SINGLE MOLECULE REAL TIME SEQUENCER, NUCLEIC ACID ANALYZER AND SINGLE MOLECULE REAL TIME SEQUENCING METHOD

• US 20110105358A1
• Filed: 06/08/2009
• Published: 05/05/2011
• Est. Priority Date: 06/23/2008
• Status: Abandoned Application

• Current Assignee: Hitachi High-Technologies Corporation (Hitachi, Ltd.)
• Original Assignee: Hitachi High-Technologies Corporation (Hitachi, Ltd.)
• Inventors: Kato, Hirokazu, Takahashi, Satoshi, Haga, Takanobu, Kumazaki, Nobutaka
• Application Number:
  US13/001,294
• Publication Number:
  US 20110105358A1
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 3/502707 characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2523/313 Irradiation, e.g. UV irradiation
• CPC Class Codes: C12Q 2523/319 Photocleavage, photolysis, photoactivation
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2561/113 Real time assay
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/628 being a surface plasmon resonance spectrometer
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: G01N 21/648 using evanescent coupling or surface plasmon coupling for the excitation of fluorescence

Abstract

An object of the present invention relates to selectively control an extension reaction within a desired area in a substrate. In the present invention, an oligo probe arranged with a caged compound at the terminal thereof is immobilized to a reaction field area in the substrate. After pouring a reaction solution into a flow cell including the reaction field area, the reaction field area alone is irradiated with light to associate the photodegradation-active protecting group at the terminal of the oligo probe that has been immobilized in the reaction field area and thus to selectively control initiation of a polymerase extension reaction. In the flow cell, a plural number of the reaction field areas are arranged at constant interval on the substrate. The flow cell immobilized to a moving stage is moved by a distance equal to the interval between the adjacent reaction field areas and then light irradiation is carried out to measure the extension reaction continuously. By repeating these operations, the base extension reaction is stably measured in the flow cell without using complicated channels or without replacing the reaction solution.

Claims

1. A single molecule real time sequencer comprising:

a nucleic acid probe having a photodegradable substance that inhibits a nucleic acid extension reaction;

a reaction field area arranged with a plurality of said nucleic acid probes;

a channel installed with a plurality of said reaction field areas;

a reagent supply mechanism for supplying a reagent to be utilized in the nucleic acid extension reaction to the channel;

an excited optical system for irradiating evanescent light to the desired reaction field area and detecting fluorescence generated; and

a reaction control optical system for irradiating the light to decompose the photodegradable substance to the desired reaction field area.

2. The single molecule real time sequencer according to claim 1, characterized in that the photodegradable substance is a photodegradable protecting group modified at the terminal of the nucleic acid probe.

3. The single molecule real time sequencer according to claim 2, characterized in that the photodegradable protecting group is a 2-nitrobenzyl type, a decyl-phenacyl type or a coumarinylmethyl type.

4. The single molecule real time sequencer according to claim 1, characterized in that a metal structure that generates a fluorescence increasing field is arranged in the reaction area field, corresponding to each of the nucleic acid probes.

5. The single molecule real time sequencer according to claim 1, characterized in that the reagent comprises four deoxynucleotides, dATP, dCTP, dTTP and dGTP, labeled with four-colored fluorescent dyes emitting each different fluorescence depending on the evanescent light, and an enzyme for carrying out the nucleic acid extension reaction.

6. The single molecule real time sequencer according to claim 1, characterized in that the excited optical system illuminates by total reflection of visible light having a wavelength range of 420 nm to 800 nm, and generates the evanescent light.

7. The single molecule real time sequencer according to claim 1, characterized in that the reaction control optical system irradiates UV light having a wavelength range of 250 nm to 400 nm.

8. The single molecule real time sequencer according to claim 1, characterized in that after the reaction control optical system irradiated light to the desired reaction area field, the channels are moved to capture, in a view thereof, the reaction area field that has the different reaction control optical system.

