Pulsed-multiline excitation for color-blind fluorescence detection

• US 7,511,811 B2
• Filed: 10/12/2005
• Issued: 03/31/2009
• Est. Priority Date: 08/28/2001
• Status: Expired due to Fees

• Current Assignee: Baylor College of Medicine and Rice University
• Original Assignee: Baylor College of Medicine and Rice University
• Inventors: Scott, Graham B. I., Kittrell, Carter, Metzker, Michael L., Curl, Robert F.
• Primary Examiner(s): Geisel; Kara E
• Application Number:
  US11/248,910
• Publication Number:
  US 20060139634A1
• Time in Patent Office: 1,266 Days
• Field of Search: 356/317, 250/459.1
• US Class Current: 356/317
• CPC Class Codes: G01J 3/021 using plane or convex mirrors, parallel phase plates, or particular reflectors
• CPC Class Codes: G01J 3/10 Arrangements of light sources specially adapted for spectrometry or colorimetry
• CPC Class Codes: G01J 3/4406 Fluorescence spectrometry
• CPC Class Codes: G01N 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6458 Fluorescence microscopy fluorescence microscopes per se G02B21/0076 and G02B21/16

Abstract

The present invention provides a technology called Pulse-Multiline Excitation or PME. This technology provides a novel approach to fluorescence detection with application for high-throughput identification of informative SNPs, which could lead to more accurate diagnosis of inherited disease, better prognosis of risk susceptibilities, or identification of sporadic mutations. The PME technology has two main advantages that significantly increase fluorescence sensitivity: (1) optimal excitation of all fluorophores in the genomic assay and (2) “color-blind” detection, which collects considerably more light than standard wavelength resolved detection. This technology differs significantly from the current state-of-the-art DNA sequencing instrumentation, which features single source excitation and color dispersion for DNA sequence identification. Successful implementation of the PME technology will have broad application for routine usage in clinical diagnostics, forensics, and general sequencing methodologies and will have the capability, flexibility, and portability of targeted sequence variation assays for a large majority of the population.

Claims

1. A method of identifying sample components comprising:

(a) preparing a sample comprising sample components, a first dye and a second dye;

(b) placing the sample in the beam path of a first excitation line and a second excitation line;

(c) sequentially firing the first excitation line and the second excitation line;

(d) collecting fluorescence signals from the samples as a function of time; and

(e) sorting the fluorescence by each excitation line'"'"'s on-time window, wherein the sample components are identified.

2. The method of claim 1, wherein the fluorescence signals are collected from discrete time periods in which no excitation line is incident on the sample, the time periods occurring between the firing of the two excitation lines.

3. The method of claim 1, wherein the absorption maxima of the first dye substantially corresponds to the excitation wavelength of the first excitation line.

4. The method of claim 1, wherein the absorption maxima of the second dye substantially corresponds to the excitation wavelength of the second excitation line.

5. The method of claim 4, further comprising a third and fourth dye and a third and fourth excitation line, wherein the absorption maxima of the third and fourth dyes substantially correspond to the excitation wavelength of the third and four excitation lines.

6. The method of claim 5, further comprising a fifth, sixth, seventh and eighth dye and a fifth, sixth, seventh and eighth excitation line, wherein the absorption maxima of the fifth, sixth, seventh and eighth dyes substantially correspond to the excitation wavelength of the fifth, sixth, seventh and eighth excitation lines.

7. The method of claim 6, further comprising a ninth, tenth, eleventh, twelfth, thirteenth, fourteenth, fifteenth, and sixteenth excitation line, wherein the absorption maxima of the ninth, tenth, eleventh, twelfth, thirteenth, fourteenth, fifteenth, and sixteenth dyes substantially correspond to the excitation wavelength of the ninth, tenth, eleventh, twelfth, thirteenth, fourteenth, fifteenth, and sixteenth excitation lines.

8. The method of claim 1, wherein at least one of said dyes is a zanthene, fluorescein, rhodamine, BODIPY, cyanine, coumarin, pyrene, phthalocyanine, phycobiliprotein, Alexa, or squariane dye.

9. The method of claim 8, wherein at least one of said dyes is a BODIPY dye.

10. The method of claim 1, wherein said sample components enable the determination of single nucleotide polymorphisms (SNPs).

11. The method of claim 10, wherein said method is for the high-throughput identification of informative SNPs.

12. The method of claim 10, wherein said SNPs are obtained directly from genomic DNA material.

13. The method of claim 10, wherein said SNPs are obtained from PCR amplified material.

14. The method of claim 10, wherein said SNPs are obtained from cloned material derived directly from genomic DNA material or PCR amplified material.

15. The method of claim 10, wherein said SNPs are obtained using a single nucleotide primer extension method.

16. The method of claim 15, wherein said single nucleotide primer extension method comprises using single unlabeled dNTPs, single labeled dNTPs, single 3′

-modified dNTPs, single base-modified 3′

-dNTPs, single alpha-thio-dNTPs or single labeled 2′

,3′

-dideoxynucleotides.

17. The method of claim 1, comprising a mini-sequencing method comprises using single unlabeled dNTPs, single labeled dNTPs, single 3′

-modified dNTPs, single base-modified 3′

-dNTPs, single alpha-thio-dNTPs or single labeled 2′

,3′

-dideoxynucleotides.

18. The method of claim 17, wherein said mini-sequencing method comprises a single nucleotide polymorphism (SNP).

19. The method of claim 18, wherein said mini-sequencing method comprises multiple SNPs.

20. The method of claim 10, wherein said SNPs are obtained using Sanger sequencing.

21. The method of claim 10, wherein the analyzing of said signals is adapted for the accurate diagnosis of inherited disease, better prognosis of risk susceptibilities, identification of sporadic mutations, or prescribing tailor-made daily drug regimens for individual patients.

22. The method of claim 1, wherein the analyzing of said signals is adapted for routine usage in clinical diagnostics, forensics applications or determining general sequencing methodologies.

23. A method of identifying sample components comprising:

(a) preparing a sample comprising sample components, a first dye and a second dye;

(b) placing the sample in the beam path of a first excitation line and a second excitation line;

(c) sequentially firing the first excitation line and the second excitation line;

(d) collecting fluorescence signals from the samples as a function of time, wherein said step of collecting fluorescence signals comprises measuring fluorescence emission using a non-dispersive detector; and

(e) sorting the fluorescence by each excitation line'"'"'s on-time window, wherein the sample components are identified.