Solution-based color compensation adjusted for temperature and electronic gains

• US 6,197,520 B1
• Filed: 08/13/1999
• Issued: 03/06/2001
• Est. Priority Date: 08/13/1999
• Status: Expired due to Term

• Current Assignee: University of Utah Research Foundation (State of Utah)
• Original Assignee: University of Utah Research Foundation (State of Utah)
• Inventors: Bernard, Philip, Pritham, Gregory, Wittwer, Carl T.
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US09/374,422
• Time in Patent Office: 571 Days
• Field of Search: 435/6, 435/91.2, 436/94
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention is directed to a method of analyzing at least two analytes at the same time using at least two fluorescent detecting entities. More particularly, the present invention relates to the use of fluorescently labeled hybridization probes to identify the genotypes of a nucleic acid sample at more than one locus by measuring fluorescence throughout a range of temperatures and correcting for temperature-dependent spectral overlap of the fluorescent probes.

Claims

1. A method for determining the presence of at least two analytes in a sample, comprising:

providing at least two detecting entities, each of said entities comprising a fluorescent label different from the fluorescent label of any of the other detecting entities, and each of said entities capable of specific binding with their respective analytes,

contacting the sample with the detecting entities to allow specific binding of the analytes and detecting entities,

exciting each of said labels with light having an appropriate wavelength for inducing fluorescence,

determining values of fluorescence of the labels in at least two different spectral channels, and

compensating said values for spectral overlap, wherein the compensating step includes correcting for temperature dependence of the fluorescent values.

2. The method of claim 1 wherein the determining step is performed throughout a range of temperatures.

3. The method of claim 2 wherein the correction for temperature dependence is performed through calculating a temperature specific overlap coefficient.

4. The method of claim 1 wherein the analytes are nucleic acid amplification products.

5. The method of claim 4 further comprising the step of determining the genotype of each of the nucleic acid amplification products.

6. The method of claim 1 further comprising the step of compensating said values for amplifier gain.

7. A method of analyzing the genotype of multiple loci of nucleic acid sequences comprising the steps of:

providing a sample of nucleic acid having a first locus and a second locus,

providing a first detecting entity, the first detecting entity comprising a first fluorescent label and having specificity for the first locus,

providing a second detecting entity, the second detecting entity comprising a second fluorescent label and having specificity for the second locus,

contacting the sample of nucleic acid with the first and second detecting entities,

exciting the first and second entities with light having the appropriate wavelength to induce fluorescence of the first and second fluorescent labels,

measuring throughout a range of temperatures a first fluorescent signal of the first detecting entity in a first spectral channel and a second fluorescent signal of the second detecting entity in a second spectral channel, and

compensating the first and second signal values for temperature dependence of the fluorescent signals.

8. The method of claim 7 wherein the compensating step is performed through calculating a temperature dependent coefficient.

9. The method of claim 8 further comprising the step of compensating for amplifier gain.

10. The method of claim 7 wherein the first detecting entity further comprises a sequence of nucleic acid complementary to at least a portion of the first locus and the second detecting entity further comprises a sequence of nucleic acid complementary to at least a portion of the second locus.

11. The method of claim 10 wherein the contacting step includes annealing the first and second detecting entities to their respective loci, and the measuring step includes monitoring fluorescent signals in the spectral channels during heating to melt the detecting entities from their respective loci.

12. The method of claim 11 wherein the contacting step is performed by lowering the temperature by 1°

C./s.

13. The method of claim 7 wherein the first fluorescent label comprises a first donor dye, a first acceptor dye, and a first pair of oligonucleotides, each oligonucleotide attached to one of the dyes, and each oligonucleotide substantially complementary to neighboring regions of the first locus.

14. The method of claim 13 wherein the second fluorescent label comprises a second donor dye, a second acceptor dye, and a second pair of oligonucleotides, each oligonucleotide attached to one of the dyes, and each oligonucleotide substantially complementary to neighboring regions of the second locus.

15. The method of claim 14 wherein the first donor dye is fluorescein and the first acceptor dye is LC Red 705.

16. The method of claim 15 wherein the second donor dye is fluorescein and the second acceptor dye is LC Red 640.

17. The method of claim 13 wherein the first locus has multiple alleles and the Mg⁺⁺ concentration is optimized to produce relatively even melting peaks for the alleles when the compensated signal values are plotted as −

dF/dT vs temperature.

18. The method of claim 13 wherein the first locus has multiple alleles and the concentration of the nucleic acid comprising the first locus is optimized to produce relatively even melting peaks for the alleles when the compensated signal values are plotted as −

dF/dT vs temperature.