9. A nucleic acid analyzer comprising:

a nucleic acid analysis device having a nucleic acid probe that hybridizes with a target nucleic acid but does not promote a nucleic acid extension reaction unless UV light is irradiated, a reaction field area arranged with a plurality of said nucleic acid probes that hybridize with different target nucleic acids, and a nucleic acid analysis device having a channel that is installed with a plurality of said reaction field areas, and that is capable of retaining a reagent to be utilized in the nucleic acid reaction;

an excited optical system for irradiating the evanescent light to the desired reaction field area and detecting fluorescence generated;

a reaction control optical system for irradiating the UV light to decompose the photodegradable substance to the desired reaction field area; and

a stage drive mechanism for moving relatively the nucleic acid analysis device to the excited optical system and the reaction control optical system, so as to irradiate evanescent light and UV light to the desired reaction field area.

10. The nucleic acid analyzer according to claim 9, characterized in that the terminal of the nucleic acid probe is modified with the photodegradable protecting group modified.

11. The nucleic acid analyzer according to claim 10, characterized in that the photodegradable protecting group is a 2-nitrobenzyl type, a decyl-phenacyl type or a coumarinylmethyl type.

12. The nucleic acid analyzer according to claim 9, characterized in that a metal structure that generates a fluorescence increasing field is arranged in the reaction area field, corresponding to each of the nucleic acid probes.

13. The nucleic acid analyzer according to claim 9, characterized in that the reagent comprises four deoxynucleotides, dATP, dCTP, dTTP and dGTP, labeled with four-colored fluorescent dyes emitting each different fluorescence depending on the evanescent light, and an enzyme for carrying out the nucleic acid extension reaction.

14. The nucleic acid analyzer according to claim 9, characterized in that the excited optical system illuminates by total reflection of visible light having a wavelength range of 420 nm to 800 nm, and generates the evanescent light.

15. The nucleic acid analyzer according to claim 9, characterized in that the reaction control optical system irradiates UV light having a wavelength range of 250 nm to 400 nm.

16. The nucleic acid analyzer according to claim 9, characterized in that after the reaction control optical system irradiates light to the desired reaction area field, the channels are moved to capture, in a view thereof, the reaction area field that has the different reaction control optical system.

17. A single molecule real time sequencing method comprising:

preparing a nucleic acid probe having a photodegradable substance that inhibits a nucleic acid extension reaction and a channel installed with a plurality of reaction field areas arranged with a plurality of said nucleic acid probes;

supplying a target nucleic acid and a reagent to be utilized in the nucleic acid extension reaction into the channel;

irradiating UV light to decompose the photodegradable substance to the desired reaction field area;

irradiating evanescent light to the desired reaction field area, and detecting fluorescence generated;

moving relatively the channel to the reaction control optical system for irradiating the UV light, and the excited optical system generating the evanescent light;

irradiating UV light to decompose the photodegradable substance to the different reaction field areas; and

irradiating evanescent light to the different reaction field area, and to detect fluorescence generated.

18. The single molecule real time sequencing method according to claim 17, characterized in that the photodegradable substance is a photodegradable protecting group modified at the terminal of the nucleic acid probe.

19. The single molecule real time sequencing method according to claim 18, characterized in that the photodegradable protecting group is a 2-nitrobenzyl type, a decyl-phenacyl type or a coumarinylmethyl type.

20. The single molecule real time sequencing method according to claim 17, characterized in that a metal structure that generates a fluorescence increasing field is arranged in the reaction area field, corresponding to each of the nucleic acid probes.

21. The single molecule real time sequencing method according to claim 17, characterized in that the reagent comprises four deoxynucleotides, dATP, dCTP, dTTP and dGTP, labeled with four-colored fluorescent dyes emitting each different fluorescence depending on the evanescent light, and an enzyme for carrying out the nucleic acid extension reaction.

22. The single molecule real time sequencing method according to claim 17, characterized in that the evanescent light is generated by total reflected illumination of visible light having a wavelength range of 420 nm to 800 nm.

23. The single molecule real time sequencing method according to claim 17, characterized in that the UV light is one having a wavelength range of 250 nm to 400 nm.