Method for genotyping and quantifying Hepatitis B Virus

• US 20040191776A1
• Filed: 03/21/2003
• Published: 09/30/2004
• Est. Priority Date: 03/21/2003
• Status: Abandoned Application

• Current Assignee: Ding-Shinn Chen, Pei-Jer Chen, Shiou-Hwei Yeh, Tsong-Chin Lin
• Original Assignee: Ding-Shinn Chen, Pei-Jer Chen, Shiou-Hwei Yeh, Tsong-Chin Lin
• Inventors: Chen, Ding-Shinn, Chen, Pei-Jer, Yeh, Shiou-Hwei, Lin, Tsong-Chin
• Application Number:
  US10/395,013
• Publication Number:
  US 20040191776A1
• Time in Patent Office: Days
• US Class Current: 435/6.14
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/706 for hepatitis

Abstract

A method for simultaneously genotyping and quantifying Hepatitis B Virus. Also disclosed are (1) a pair of primers containing, respectively, the sequences of SEQ ID NOs: 13 and 14, SEQ ID NOs: 17 and 14, or SEQ ID NOs: 20 and 6, each primer being 8-50 nucleotides in length; (2) a pair of probes, containing, respectively, the sequences of SEQ ID NOs: 18 and 19, SEQ ID NOs: 15 and 16, or SEQ ID NOs: 21 and 22, each probe being 9-50 nucleotides in length; (3) a nucleic acid obtained from amplification of a Hepatitis B Virus nucleic acid template, containing the sequence selected from SEQ ID NOs: 15, 19, or 22, or its complementary sequence, the nucleic acid being 100-1,000 nucleotides in length.

Claims

1. A pair of primers for amplifying a target nucleic acid of Hepatitis B Virus, comprising, respectively, the sequences of SEQ ID NOs:

13 and 14, SEQ ID NOs;

17 and 14, or SEQ ID NOs;

20 and 6, wherein each primer is 8-50 nucleotides in length.

2. The pair of primers of claim 1, wherein each primer is 15-40 nucleotides in length.

3. The pair of primers of claim 2, wherein each primer is 18-30 nucleotides in length.

4. The pair of primers of claim 1, the pair of primers comprise, respectively, the sequences of SEQ ID NOs:

9 and 10, SEQ ID NOs;

1 and 2, or SEQ ID NOs;

5 and 6.

12. A kit for simultaneously identifying a single nucleotide polymorphism in a target nucleic acid of Hepatitis B Virus and quantifying the target nucleic acid, comprising a pair of primes of claim 1 and a pair of probes of claim 2.

13. The kit of claim 12, further comprising a second pair of primers of claim 1.

14. The kit of claim 13, further comprising a third pair of primers of claim 1.

15. The kit of claim 12, further comprising a second pair of probes of claim 2.

16. The kit of claim 15, further comprising a third pair of probes of claim 2.

5. A pair of probes for identifying a single nucleotide polymorphism in a target nucleic acid of Hepatitis B Virus, comprising, respectively, the sequences of SEQ ID NOs:

18 and 19, SEQ ID NOs;

15 and 16, or SEQ ID NOs;

21 and 22, wherein each probe is 9-50 nucleotides in length.

6. The pair of probes of claim 5, wherein each probe is 15-40 nucleotides in length.

7. The pair of probes of claim 6, wherein each probe is 18-30 nucleotides in length.

8. The pair of probes of claim 5, wherein the pair of probes comprise, respectively, the sequences of SEQ ID NOs:

3 and 4, SEQ ID NOs;

11 and 12, or SEQ ID NOs;

7 and 8.

9. A nucleic acid obtained from amplification of a Hepatitis B Virus nucleic acid template, comprising a sequence selected from the group consisting of SEQ ID NOs:

15, 19, and 22, or a sequence complementary thereto, wherein the nucleic acid is 100-1,000 nucleotides in length.

