling said DNA by a method as claimed in claim 1,

under hybridization conditions, contacting said fragments to a plurality of nucleic acid probes termed capture probes, the plurality of capture probes being attached to a solid support and the plurality of capture probes covering in its entirety at least the polymorphism to be studied, and

detecting any hybrids formed between the labeled fragments and at least part of the nucleic acid probes using the marker and deducing therefrom the polymorphism of the target DNA.

25. The method as claimed in claim 24, comprising, in addition, a denaturation step after the fragmentation and labeling step.

26. The method as claimed in claim 25, wherein the fragmentation, labelings and denaturation are carried out in a single step.

27. The method as claimed in claim 24, wherein the solid support contains at least ten (10) nucleic acid probes of different sequences.

28. The method as claimed in claim 4, wherein the pH of the acidic medium is less than 4.

29. The method as claimed in claim 24, wherein the solid support contains at least four hundred (400) nucleic acid probes of different sequences.

30. The method as claimed in claim 24, wherein the solid support contains at least one thousand (1000) nucleic acid probes of different sequences.

31. A method for detecting a target nucleic acid, comprising:

fragmenting and labeling a deoxyribonucleic acid (DNA) by a method according to claim 1, wherein the fragment that is attached to the marker is sufficiently specific for the target nucleic acid,

under hybridization conditions, contacting the fragment that is attached to the marker with potential target nucleic acid, and

detecting any hybrid formed using the marker.