Method for analyzing a nucleotide sequence

• US 5,728,526 A
• Filed: 06/07/1995
• Issued: 03/17/1998
• Est. Priority Date: 06/07/1995
• Status: Expired due to Fees

• Current Assignee: Douglas C. Barclay
• Original Assignee: Oncor, Inc
• Inventors: Nazarenko, Irina, George, Albert L. Jr., Bhatnagar, Satish K.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US08/472,239
• Time in Patent Office: 1,014 Days
• Field of Search: 435/6, 435/91.2, 435/91.1, 435/24.3, 435/24.31, 536/24.32, 536/24.33
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 2561/125 Ligase Detection Reaction [LDR]
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

A method for analyzing a target nucleotide sequence which exists in a first state or a different second state which makes the method particularly useful for determining point mutations. The method uses a first polynucleotide which is immobilized on a solid support and which is at least partially complementary to a first segment of the target nucleotide sequence. By means of a series of steps, a product of the first polynucleotide and a further polynucleotide that contains a detectable label can be obtained. When the state to be analyzed occurs in a rare population, amplification can be conducted so that substantially only amplification of the target nucleotide sequence in one of the states is attained. The method can be used to analyze multiple target sequences simultaneously. A kit which can be used in the method is also set forth.

Claims

1. A method for analyzing a target nucleotide sequence having a first segment, a second segment and a third segment therebetween which third segment is formed of at least one nucleotide but which is formed of less than four different nucleotides wherein the third segment has a nucleotide or nucleotide sequence in a first state or a different second state, said method comprising:

a) providing a first polynucleotide which is immobilized on a solid support and which is at least partially complementary to the first segment of the target nucleotide sequence;

b) hybridizing the first polynucleotide to the first segment of the target nucleotide sequence under conditions suitable for hybridization;

c) providing a second polynucleotide which is at least partially complementary to the second segment of the target nucleotide sequence;

d) hybridizing the second polynucleotide to the second segment of the target nucleotide sequence under conditions suitable for hybridization wherein a gap of at least one nucleotide is present between one end of the first polynucleotide and one end of the second polynucleotide;

e) providing at least one nucleotide selected such that all the nucleotides which are complementary to the third segment are provided for only one of the first state or the second state and less than all the nucleotides complementary to the third segment are provided for the other state, the nucleotide or nucleotides being provided under conditions whereby the nucleotide or nucleotides form an extended portion of one of the first or second polynucleotide that is complementary to the nucleotides(s) of the third segment of the target nucleic acid sequence in one of the states;

f) linking the polynucleotide with the extended portion to the other polynucleotide under conditions whereby a fused product is formed comprised of the first polynucleotide, the second polynucleotide and the extended portion therebetween;

g) separating the fused product from the target nucleotide sequence and any non-linked second polynucleotide by treatment with exonuclease to digest target nucleotide sequence and non-linked second polynucleotide, and washing;

h) amplifying at least a portion of the fused product wherein the portion contains the extended portion under conditions suitable to form an amplified product containing the first polynucleotide and a detectable label, the amplifying being conducted to obtain a sufficient quantity of amplified product to detect the detectable label; and

i) detecting the presence of the label of the amplified product.

2. The method of claim 1 wherein the support is selected from the group consisting of glass, cellulosic material and polymeric material.

3. The method of claim 2 wherein the cellulosic material is nitrocellulose.

4. The method of claim 2 wherein the polymeric material is selected from the group consisting of polystyrene, polypropylene, polyethylene, dextran, polyamide, polyacrylamide, and agarose.

5. The method of claim 1 wherein the target nucleotide sequence is present in a DNA strand which has been denatured before being hybridized to the first polynucleotide.

6. The method of claim 1 wherein the first and second polynucleotides are provided simultaneously.

7. The method of claim 1 wherein the third segment consists of a single nucleotide.

8. The method of claim 1 wherein steps e) and f) are conducted simultaneously in the presence of polymerase and ligase.

9. The method of claim 1 wherein step g) is conducted by denaturing the fused product from the target nucleotide sequence and washing.

10. The method of claim 1 wherein the amplification of step h) is conducted by:

i) hybridizing a third polynucleotide to the fused product;

ii) extending the third polynucleotide so that the extended third polynucleotide is complementary to the extended portion of the fused product and at least a portion of the first polynucleotide and the second polynucleotide of the fused product;

iii) separating the extended third polynucleotide from the fused product;

iv) providing a fourth polynucleotide which contains a detectable label and is at least partially complementary to the extended portion of the third polynucleotide;

v) linking the fourth polynucleotide with the first polynucleotide to form the amplified product; and

vi) repeating steps i) through v) to obtain a sufficient quantity of the amplified product to detect the detectable label.

