Detection of target nucleic acid molecules using thermostable 5' nuclease

• US 5,837,450 A
• Filed: 06/06/1995
• Issued: 11/17/1998
• Est. Priority Date: 12/07/1992
• Status: Expired due to Term

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Third Wave Technologies Incorporated (Hologic Incorporated)
• Inventors: Dahlberg, James E., Lyamichev, Victor I., Brow, Mary Ann D.
• Primary Examiner(s): Zitomer, Stephanie W.
• Assistant Examiner(s): REES, DIANE
• Application Number:
  US08/471,066
• Time in Patent Office: 1,260 Days
• Field of Search: 536/24.3, 536/24.33, 536/24.32, 536/350, 435/6, 435/5, 435/91.2, 435/199, 435/194
• US Class Current: 435/6.18
• 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: C07K 14/4746 p53
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 9/1252 DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase
• CPC Class Codes: C12N 9/14 Hydrolases (3)
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6823 Release of bound markers
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/705 for herpetoviridae, e.g. herpes simplex, varicella zoster
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2527/101 Temperature
• CPC Class Codes: C12Q 2537/149 Sequential reactions
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

A means for cleaving a nucleic acid cleavage structure in a site-specific manner is disclosed. A cleaving enzyme having 5'"'"' nuclease activity without interfering nucleic acid synthetic ability is employed as the basis of a novel method of detection of specific nucleic acid sequences.

Claims

1. A method of detecting the presence of a nucleic acid molecule comprising:

a) providing;

i) a thermostable 5'"'"' nuclease derived from a thermostable polymerase modified to have reduced synthetic activity, wherein said 5'"'"' nuclease is capable of cleaving a linear nucleic acid duplex structure so as to create substantially a single, single-stranded nucleic acid cleavage product,

ii) a target nucleic acid having a first and a second portion,

iii) a first oligonucleotide complementary to said first portion of said target nucleic acid, and

iv) a second oligonucleotide having a 5'"'"' and a 3'"'"' end, said second oligonucleotide comprising a 5'"'"' region and a 3'"'"' region, wherein said 3'"'"' region is complementary to said second portion of said target nucleic acid and said 5'"'"' region is non-complementary to said target nucleic acid and provides a single-stranded arm;

b) mixing said 5'"'"' nuclease, said target nucleic acid, said first oligonucleotide and said second oligonucleotide under conditions wherein said first oligonucleotide and said 3'"'"' region of said second oligonucleotide are annealed to said target nucleic acid sequence so as to create a first cleavage structure and cleavage of said first cleavage structure results in the liberating of said single-stranded arm of said second oligonucleotide to generate a first signal oligonucleotide and a cleaved second oligonucleotide; and

c) detecting the presence of said first signal oligonucleotide.

2. The method of claim 1 further comprising:

a) providing;

i) a plurality of third oligonucleotides, each having a 5'"'"' and a 3'"'"' end, each of said third oligonucleotides comprising a 5'"'"' region and a 3'"'"' region, wherein said 3'"'"' region is complementary to said 5'"'"' region of said second oligonucleotide; and

ii) a plurality of fourth oligonucleotides, each having a 5'"'"' and a 3'"'"' end, each of said fourth oligonucleotides comprising a 5'"'"' region and a 3'"'"' region, wherein said 3'"'"' region is complementary to said 5'"'"' region of said third oligonucleotide;

b) reacting said first signal oligonucleotide with one of said plurality of third oligonucleotides under conditions wherein said first signal oligonucleotide anneals to the 3'"'"' region of said third oligonucleotide so as to create a second cleavage structure and cleavage of said second cleavage structure results in the liberating of said 5'"'"' region of said third oligonucleotide to generate a second signal oligonucleotide and a cleaved third oligonucleotide, said second signal oligonucleotide complementary to said 3'"'"' region of said fourth oligonucleotide;

c) reacting said second signal oligonucleotide with one of said plurality of fourth oligonucleotides under conditions wherein said second signal oligonucleotide anneals to the 3'"'"' region of said fourth oligonucleotide so as to create a third cleavage structure and cleavage of said third cleavage structure results in the liberating of said 5'"'"' region of said fourth oligonucleotide to generate a second molecule of said first signal oligonucleotide and a cleaved fourth oligonucleotide; and

d) detecting the presence of said first and second signal oligonucleotides.

