Device for sequencing nucleic acid molecules

• US 20050227231A1
• Filed: 10/02/2002
• Published: 10/13/2005
• Est. Priority Date: 10/04/2001
• Status: Abandoned Application

• Current Assignee: Dimitri Tcherkassov
• Original Assignee: Dimitri Tcherkassov
• Inventors: Tcherkassov, Dimitri
• Application Number:
  US10/491,557
• Publication Number:
  US 20050227231A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G01N 33/54366 Apparatus specially adapted for solid-phase testing

Abstract

The invention relates to a device for the automatic determination of nucleic acid sequences. The sequencing reaction occurs by the parallel sequential construction of the strands complementary to individually-fixed single-strand nucleic acid chains. The automatic sequencing carries out said sequential construction and detects electromagnetic radiation from individual marked nucleotides (NT*s) incorporated in the complementary strands. The sequence of the immobilised nucleic acid chain is determined from the order of the incorporated NT*s.

Claims

1. Automated sequencing device for parallel sequencing of a population of individual nucleic acid chain molecules fixed on a plane surface, this sequencing occurring by the sequential construction of a strand complementary to the fixed nucleic acid chain concerned with the nucleotides reversibly labelled with fluorescent dyes, the sequential construction taking place in cyclic reactions. This automated sequencing device comprises the following elements:

An optical system for the detection of signals of individual molecules, which system comprises the following components;

A source of electromagnetic radiation for the excitation of the fluorescence of dyes which are coupled to the modified nucleotides,

A device for focusing the electromagnetic radiation used for the excitation of fluorescence and for collecting emitted electromagnetic radiation (fluorescence signals) of individual dye molecules which are coupled to the modified nucleotide molecules incorporated into the strands complementary to the nucleic acid chains to be sequenced,

A filter device for selecting wavelengths of the electromagnetic radiation used for the excitation of the fluorescence and of electromagnetic radiation collected (fluorescence signals),

A detection device for the detection of the electromagnetic radiation, selected by the filter device (fluorescence signals), of individual dye molecules which are coupled to the modified nucleotide molecules incorporated into the strands complementary to the nucleic acid chains to be sequenced,

A translation device for the translation of the reaction platforms during scanning of the surface and for changing over between reaction platforms during the cycle steps,

One or several reaction platforms on the translation device for the execution of sequential reaction cycles with immobilised nucleic acid chains, these platforms permitting a simultaneous detection of the signals of many individual dye molecules which are coupled to modified nucleotide molecules incorporated into the strands complementary to the nucleic acid chains to be sequenced,

A housing for retaining the optical system, detection device and translation device,

An analytical device for the determination of sequences of fixed nucleic acid chains by way of signals, detected by the detection device, of individual modified nucleotides molecules to be incorporated into strands complementary to the nucleic acid chains to be sequenced,

A control device for controlling

a) the cycles in the reaction platform

b) the optical system

c) the translation device

d) the analysis device

2. Automated sequencing device according to claim 1 characterised in that the electromagnetic radiation used for the excitation of fluorescence is passed onto the reaction surface in the epifluorescence mode.

3. Automated sequencing device according to claim 1 characterised in that the optical system, the translation device and the housing are part of a fluorescence microscope.

4. Automated sequencing device according to claim 1 to 3 characterised in that the source of electromagnetic radiation is a lamp.

5. Automated sequencing device according to claim 4 characterised in that the source of the electromagnetic radiation is a mercury vapour lamp.

6. Automated sequencing device according to claim 1 to 3 characterised in that the source of electromagnetic radiation is one or several lasers.

7. Automated sequencing device according to claim 1 characterised in that the nucleic acid chains are fixed on a plane surface in the form of nucleic acid chain primer complexes.

8. Automated sequencing device according to claim 1 characterised in that several fluorescence signals of individual NT*s incorporated into different NACs and/or NACFs are detected simultaneously.

9. Automated sequencing device according to claim 1 characterised in that several nucleic acid chains are sequenced simultaneously.

10. Automated sequencing device according to claim 1 characterised in that it carries out the following process for the parallel sequence analysis of nucleic acid sequences (nucleic acid chains, NACs or their fragments, NACFs) whereby a cyclic build-up reaction of the complementary strand of the NACs and/or NACFs is carried out using one or several primers and one or several polymerases by

a) adding, to the NAC primer complexes or NACF primer complexes bound to the surface, a solution containing one or several polymerases and one to four modified nucleotides (NTs*) which are labelled with fluorescent dyes, the fluorescent dyes present on the NTs* in the case of the simultaneous use of at least two NTs* being selected such that it is possible to distinguish between the NTs* used by measuring different fluorescence signals, the NTs* being structurally modified such that the polymerase, following the incorporation of such an NT* into a growing complementary strand, is not capable of incorporating a further NT* into the same strand,

b) incubating the stationary phase obtained in stage a) under conditions suitable for extending the complementary strands, the complementary strands being extended in each case by one NT*,

c) washing the stationary phase obtained in stage b) under conditions suitable for removing NTs* not incorporated into a complementary strand,