11. The method of claim 10 wherein the third poly nucleotide is complementary to at least the extended portion of the fused product.

12. The method of claim 10 wherein the fourth polynucleotide is linked with the first polynucleotide in the presence of polymerase, ligase and four different nucleotides.

13. The method of claim 1 wherein the detectable label is selected from the group consisting of biotin, digoxigenin, phenyloxazolone, and fluorescing material.

14. The method of claim 1 wherein the first polynucleotide is immobilized on the solid support so that the 5'"'"' end is adjacent the gap.

15. The method of claim 1 wherein the first polynucleotide is immobilized on the solid support so that the 3'"'"' end is adjacent the gap.

16. The method of claim 1 wherein the target nucleotide sequence is DNA.

17. The method of claim 1 wherein the first polynucleotide is immobilized on the solid support so that the 3'"'"' end is adjacent the gap and amplification of step h) is conducted by:

i) hybridizing a third polynucleotide to the fused product;

ii) extending the third polynucleotide so that the extended third polynucleotide is complementary to the extended portion of the fused product and at least a portion of the first polynucleotide and the second polynucleotide of the fused product;

iii) separating the extended third polynucleotide from the fused product;

iv) providing polymerase and nucleotides, at least one of the nucleotides containing a detectable label, and extending the first polynucleotide to be complementary to the extended third polynucleotide so as to form the amplified product;

v) repeating steps i) through iv) to obtain a sufficient quantity of the amplified product to detect the detectable label.

18. The method of claim 1 wherein subsequent to the amplification step h), the solid support is treated to remove materials not immobilized thereon.

19. The method of claim 1 wherein the solid support is comprised of polypropylene.

20. The method of claim 1 wherein the first and second polynucleotides are hybridized to the first and second segments simultaneously.

21. The method of claim 1 wherein the second polynucleotide has a 3'"'"' end adjacent the gap and has a portion at the 5'"'"' end which is not complementary to any portion of the target nucleotide sequence and wherein the amplification also amplifies the non-complementary portion of the second polynucleotide.

22. The method of claim 21 wherein the amplification of step h) is conducted by:

i) hybridizing a third polynucleotide to the fused product;

ii) extending the third polynucleotide so that the extended third polynucleotide is complementary to the extended portion of the fused product and at least a portion of the first polynucleotide and the second polynucleotide of the fused product including the non-complementary portion of the second polynucleotide;

iii) separating the extended third polynucleotide from the fused product;

iv) providing a fourth polynucleotide which is at least partially complementary to the extended portion of the third polynucleotide which is complementary to the non-complementary portion of the second polynucleotide;

v) extending the fourth polynucleotide to the first polynucleotide;

vi) linking the fourth polynucleotide with the first polynucleotide to form the amplified product containing the detectable label; and

vii) repeating steps i) through vi) to obtain a sufficient quantity of the amplified product to detect the detectable label.

23. The method of claim 22 wherein the fourth polynucleotide contains the detectable label.

24. The method of claim 23 wherein the polynucleotide having a 3'"'"' end adjacent the gap is modified so that the 3'"'"' terminal nucleotide is a dideoxynucleotide.

25. The method of claim 1 wherein multiple target nucleotide sequences are analyzed simultaneously.

26. The method of claim 25 wherein a first polynucleotide immobilized on a solid support is provided for each target sequence analyzed and the solid support is divided into a grid and wherein step (e) is conducted by providing a different single nucleotide in each section of the grid.

27. A method for analyzing a target nucleotide sequence having a first segment, a second segment and a third segment therebetween which third segment is formed of at least one nucleotide but which is formed of less than four different nucleotides wherein the third segment has a nucleotide or nucleotide sequence in a first state or a different second state, said method comprising:

a) providing a first polynucleotide which is immobilized on a solid support and which is at least partially complementary to the first segment of the target nucleotide sequence;

b) providing a second polynucleotide which is at least partially complementary to the second segment of the target nucleotide sequence;

c) hybridizing the second polynucleotide to the second segment of the target nucleotide sequence under conditions suitable for hybridization;

d) providing at least one nucleotide selected such that all the nucleotides which are complementary to the third segment are provided for only one of the first state or the second state and less than all the nucleotides complementary to the third segment are provided for the other state, the nucleotide or nucleotides being provided under conditions whereby the nucleotide or nucleotides form an extended portion of the second polynucleotide that is complementary to the nucleotides(s) of the third segment of the target nucleic acid sequence in one of the states;

