Applications with and methods for producing selected interstrand cross-links in nucleic acids

• US 6,406,850 B2
• Filed: 12/03/1999
• Issued: 06/18/2002
• Est. Priority Date: 12/03/1998
• Status: Expired due to Term

• Current Assignee: Leica Biosystems Newcastle Ltd. (Danaher Corporation)
• Original Assignee: Kreatech Biotechnology BV (Danaher Corporation)
• Inventors: van Gijlswijk, R. P. M., Houthoff, Hendrik-Jan, Tanke, Hendrikus Johannes, Volkers, Herman, Raap, Anton Klaas, Heetebrij, Robert
• Primary Examiner(s): Fredman, Jeffrey
• Assistant Examiner(s): Chakrabarti, Arun K.
• Application Number:
  US09/454,404
• Publication Number:
  US 20020012915A1
• Time in Patent Office: 928 Days
• Field of Search: 435/6, 435/91.2, 536/24, 536/26.6, 536/24.32, 536/26.7, 536/26.8, 436/536
• US Class Current: 435/6.12
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2523/101 Crosslinking agents, e.g. psoralen
• CPC Class Codes: C12Q 2525/107 incorporating a peptide nucleic acid
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2563/137 Metal/ion, e.g. metal label
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels

Abstract

The Invention relates to a method for providing at least one selected sequence in a nucleic acid with interstrand cross-links. The method comprises hybridizing at least one selected single strand sequence with a complementary single strand nucleic acid or a functional analogue thereof. The selected sequence or complementary nucleic acid or both comprise a cross-linking agent. The invention also relates to a method, referred to as COBRA, for the labeling of a set of at least two bio-organic molecules with a set of at least two colors, comprising generating said set of colors through combining ratio labeling with binary labeling.

Claims

1. A method for preventing hybridization of a repetitive chromosomal nucleic acid sequence, while permitting hybridization of a unique chromosomal nucleic acid sequence, the method comprising the steps of:

providing a nucleic acid sequence that is complementary to the repetitive sequence, wherein the complementary sequence or the repetitive sequence or both comprise a cross-linking agent, the cross-linking agent being capable of cross-linking the complementary sequence to the repetitive sequence when the complementary sequence is hybridized to the repetitive sequence; and

hybridizing the repetitive nucleic acid sequence to its complementary sequence in the presence of the unique sequence, thereby cross-linking the complementary sequence to the repetitive sequence;

whereby the cross-linked repetitive sequence is prevented from further hybridizing, while the unique sequence is permitted to hybridize.

2. The method according to claim 1, wherein the complementary nucleic acid sequence is DNA, RNA or PNA.

3. The method according to claim 1, wherein the repetitive nucleic acid sequence is DNA.

4. The method according to claim 1, wherein at least two repetitive nucleic acid sequences are hybridized to complementary sequences comprising cross-linking agents.

5. The method according to claim 1, wherein the cross-linking agent comprises a transition metal.

6. The method according to claim 1, wherein the transition metal is platinum.

7. The method according to claim 1, wherein the cross-linking agent is (trans)-dichlorodiammineplatinum.

8. A method for preventing hybridization of a repetitive chromosomal nucleic acid sequence, while permitting hybridization of a unique chromosomal nucleic acid sequence, the method comprising the steps of:

providing a nucleic acid sequence that is complementary to the repetitive sequence and that comprises a cross-linking agent capable of cross-linking the complementary sequence to the repetitive sequence when the complementary sequence is hybridized to the repetitive sequence; and

hybridizing the repetitive nucleic acid sequence to its complementary sequence in the presence of the unique sequence, thereby cross-linking the complementary sequence to the repetitive sequence;

whereby the cross-linked repetitive sequence is prevented from further hybridizing, while the unique sequence is permitted to hybridize.

9. The method according to claim 8, wherein the complementary nucleic acid sequence is DNA, RNA, or PNA.

10. The method according to claim 8, wherein the repetitive nucleic acid sequence is DNA.

11. The method according to claim 8, wherein at least two repetitive nucleic acid sequences are hybridized to complementary sequences.