3. The method of claim 2, wherein said second molecule of said first signal oligonucleotide anneals to a second molecule of said plurality of third oligonucleotides under conditions such that a second molecule of said second signal oligonucleotide is generated.

4. The method of claim 1, wherein said second oligonucleotide is attached via its 3'"'"' end to a first solid support.

5. The method of claim 2, wherein said plurality of third oligonucleotides are attached via their 3'"'"' ends to a second solid support.

6. The method of claim 2, wherein said plurality of fourth oligonucleotides are attached via their 3'"'"' ends to a third solid support.

7. The method of claim 1, wherein said first and second oligonucleotides are present in excess relative to said target nucleic acid.

8. The method of claim 1, wherein a portion of the amino acid sequence of said 5'"'"' nuclease is homologous to a portion of the amino acid sequence of a thermostable DNA polymerase derived from a eubacterial thermophile of the genus Thermus.

9. The method of claim 8, wherein said thermophile is selected from the group consisting of Thermus aquaticus, Thermus flavus and Thermus thermophilus.

10. The method of claim 9, wherein said nuclease is encoded by a DNA sequence selected from the group consisting of SEQ ID NOS:

9, 10, 12, 30 and 31.

11. A method of detecting the presence of a nucleic acid molecule comprising:

a) providing;

i) a thermostable 5'"'"' nuclease derived from a thermostable polymerase modified to have reduced synthetic activity,

ii) a target nucleic acid,

iii) an oligonucleotide complementary to a portion of said target nucleic acid, said oligonucleotide being present in excess relative to said target nucleic acid;

b) mixing said thermostable 5'"'"' nuclease, said target nucleic acid and said oligonucleotide under conditions wherein a first molecule of said oligonucleotide anneals to said target nucleic acid so as to create a duplex nucleic acid substrate thereby permitting the digestion of said oligonucleotide and the release of said digested oligonucleotide from said target nucleic acid structure.

12. The method of claim 11 further comprising annealing a second molecule of said oligonucleotide to said target nucleic acid structure followed by digestion of the second molecule thereby releasing said digested second molecule of said oligonucleotide and thereby permitting subsequent molecules of oligonucleotides to anneal to said target followed by nucleolytic digestion so as to permit a cycle of annealing, digestion and release of digested oligonucleotides.

13. The method of claim 12 further comprising detecting the presence of said digested oligonucleotides.

14. The method of claim 11, wherein said oligonucleotide comprises a label.

15. The method of claim 14, wherein said label comprises a 5'"'"' end label.

16. The method of claim 15, where in said end label comprises a radioactive label.

17. The method of claim 14, wherein said labelled oligonucleotide comprises two fluorescent labels located in close proximity on said oligonucleotide such that prior to nucleolytic digestion of said oligonucleotide the emission of said fluorescent labels is quenched and wherein nucleolytic digestion of said fluorescently labelled oligonucleotide results in a detectable emission from said fluorescent labels.

18. The method of claim 11, wherein a portion of the amino acid sequence of said thermostable 5'"'"' to 3'"'"' exonuclease is homologous to a portion of the amino acid sequence of a thermostable DNA polymerase derived from a eubacterial thermophile of the genus Thermus.

19. The method of claim 18, wherein said thermophile is selected from the group consisting of Thermus aquaticus, Thermus flavus and Thermus thermophilus.

20. The method of claim 19, wherein said exonuclease is encoded by a DNA sequence selected from the group consisting of SEQ ID NOS:

9-12, 21, 30 and 31.