Multiple tag labeling method for DNA sequencing

• US 5,436,130 A
• Filed: 10/26/1993
• Issued: 07/25/1995
• Est. Priority Date: 03/19/1992
• Status: Expired due to Fees

• Current Assignee: Regents of the University of California (University of California)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Quesada, Mark A., Mathies, Richard A., Huang, Xiaohua C.
• Primary Examiner(s): Parr, Margaret
• Assistant Examiner(s): MYERS, CARLA J
• Application Number:
  US08/143,377
• Time in Patent Office: 637 Days
• Field of Search: 435/6, 435/915, 436/164, 436/172, 436/173, 935/77
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 27/44721 by optical means
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

Claims

1. A method of determining the sequence of DNA which comprises the steps of

processing said DNA to form four sets of DNA sequencing fragments where one set contains fragments terminating in G, a second set contains fragments terminating in A, a third set contains fragments terminating in T, and a fourth set contains fragments terminating in C, such that selected mole fractions of each one of selected sets of sequencing fragments is tagged with a first fluorophore which fluoresces at a first wavelength and such that different selected mole fractions of each one of selected sets of sequencing fragments is tagged with a second fluorophore which fluoresces at a second wavelength and in which one of said sets of sequencing fragments is comprised of a mixture of selected mole fractions of fragments where one mole fraction is labeled with the first fluorophore and the other mole fraction is labeled with the second fluorophore,

separating said sets of tagged DNA sequencing fragments in a single channel or lane, and

determining the sequence of said sequencing fragments by detecting the ratio of fluorescence intensity at the first and second wavelengths as a function of time or position.

2. The method of claim 1 where the separation is performed electrophoretically in a capillary, gel-filled capillary or slab gel.

3. The method of claim 1 where the tagging of the sets of DNA sequencing fragments with the first and second fluorophores is performed by synthesizing a selected set of sequencing fragments by using selected mole fractions of two DNA primers, one of which is labeled with the first fluorophore and the other of which is labeled with the second fluorophore.

4. The method of claim 1 where the tagging of the sets of DNA sequencing fragments with the first and second fluorophores is performed by using selected mole fractions of two different fluorescently labeled terminators in the synthesis of the selected set of sequencing fragments, one of which is labeled with the first fluorophore and the other of which is labeled with the second fluorophore.

5. The method of claim 3 in which one of the sets of DNA sequencing fragments is synthesized with equal mole fraction ratios of primers labeled with the first and second fluorophores, a second one of the sets of DNA sequencing fragments is synthesized with a unity mole fraction of a primer labeled with the first fluorophore, a third one of the sets of DNA sequencing fragments is synthesized with a unity mole fraction of a primer labeled with the second fluorophore, and the fourth one of the sets of DNA sequencing fragments is unlabeled.

6. The method of claim 4 in which one of the sets of DNA sequencing fragments is synthesized with equal mole fractions of terminators labeled with the first and second fluorophores, a second of the sets of DNA sequencing fragments is synthesized with a unity mole fraction of a terminator labeled with the first fluorophore, a third of the sets of DNA sequencing fragments is synthesized with a unity mole fraction of a terminator labeled with a second fluorophore, and the fourth of the sets of DNA sequencing fragments is unlabeled.

7. The method of claims 5 or 6 in which the sequencing fragments terminating in G, A, T and C are identified by determining the ratio of intensity of the fluorescence at the first and second wavelength.

8. The method of claim 3 in which a first of said sets of DNA sequencing fragments is synthesized with unity mole fraction of primer labeled with a first fluorophore, a second of said sets of DNA sequencing fragments is synthesized with unity mole fraction of primer labeled with a second fluorophore, a third of said sets of DNA sequencing fragments is synthesized with equal mole fractions of primers labeled with said first and second fluorophores and the fourth set of DNA sequencing fragments is synthesized with unequal mole fractions of primers labeled with said first and second fluorophores.

9. The method of claim 4 in which a first of said sets of DNA sequencing fragments is synthesized with unity mole fraction of terminator labeled with a first fluorophore, a second of said sets of DNA sequencing fragments is synthesized with unity mole fraction of a terminator labeled with a second fluorophore, a third of said sets of DNA sequencing fragments synthesized with equal mole fractions of terminators labeled with said first and second fluorophores and the fourth set of DNA sequencing fragments is synthesized with unequal mole fractions of terminators labeled with said first and second fluorophores.

10. The method of claims 8 or 9 in which the sequencing fragments terminating in G, A, T and C are identified by determining the ratio of intensity of the fluorescence at the first and second wavelength.

11. The method as in claims 8 or 9 in which each of the sets of DNA fragments is coded with a different mole fraction ratio of the fluorophores that emit at first and second wavelengths.

12. A method of determining the sequence of DNA which comprises the steps of

processing sets of DNA sequencing fragments such that different selected mole fractions of each one of selected sets of sequencing fragments is tagged with fluorophores which emit fluorescence at different wavelengths with one of said sets of sequencing fragments is comprised of a mixture of selected mole fractions of fragments where one mole fraction is labeled with a fluorophore which fluoresces at a first wavelength and the other mole fraction is labeled with a fluorophore which fluoresces at a second wavelength,

separating said sets of tagged DNA sequencing fragments in a single channel or lane, and

determining the sequence of each of said sequencing fragments by detecting the ratio of fluorescence intensity at different wavelengths as a function of time or position.

13. The method of claim 12 where the separation is performed electrophoretically in a capillary, gel-filled capillary or slab gel.

14. The method of claim 12 in which the tagging is performed by synthesizing the DNA sequencing fragments using labeled DNA primers.

15. The method of claim 12 in which the tagging is performed by terminating the synthesis of the DNA sequencing fragments using dye-labeled terminators.

16. The method of claims 14 or 15 in which the fluorophores are selected to emit fluorescence at two wavelengths.

17. The method of claims 14 or 15 in which the fluorophores are selected to emit fluorescence at three wavelengths.

18. A method of determining the sequence of DNA which comprises the steps of

processing sets of DNA sequencing fragments terminating in G, A, T and C, where each one of said selected sets of sequencing fragments is labeled with a selected ratio of two or more radio-isotopes having the same mobility shift and one set of sequencing fragments is comprised of a mixture of selected mole fractions of fragments, one of which is labeled with one radio-isotope and the other of which is labeled with a second radio-isotope,

separating said sets of tagged DNA sequencing fragments in a single channel or lane, and

determining the sequence of said sequencing fragments by detecting the ratio of isotopes as a function of position or time.

19. The method of claim 18 where the separation is performed electrophoretically in a capillary, gel-filled capillary, or slab gel.

20. The method of claim 18 where the isotopes are radioactive and they are detected based on the different energy of their radioactive emission.

21. The method of claim 18 where the isotopes are stable and they are detected by using a mass spectrometer.

22. A method of determining the sequence of DNA which comprises the steps of

processing sets of DNA sequencing fragments where one set contains fragments terminating in G, a second set contains fragments terminating in A, a third set contains fragments terminating in T, and a fourth set contains fragments terminating in C,

tagging selected mole fractions of each one of selected sets of sequencing fragments with a first tag which provides a first signal,

tagging different selected mole fractions of each one of selected sets of sequencing fragments with a second tag which provides a second signal,

tagging two different mole fractions of one set of sequencing fragment with two different tags which simultaneously provide first and second signals,

separating said sets of tagged DNA sequencing fragments in a single channel or lane, and

determining the sequence of said sequencing fragments by detecting the ratio of intensity of the first and second signals as a function of time or position.