Evanescence-based multiplex sequencing method

• US 8,017,319 B2
• Filed: 12/18/2002
• Issued: 09/13/2011
• Est. Priority Date: 12/19/2001
• Status: Active Grant

• Current Assignee: Rudolf Rigler
• Original Assignee: Rudolf Rigler
• Inventors: Rigler, Rudolf
• Primary Examiner(s): Kapushoc; Stephen
• Assistant Examiner(s): BHAT, NARAYAN KAMESHWAR
• Application Number:
  US10/499,547
• Publication Number:
  US 20070020626A1
• Time in Patent Office: 3,191 Days
• Field of Search: 385/129, 435/6, 435/283.1, 435/287.2, 536/23.1
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target

Abstract

The invention relates to a method and a device for evanescence-based multiplex sequencing of nucleic acid molecules immobilized on a support.

Claims

1. Method for sequencing nucleic acids comprising the steps:

(a) providing an at least partially optically transparent support with a multitude of identical nucleic acid molecules immobilized thereon wherein the nucleic acid molecules carry several fluorescent marker groups,

(b) progressive cleavage of individual nucleotide building blocks from the immobilized identical nucleic acid molecules, and

(c) simultaneous determination of the base sequence of the plurality of nucleic acid molecules based on a time-dependent change in the fluorescence of the nucleic acid molecules and the time-dependent change in the fluorescence of the cleaved nucleotide building blocks caused by the cleavage of nucleotide building blocks, wherein the fluorescence is produced by beaming light into the support and generating an evanescent excitation field by internal reflection at the support surface in the area of the immobilized nucleic acid molecules, wherein the molecule sequencing is single molecule sequencing, wherein the cleavage of said multitude of individual nucleotide building blocks from a plurality of single immobilized nucleic acid molecules is measured and carried out in one single step by using a reagent selected from the group consisting of a single strand-specific exonuclease and a double strand-specific exonuclease, and wherein each nucleic acid molecule is measured separately and the measurements of each individual nucleic acid molecule are carried out in parallel by means of a detection matrix.

2. Method as claimed in claim 1, wherein a support made of glass, plastics, quartz or a composite containing one or more of these materials is used.

3. Method as claimed in claim 1, wherein a total internal reflection is generated at the support surface.

4. Method as claimed in claim 1, wherein the nucleic acid molecules are labelled in such a manner that at least 50% of all nucleotide building blocks of one base type carry a fluorescent marker group.

5. Method as claimed in claim 4, wherein essentially all nucleotide building blocks of one base type carry a fluorescent marker group.

6. Method as claimed in claim 1, wherein the exonuclease is selected from the group consisting of T7 DNA polymerase, E. coli exonuclease I and E. coli exonuclease III.

7. Method as claimed in claim 1, wherein the evanescent field is generated by beaming in light using a widened laser.

8. Method as claimed in claim 1, wherein the evanescent field is generated at multiple areas on the support by irradiating it with multiple laser beams or/and by means of multiple internal reflections.

9. Method as claimed in claim 1, wherein the detection matrix includes an electronic matrix selected from the group consisting of a CCD camera and an avalanche photodiode matrix.

10. Method as claimed in claim 1, wherein the fluorescence excitation and detection is carried out in several steps and in each case on a portion of the nucleic acid strands to be examined.

11. Method as claimed in claim 1, wherein a convection flow away from the support is generated during the determination.

12. Method as claimed in claim 1, wherein the fluorescent marker groups are at least partially quenched when they are incorporated into the nucleic acid strands and the fluorescence intensity is increased after cleavage.

13. Method as claimed in claim 1, wherein the cleavage of said multitude of individual nucleotide building blocks from a plurality of single immobilized nucleic acid molecules is measured and carried out in one single step by using a single nucleic acid strand which is digested and a single strand-specific exonuclease reagent.