10. The nucleic acid of claim 9, wherein the nucleic acid is 200-700 nucleotides in length.

11. The nucleic acid of claim 10, wherein the nucleic acid is 300-500 nucleotides in length.

17. A method for simultaneously identifying a single nucleotide polymorphism (SNP) in a target nucleic acid from a Hepatitis B Virus (HBV) and quantifying the target nucleic acid, comprising:

providing a first probe that is identical or complementary to a first sequence of the target nucleic acid that covers a base corresponding to the SNP; and

a second probe that is identical or complementary to a second sequence of the target nucleic acid that does not cover the base corresponding to the SNP;

amplifying, by a polymerase chain reaction with a pair of primers, the target nucleic acid to form a double-stranded nucleic acid product containing the first sequence and the second sequence;

hybridizing to the nucleic acid product in a solution to form a first duplex with the first probe that is covalently bounded to a first fluorophore and to form a second duplex with the second probe that is covalently bounded to a second fluorophore, one of the first and second fluorophores being a donor fluorophore and the other being an acceptor fluorophore, so that, when the first probe and the second probe are hybridized to the nucleic acid product, the donor fluorophore and the acceptor fluorophore are in close proximity to allow fluorescence resonance energy transfer therebetween;

heating the solution to an elevated temperature that is above the melting temperature of the duplex formed by the first probe and its complementary sequence;

identifying the SNP by monitoring fluorescent emission change of the acceptor fluorophore upon irradiation of the donor fluorophore with an excitation light, the change being a function of the elevated temperature; and

quantifying the target nucleic acid by monitoring the fluorescent emission of the acceptor fluorophore.

18. The method of claim 17, wherein the quantifying step is conducted by comparing the intensity of the fluorescent emission to a predetermined value.

19. The method of claim 18, wherein the first and second probes hybridize to the same strand of the nucleic acid product.

20. The method of claim 17, wherein the first and second probes hybridize to the same strand of the nucleic acid product.

21. The method of claim 20, wherein the identifying step is conducted by

generating a first derivative melting curve of the first duplex;

determining a temperature value corresponding to a melting peak on the curve; and

comparing the temperature value with the melting temperature of the duplex formed by the first probe and its complementary sequence,

whereby a single nucleotide polymorphism in the target nucleic acid is present when the temperature value is lower than the melting temperature and is absent when the temperature value is the same as the melting temperature.

22. The method of claim 17, wherein the identifying step is conducted by

generating a first derivative melting curve of the first duplex;

determining a temperature value corresponding to a melting peak on the curve; and

comparing the temperature value with the melting temperature of the duplex formed by the first probe and its complementary sequence,

whereby a single nucleotide polymorphism in the target nucleic acid is present when the temperature value is lower than the melting temperature and is absent when the temperature value is the same as the melting temperature.

23. The method of claim 22, wherein the quantifying step is conducted by comparing the intensity of the fluorescent emission to a predetermined value.

24. The method of claim 23, wherein the first and second probes hybridize to the same strand of the nucleic acid product.

25. The method of claim 17, wherein the pair of probes comprise, respectively, the sequences of SEQ ID NOs:

15 and 16, SEQ ID NOs;

18 and 19, or SEQ ID NOs;

21 and 22.

26. The method of claim 25, wherein the corresponding pair of primers comprise, respectively, the sequences of SEQ ID NOs:

13 and 14, SEQ ID NOs;

17 and 14, or SEQ ID NOs;

20 and 6.

27. The method of claim 26, wherein the identifying step is conducted by

generating a first derivative melting curve of the first duplex;

determining a temperature value corresponding to a melting peak on the curve; and

comparing the temperature value with the melting temperature of the duplex formed by the first probe and its complementary sequence,

whereby a single nucleotide polymorphism in the target nucleic acid is present when the temperature value is lower than the melting temperature and is absent when the temperature value is the same as the melting temperature.

28. The method of claim 27, wherein the quantifying step is conducted by comparing the intensity of the fluorescent emission to a predetermined value.

29. The method of claim 28, wherein the first and second probes hybridize to the same strand of the nucleic acid product.