Process for sequencing nucleic acids

• US 5,124,247 A
• Filed: 12/11/1989
• Issued: 06/23/1992
• Est. Priority Date: 12/09/1988
• Status: Expired due to Fees

• Current Assignee: European Molecular Biology Laboratory
• Original Assignee: European Molecular Biology Laboratory
• Inventors: Ansorge, Wilhelm
• Primary Examiner(s): Wax, Robert A.
• Assistant Examiner(s): Zitomer, Stephanie W.
• Application Number:
  US07/448,726
• Time in Patent Office: 925 Days
• Field of Search: 435/6, 435/91, 436/501, 436/94, 935/77, 935/78, 536/26, 536/27, 536/28, 536/29
• US Class Current: 435/6.11
• 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: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2527/137 Concentration of a component of medium
• CPC Class Codes: C12Q 2535/101 Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

For the sequencing of nucleic acids by enzymatic extension of an oligonucleotide primer in the presence of a polymerase, the four deoxyribonucleoside triphosphates, one of the four dideoxynucleoside triphosphates and the nucleic acid to be sequenced as template in each of four different preparations, labelling of the nucleic acid fragments which form and which are dependent on the dideoxynucleoside triphosphate used, separation by gel electrophoresis of the preparations containing the fragments and detection of the sequence via the label, at least two of the dideoxynucleoside triphosphates are used in different amounts together in one preparation and the fragments are differentiated by the intensity of the labelling signal of the bands in the gel or in another separation procedure.

Claims

1. Method for sequencing a nucleic acid comprising:

(a) combining

(i) an oligonucleotide primer,

(ii) a nucleic acid to be sequenced,

(iii) four deoxyribonucleoside triphosphates,

(iv) a polymerase, and

(v) at least three dideoxyribonucleoside triphosphates in different amounts, under conditions favoring extension of said oligonucleotide primer to form nucleic acid fragments complementary to the nucleic acid to be sequenced;

(b) labelling the nucleic acid fragments formed;

(c) separating the nucleic acid fragments by gel electrophoresis; and

(d) determining nucleic acid sequence by determination of position of incorporated dideoxynucleoside triphosphates in said labelled nucleic acid fragments, wherein said dideoxynucleoside triphosphates are differentiated from each other by intensity of the label in the nucleic acid sequence.

2. Method of claim 1, wherein said three dideoxynucleoside triphosphates are combined with (i), (ii), (iii) and (iv) in two preparations, a first preparation containing different amounts of two dideoxynucleotide triphosphates and a second preparation containing a third dideoxynucleotide triphosphate.

3. Method of claim 1, comprising combining four different dideoxynucleoside triphosphates in different amounts with (i), (ii), (iii) and (iv).

4. Method of claim 3, wherein different amounts of said four dideoxynucleotide triphosphates are combined with (i), (ii), (iii) and (iv) in one preparation.

5. Method of claim 3, wherein different amounts of two different dideoxynucleotides are combined with (i), (ii), (iii) and (iv) in a first preparation and different amounts of a third and a fourth dideoxynucleotide triphosphate are combined with (i), (ii), (iii) and (iv) in a second preparation.

6. Method of claim 2, wherein the two said dideoxyribonucleoside triphosphates present in said first preparation are present in a ratio of about 2:

1.

7. Method of claim 3, wherein said four dideoxynucleotide triphosphates are used in a ratio of at least 4:

3;

2;

1.

8. Method of claim 1, wherein said nucleic acid fragments are labelled with a fluorescent dye.

9. Method of claim 8, comprising labelling said nucleic acid fragments by coupling said fluorescent dye to said oligonucleotide primer.

10. Method of claim 9, wherein said fluorescent dye is bound, via a linker, to a 5'"'"'-phosphate group of said oligonucleotide primer.

11. Method of claim 8, wherein said fluorescent dye is bound, via a linker to at least one deoxynucleoside triphosphate or at least one dideoxynucleoside triphosphate.

12. Method of claim 11, wherein said fluorescent dye is bound via a linker to one deoxynucleoside triphosphate.

13. Method of claim 11, wherein said fluroescent dye is bound, via a linker, to a C5 position of a pyrimidine.

14. Method of claim 11, wherein said fluorescent dye is bound, via a linker, to a N7, C7 or C8 position of a purine.

15. Method of claim 10 or 11, wherein said linker is a straight chain or branched amino hydrocarbon or a straight chain or branched mercapto hydrocarbon, wherein said hydrocarbon contains an unbranched chain having 3 or more carbon atoms.

16. Method of claim 15, wherein said linker is an aminoalkyl, aminoalkenyl or aminoalkynyl group.

17. Method of claim 1, comprising sequencing a single stranded nucleic acid.

18. Method of claim 1, comprising sequencing a double stranded nucleic acid.

19. Method of claim 8, wherein said fluorescent dye is fluorscein, a fluorescent fluorescin analogue, or rhodamine.

20. Method of claim 2 or 5, wherein said two dideoxynucleoside triphosphates are used in a ratio of X:

1, wherein X is a whole number from 5 to 7.

21. Method of claim 3 or 4, wherein said four different dideoxynucleotide triphosphates are used in a ratio of 16:

8;

4;

1.

22. Method of claim 1, wherein said polymerase is Klenow fragment of DNA polymerase I, T7 DNA polymerase, modified T7 DNA polymerase, Taq polymerase or reverse transcriptase.

23. Method of claim 1, wherein said polymerase is T7 DNA polymerase.

24. Method of claim 1, further comprising subjecting said nucleic acid sequence to be determined to polymerase chain reaction prior to determining its sequence to increase the amount of said nucleic acid sequence, separating double stranded nucleic acids thus produced, and using one of the double strands to determine said nucleic acid sequence.

25. Method of claim 8, further comprising exciting said fluorescent dye with a laser in step (d).