e) hybridizing the first polynucleotide to the first segment of the target nucleotide sequence under conditions suitable for hybridization;

f) linking the polynucleotide with the extended portion to the other polynucleotide under conditions whereby a fused product is formed comprised of the first polynucleotide, the second polynucleotide and the extended portion therebetween;

g) separating the fused product from the target nucleotide sequence and any non-linked second polynucleotide by treatment with exonuclease to digest target nucleotide sequence and non-linked second polynucleotide, and washing;

h) amplifying at least a portion of the fused product wherein the portion contains the extended portion under conditions suitable to form an amplified product containing the first polynucleotide and a detectable label, the amplifying being conducted to obtain a sufficient quantity of amplified product to detect the detectable label; and

i) detecting the presence of the label of the amplified product.

28. The method of claim 27 wherein subsequent to the amplification step h), the solid support is treated to remove materials not immobilized thereon.

29. The method of claim 27 wherein the solid support is comprised of polypropylene.

30. The method of claim 27 wherein the amplified product comprises the first polynucleotide and a labeled polynucleotide.

31. The method of claim 27 wherein the second polynucleotide has a 3'"'"' end adjacent the gap and has a portion at the 5'"'"' end which is not complementary to any portion of the target nucleotide sequence and wherein the amplification also amplifies the non-complementary portion of the second polynucleotide.

32. The method of claim 31 wherein the amplification of step h) is conducted by:

i) hybridizing a third polynucleotide to the fused product;

ii) extending the third polynucleotide so that the extended third polynucleotide is complementary to the extended portion of the fused product and at least a portion of the first polynucleotide and the second polynucleotide of the fused product including the non-complementary portion of the second polynucleotide;

iii) separating the extended third polynucleotide from the fused product;

iv) providing a fourth polynucleotide which is at least partially complementary to the extended portion of the third polynucleotide which is complementary to the non-complementary portion of the second polynucleotide;

v) extending the fourth polynucleotide to the first polynucleotide;

vi) linking the fourth polynucleotide with the first polynucleotide to form the amplified product containing the detectable label; and

vii) repeating steps i) through vi) to obtain a sufficient quantity of the amplified product to detect the detectable label.

33. The method of claim 32 wherein the fourth polynucleotide contains the detectable label.

34. The method of claim 27 wherein multiple target nucleotide sequences are analyzed simultaneously.

35. The method of claim 34 wherein a first polynucleotide immobilized on a solid support is provided for each target sequence analyzed and the solid support is divided into a grid and wherein step (d) is conducted by providing a different single nucleotide in each section of the grid.

36. The method of claim 27 wherein the third segment consists of a single nucleotide.

37. The method of claim 27 wherein the target nucleotide sequence is DNA.

38. A method for analyzing a target nucleotide sequence having a first segment, a second segment and a third segment therebetween which third segment is formed of at least one nucleotide but which is formed of less than four different nucleotides wherein the third segment has a nucleotide or nucleotide sequence in a first state or a different second state, said method comprising:

a) providing a first polynucleotide which is immobilized on a solid support and which is at least partially complementary to the first segment of the target nucleotide sequence;

b) hybridizing the first polynucleotide to the first segment of the target nucleotide sequence under conditions suitable for hybridization;

c) providing a second polynucleotide which is at least partially complementary to the second segment of the target nucleotide sequence;

d) hybridizing the second polynucleotide to the second segment of the target nucleotide sequence under conditions suitable for hybridization wherein a gap of at least one nucleotide is present between one end of the first polynucleotide and one end of the second polynucleotide, and wherein the polynucleotide having a 3'"'"' end adjacent the gap is modified so that ligation across the gap is inhibited;

e) providing at least one nucleotide selected such that all the nucleotides which are complementary to the third segment are provided for only one of the first state or the second state and less than all the nucleotides complementary to the third segment are provided for the other state, the nucleotide or nucleotides being provided under conditions whereby the nucleotide or nucleotides form an extended portion of one of the first or second polynucleotide that is complementary to the nucleotides(s) of the third segment of the target nucleic acid sequence in one of the states;

f) linking the polynucleotide with the extended portion to the other polynucleotide under conditions whereby a fused product is formed comprised of the first polynucleotide, the second polynucleotide and the extended portion therebetween;

g) separating the fused product from the target nucleotide sequence and any non-linked second polynucleotide;

h) amplifying at least a portion of the fused product wherein the portion contains the extended portion under conditions suitable to form an amplified product containing the first polynucleotide and a detectable label, the amplifying being conducted to obtain a sufficient quantity of amplified product to detect the detectable label; and

i) detecting the presence of the label of the amplified product.