DNA sequencing using multiple fluorescent labels being distinguishable by their decay times

• US 6,447,724 B1
• Filed: 12/15/1998
• Issued: 09/10/2002
• Est. Priority Date: 08/11/1998
• Status: Expired due to Term

• Current Assignee: Caliper Holdings Incorporated
• Original Assignee: Caliper Holdings Incorporated
• Inventors: Jensen, Morten, Parce, J. Wallace
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/213,297
• Time in Patent Office: 1,365 Days
• Field of Search: 422/99, 422/55, 422/68.1, 422/58, 422/82.05, 435/6, 435/91.1, 435/91.2
• US Class Current: 422/68.1
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2561/12 Fluorescence lifetime measurement
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: G01N 15/06 Investigating concentration of particle suspensions by weighing G01N5/00; investigating sedimentation of particle suspensions G01N15/04; investigating individual particles G01N15/10
• CPC Class Codes: G01N 15/075 by optical means
• CPC Class Codes: G01N 2021/6413 Distinction short and delayed fluorescence or phosphorescence
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 21/6408 with measurement of decay time, time resolved fluorescence

Abstract

A method is provided for identifying components of a mixture by labeling the individual components with fluorescent agents having different fluorescence lifetimes. The components are subsequently separated, fluorescent labels detected and their lifetimes measured. Based on the measured fluorescent lifetimes, the components of mixtures of small organic molecules, polymers, peptides, saccharides and nucleic acids can be identified.

Claims

1. A method of distinguishing between a plurality of fluorescent species, wherein each of said fluorescent species has a fluorescence emission, said emission having a characteristic fluorescence lifetime, said method comprising:

(a) electrokinetically transporting each of said fluorescent species through a microfluidic

(b) detecting each of said fluorescent species in said channel; and

,

(c) identifying each of said fluorescent species by measuring said characteristic fluorescence lifetime.

2. The method according to claim 1, wherein said microfluidic channel is in a microfluidic apparatus comprising two or more intersecting channels.

3. The method according to claim 2, wherein said microfluidic apparatus comprises:

a glass or polymer body having at least two intersecting channels disposed therein, at least one of said two intersecting channels having at least one cross-sectional dimension in the range of from about 0.1 to about 500 μ

m.

5. The method of claim 1 or claim 4, wherein one or more member of the plurality of fluorescent species comprises an organic molecule, an amino acid, a peptide, a polypeptide, a protein, a nucleotide, a nucleoside, a dideoxynucleoside, a dideoxynucleotide, a deoxynucleoside, a deoxynucleotide, a nucleotide analog, a nucleoside analog, a polynucleotide, a nucleic acid, a sequencing reaction product, a PCR reagent, a nucleic acid template, a nucleic acid primer, an antibody, an antigen, a ligand, a receptor, an enzyme, an enzyme substrate, a monomer, a polymer, a drug, a sugar, a polysaccharide, a lipid, a liposome, a micelle, a toxin, or a cell.

6. The method of claim 1 or claim 4, wherein one or more member of the plurality of fluorescent species comprises dansyl, fluorescein, 8-anilino-1-napthalene sulfonate, pyrene, ethenoadenosine, ethidium bromide prollavine monosemicarbazide, p-terphenyl, 2,5-diphenyl-1,3,4-oxadiazole, 2,5-diphenyloxazole, p-bis[2-(5-phenyloxazolyl)]benzene, 1,4-bis-2-(4-methyl-5-phenyloxazolyl)benzene, or lanthanide chelate.

7. The method of claim 1 or claim 4, wherein each of said fluorescent species has an emission maximum and at least a first fluorescent species and a second fluorescent species comprise the substantially the same emission maximum.

8. The method of claim 1 or claim 4, wherein each of said fluorescent species has an emission maximum and at least a first fluorescent species and a second fluorescent species comprise a substantially different emission maximum.

9. The method of claim 1 or claim 4, wherein said characteristic fluorescence lifetime comprises about 0.1 nanosecond to about 4000 nanoseconds.

10. The method of claim 9, wherein said characteristic fluorescence lifetime comprises about 0.1 nanosecond to about 1000 nanoseconds.

11. The method of claim 10, wherein said characteristic fluorescence lifetime comprises about 0.1 nanosecond to about 100 nanoseconds.

12. The method of claim 1 or claim 4, wherein at least a first fluorescent species and a second fluorescent species have characteristic fluorescence lifetimes that differ by at least about 5 nanoseconds.

13. The method of claim 1, wherein said electrokinetically transporting further comprises electrokinetically separating.

14. The method of claim 1 or claim 4, said detecting comprising detecting by pulse or by phase modulation.

15. The method of claim 14, wherein said detecting by pulse comprises exciting said fluorescent species with a pulse of light and measuring time-dependent decay of fluorescence.

16. The method of claim 14, wherein said detecting by phase modulation comprises exciting said fluorescent species with sinusoidally modulated light.

17. The method of claim 3, the microfluidic apparatus further comprising a detection station, said detection station comprising an optical system, an excitation source, and a detector.

18. The method of claim 1 or claim 4, wherein said plurality of fluorescent species comprises one or more fluorescent nucleotide, fluorescent nucleotide analog, or fluorescent dideoxynucleotide.

19. The method of claim 18, the method further comprising contacting said plurality of fluorescent species with one or more sequencing reagent prior to step (a), thereby performing a sequencing reaction.

20. The method of claim 19, wherein the one or more sequencing reagent is selected from one or more of:

a nucleic acid polymer, a nucleic acid template, a nucleic acid primer, a fluorescently labeled nucleic acid, a polymerase, an exonuclease, an endonuclease, a metal ion, a chelating agent, surfactant, an acid, a base, a solvent, a buffer, and a catalyst.

21. The method of claim 19, wherein performing the sequencing reaction comprises producing a plurality of nucleic acid polymers complementary to a region of a nucleic acid template, and wherein step (a) comprises electrokinetically separating the plurality of nucleic acid polymers.

22. The method of claim 21, wherein the nucleic acid template ranges in size from about 2 to about 100,00 bases.

23. The method of claim 22, wherein the nucleic acid template ranges in size from about 100 to about 10,000 bases.

24. The method of claim 23, wherein the nucleic acid template ranges in size from a bout 300 to about 5000 bases.

4. A method of distinguishing between a plurality of fluorescent species, wherein each of said fluorescent species has a fluorescence emission, said fluorescence emission having a characteristic fluorescence lifetime, the method comprising:

(a) electrokinetically separating each of said fluorescent species;

(b) detecting each of said fluorescent species; and

,

(c) identifying each of said fluorescent species by measuring said characteristic fluorescence lifetime.