12. The method according to claim 8, wherein the cross-linking agent comprises a transition metal.

13. The method according to claim 8, wherein the transition metal is platinum.

14. The method according to claim 8, wherein the cross-linking agent is (trans)-dichlorodiammineplatinum.

15. A method for increasing the number of a single stranded unique chromosomal DNA sequence relative to the number of a single stranded repetitive chromosomal DNA sequence, the method comprising the steps of:

providing a nucleic acid sequence that is complementary to the repetitive DNA sequence, wherein the complementary sequence or the repetitive DNA sequence or both comprise a cross-linking agent, the cross-linking agent capable of cross-linking the complementary sequence to the repetitive DNA sequence when the complementary sequence is hybridized to the repetitive DNA sequence; and

hybridizing the repetitive DNA sequence to its complementary sequence in the presence of the unique DNA sequence, thereby cross-linking the complementary sequence to the repetitive DNA sequence;

whereby the cross-linked repetitive DNA sequence is prevented from further hybridizing and/or replicating, and the number of the single stranded unique DNA sequence relative to the number of the single stranded repetitive DNA sequence is increased.

16. The method according to claim 15, wherein the complementary sequence is DNA, RNA, or PNA.

17. The method according to claim 15, wherein at least two repetitive sequences are hybridized to complementary sequences comprising cross-linking agents.

18. The method according to claim 15, wherein the cross-linking agent comprises a transition metal.

19. The method according to claim 15, wherein the transition metal is platinum.

20. The method according to claim 15, wherein the cross-linking agent is (trans)-dichlorodiammineplatinum.

21. A method for selectively replicating a unique chromosomal nucleic acid sequence in the presence of a repetitive chromosomal nucleic acid sequence, the method comprising the steps of:

providing a nucleic acid sequence that is complementary to the repetitive sequence and that comprises a cross-linking agent capable of cross-linking the complementary sequence to the repetitive sequence when the complementary sequence is hybridized to the repetitive sequence;

hybridizing the repetitive nucleic acid sequence to its complementary sequence, thereby cross-linking the complementary sequence to the repetitive sequence; and

selectively replicating the unique sequence in the presence of the repetitive sequence cross-linked to its complementary sequence.

22. The method according to claim 21, wherein the complementary sequence is DNA, RNA, or PNA.

23. The method according to claim 21, wherein the repetitive sequence is DNA.

24. The method according to claim 21, wherein at least two repetitive sequences are hybridized to complementary sequences.

25. The method according to claim 21, wherein the cross-linking agent comprises a transition metal.

26. The method according to claim 21, wherein the transition metal is platinum.

27. The method according to claim 21, wherein the cross-linking agent is (trans)-dichlorodiammineplatinum.

28. A method for preparing probes suitable for detecting unique sequences of a target chromosome, the chromosome comprising unique DNA sequences and repetitive DNA sequences, the method comprising the steps of:

providing fragments of the chromosome;

providing nucleic acid sequences that are complementary to the repetitive DNA sequences, wherein the complementary sequences or the repetitive DNA sequences or both comprise a cross-linking agent, the cross-linking agent capable of cross-linking the complementary sequences to the repetitive DNA sequences when the complementary sequences are hybridized to the repetitive DNA sequences;

hybridizing the repetitive DNA sequences to the complementary sequences in the presence of the unique DNA sequences, thereby cross-linking the complementary sequences to the repetitive DNA sequences, whereby the cross-linked repetitive DNA sequences are prevented from further hybridizing; and

labeling the unique DNA sequences;

wherein the labeled, unique DNA sequences are suitable for detecting unique DNA sequences of the target chromosome.

29. The method according to claim 28, further comprising replicating the unique DNA sequences after the repetitive DNA sequences have been cross-linked to the complementary sequences.

30. The method according to claim 28, wherein the complem entary sequence is DNA, RNA, or PNA.

31. The method according to claim 28, wherein the cross-inking agent comprises a transition metal.

32. The method according to claim 31, wherein the transition metal is platinum.

33. The method according to claim 28, wherein the cross-linking agent is (trans)-dichlorodiammineplatinum.

34. The method according to claim 28, wherein the nucleic acid sequences complementary to the repetitive DNA sequences are fragments of a chromosome other than the target chromosome.

35. The method according to claim 28, wherein the nucleicacid sequences complementary to the repetitive DNA sequences comprise the cross-linking agent.

36. Probes suitable for detecting unique sequences of a target chromosome prepared in accordance with claim 28.

37. Probes according to claim 36, wherein the cross-linking agent comprises a transition metal.

38. Probes according to claim 37, wherein the transition metal is platinum.

39. Probes according to claim 38, wherein the cross-linking agent is (trans)-dichlorodiarnuineplatinum.