d) detecting the individual NTs* incorporated into complementary strands by measuring the characteristic signal of the fluorescent dye concerned, the relative position of the individual fluorescence signals on the reaction surface being simultaneously determined,

e) cleaving off the fluorescent dyes and the group leading to termination from the NTs* added into the complementary strand in order to produce non-labelled (NTs or) NACs or NACFs,

f) washing the stationary phase obtained in stage e) under conditions suitable for removing the fluorescent dyes and the group,

stages a) to f) being repeated several times, if necessary,

whereby the relative position of individual NAC primer complexes or NACF primer complexes on the reaction surface and the sequence of these NACs or NACFs are determined by specific allocation, to the NTs, of the fluorescence signals detected in stage d) in successive cycles at the positions concerned.

11. Automated sequencing device according to claim 1 characterised in that it carries out the following process for the parallel sequence analysis of nucleic acid sequences (nucleic acid chains, NACFs) whereby

fragments (NACFs) of single-strand NACs with a length of approx. 50 to 1000 nucleotides are produced which may represent overlapping partial sequences of a total sequence,

the NACFs are bound in a random arrangement on a reaction surface by using a uniform primer or several different primers in the form of NACF primer complexes,

a cyclic build-up reaction of the complementary strand of the NACFs is carried out using one or several polymerases by

a) adding, to the NACF primer complexes bound to the surface, a solution containing one or several polymerases and one to four modified nucleotides (NTs*) which are labelled with fluorescent dyes, the fluorescent dyes present on the NTs* in the case of the simultaneous use of at least two NTs* being selected such that it is possible to distinguish between the NTs* used by measuring different fluorescence signals, the NTs* being modified structurally such that the polymerase, following the incorporation of such an NT* into a growing complementary strand, is not capable of incorporating a further NT* into the same strand,

b) incubating the stationary phase obtained in stage a) under conditions suitable for extending the complementary strands, the complementary strands being extended in each case by one NT*,

c) washing the stationary phase obtained in stage b) under conditions suitable for removing NTs* not incorporated into a complementary strand,

d) detecting the individual NTs* incorporated into complementary strands by measuring the characteristic signal of the fluorescent dye concerned, the relative position of the individual fluorescence signals on the reaction surface being simultaneously determined,

e) cleaving off the fluorescent dyes and the group leading to termination from the NTs* added into the complementary strand in order to produce non-labelled (NTs or) NACFs,

f) washing the stationary phase obtained in stage e) under conditions suitable for removing the fluorescent dyes and the group,

stages a) to f) being repeated several times, if necessary,

whereby the relative position of individual NACF primer complexes on the reaction surface and the sequence of these NACFs are determined by the specific allocation, to the NTs, of the fluorescence signals detected in stage d) in successive cycles at the positions concerned.

12. Automated sequencing device according to claim 1 characterised in that it carries out the following process for the highly parallel analysis of gene expression, whereby

single-strand gene products are provided,

the gene products are bound in a random arrangement on a reaction surface by using a uniform primer or several different primers in the form of gene product primer complexes,

a cyclic build-up reaction of the complementary strand of the gene product is carried out using one or several polymerases by

a) adding, to the gene product primer complexes bound to the surface, a solution containing one or several polymerases and one to four modified nucleotides (NTs*) which are labelled with fluorescent dyes, the fluorescent dyes present on the NTs* in the case of the simultaneous use of at least two NTs* being selected such that it is possible to distinguish between the NTs* used by measuring different fluorescence signals, the NTs* being modified structurally such that the polymerase, following the incorporation of such an NT* into a growing complementary strand, is not capable of incorporating a further NT* into the same strand,

b) incubating the stationary phase obtained in stage a) under conditions suitable for extending the complementary strands, the complementary strands being extended in each case by one NT*,

c) washing the stationary phase obtained in stage b) under conditions suitable for removing NTs* not incorporated into a complementary strand,

d) the individual NTs* incorporated into complementary strands by measuring the characteristic signal of the fluorescent dye concerned, the relative position of the individual fluorescence signals on the reaction surface being simultaneously determined,

e) cleaving off the fluorescent dyes and the group leading to termination from the NTs* added into the complementary strand in order to produce non-labelled (NTs or) gene products,

f) washing the stationary phase obtained in stage e) under conditions suitable for removing the fluorescent dyes and the group,

stages a) to f) being repeated several times, if necessary,

whereby the relative position of individual gene product primer complexes on the reaction surface and the sequence of these gene products are determined by the specific allocation, to the NTs, of the fluorescence signals detected in stage d) in successive cycles at the positions concerned and the identity of the gene products is determined from the partial sequences determined.

13. Reaction platform according to claim 1 for carrying out reaction steps, which platform comprises the following elements:

a replaceable chip with one or several microfluid channels

a distribution device for controlling the replacement of the solution in the chip

a thermostat unit for controlling the temperature in the chip.

14. Automated sequencing device according to claim 1 to 3 characterised in that the source of electromagnetic radiation is one or several laser diodes.