Patent Application
20110105358
The present invention relates to an analysis method for a nucleic acid sequence and an analyzer of the nucleic acid sequence. More specifically, the present invention relates to a method and a device to decode a base sequence of, for example, a nucleic acid such as DNA or RNA.
A human genome plan, where 3 billion dollars of budget has been spent from 1990 to 2005, enabled to read a part easiest to decode (93% of the whole parts) 2 to 3 years earlier than originally planned, and has left, as a property, a technology or a method required in decoding, as shown in the Non Patent Literature 1. Such technology has shown further improvement thereafter, and at present, genome decoding becomes possible in precision practically endurable in a cost of about 20 million dollars ($2×107). Decoding of a large scale base sequence in this high cost is still limited only by a special decoding center, or a research project obtained a high amount of budget. However, cost reduction in sequence determination will enable to handle much larger quantity of genome by many parties. For example, it becomes possible to compare genomes of a patient and a healthy person, and as a result, enhancement of value of genome information is expected. As shown in the Non Patent Literature 2, acquisition of such a fundamental data is expected to largely contribute to development of personalized medical treatment in the future.
Under such circumstances, two programs for “Innovative genome sequence determination technology”, under financial support by The National Institutes of Health (NIH), aim at human genome decoding by 100 thousand dollars ($1×105) for one person till 2009, and by thousand dollars ($1×103) till 2014, namely, development of what is called “thousand dollars genome” decoding technology.
As shown in the Non Patent Literature 3, there have been commercialized already several next generation sequencers. These technologies have already attained 1/10 to 1/100 level cost as compared with conventional technology. In addition, number of bases measurable by one time analysis has attained an order of 109. However, enhancement of these sequencers in view of cost has nearly saturated, and it is estimated that attainment of the “thousand dollars genome” by a device and a system already commercialized is difficult.
In addition, the next generation sequencers now available on the market are capable of decoding a base sequence of up to about 109, however, they require running time of 2 to 3 days only for sequence decoding of a data volume as large as about 109. In a practical medical field, for genome sequence decoding on an individual basis to be a routine work, not only cost reduction but also high speed sequence decoding are necessary.
One promising sequence technology, expected under these circumstances, is a single molecule real time sequencing method, namely, a method for measuring by real time directly in a single molecule level, at a field of an enzyme reaction. The single molecule real time sequencing method carries out fluorescence detection in real time where base extension is carried out. Therefore, it is capable of carrying out base sequence decoding in dramatically high speed. In addition, in the single molecule real time sequencing method, amplification of a sample by PCR is not required, and thus dramatic cost reduction is also possible. Therefore, the single molecule real time sequencing method is one of the most promising technologies for attaining the “thousand dollars genome”.
The Non Patent Literature 4 has disclosed one of the single molecule real time sequencing methods. In this Literature, a measurement method is adopted for energy fluorescence transfer to acceptor-nucleotide accompanying with the extension reaction of nucleic acid, by immobilization of polymerase modified with a donor fluorescence body on a substrate.
In addition, as technology for controlling various biological processes proceeding in a cell, and analyzing it in real time, a caged compound can be included. The caged compound is a generic term for one that modifies a biologically active molecule by a photodegradable protecting group to deactivate temporarily. It has a name of the “caged compound” to mean a molecule to have biological activity slept by putting it in a cage. By irradiation of light with an optimal wavelength for the compound onto the caged compound, the protecting group is dislocated only at the site irradiated in an instant of light irradiation, resulting in expression of original biological activity. That is, it becomes possible to control temporal and spatial dynamics of a chemical reaction by irradiation of light. In the Patent Literatures 1 and 2, the caged compound is used to prepare a pool of oligo nucleotides. However, this method uses a sequential reaction, and is a method for sequentially decomposing the caged compound bound to the terminal, accompanying with the reaction. Therefore, this method is not used for real time analysis. In addition, a target of this method is multi-molecules and not a single molecule.
As a problem of the single molecule real time sequencing method, control of initiation of the extension reaction is included. In general, in the extension reaction, fluorescence from a single molecule immobilized on a substrate is detected with a CCD camera through an objective lens. However, because the objective lens has limited observable view, it cannot observe the whole surface of substrate at one time. On the other hand, in a real time reaction, the extension reaction is initiated with pouring a reaction solution. Therefore, it is necessary to initiate the extension reaction only at the substrate area observable with the objective lens, and establish a reaction system where the reaction does not proceed at other areas. In order to attain this, it is considered a method for dividing a flow cell to a plurality of reaction fields, and sending a liquid to these reaction fields independently or sequentially. However, decoding of human genome requires several-hundred or more reaction fields, and thus preparation of complicated channels. In addition, to correctly send a liquid to a plurality of the reaction fields independently or sequentially, plural units of high performance pumps are required. Furthermore, to stably send the liquid to a plurality of the reaction fields independently or sequentially is predicted to be extremely difficult due to generation problems of pressure loss, air bubbles, contamination causing measurement noise and the like. Still more, the complicated channels and a plurality of pumps have drawback of increasing cost. Accordingly, it has been required a methodology for initiating the extension reaction only at a desired area in the substrate, without preparing the complicated channels.
An object of the present invention relates to selectively control the extension reaction in a desired area in the substrate.
The present invention immobilizes an oligo probe arranged with a caged compound at the terminal thereof 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 dissociate the photodegradation-active protecting group at the terminal of the oligo probe that has been immobilized in said reaction field area to control initiation of a polymerase extension reaction selectively. In the flow cell, a plural number of the reaction field areas are arranged at constant interval on the substrate. The flow cell immobilized in 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.
According to the present invention, a real time base extension reaction can be measured without using a flow cell configured by complicated channels and a liquid sending mechanism. In addition, because a simple channel system can be adopted, problems such as generation of air bubbles, and liquid leakage in the channels accompanying with sending the liquid can be prevented beforehand, and also preparation cost of the flow cell can be reduced.
An Embodiment discloses a single molecule real time sequencer having: 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 the evanescent light to the desired reaction field area and detecting the fluorescence generated; and a reaction control optical system for irradiating the light to decompose the photodegradable substance to the desired reaction field area.
In addition, an Embodiment discloses a nucleic acid analyzer having: 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 the nucleic acid probes that hybridize with different target nucleic acids, and 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 the fluorescence generated; a reaction control optical system for irradiating 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.
In addition, an Embodiment discloses a single molecule real time sequencing method comprising: to prepare 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; to supply a target nucleic acid and a reagent to be utilized in the nucleic acid extension reaction, in the channel; to irradiate UV light to decompose the photodegradable substance to the desired reaction field area, to irradiate evanescent light to the desired reaction field area, and to detect fluorescence generated; to move relatively the channel to the reaction control optical system for irradiating the UV light, and the excited optical system generating evanescent light; to irradiate UV light to decompose the photodegradable substance to the different reaction field areas, to irradiate evanescent light to the different reaction field area, and to detect fluorescence generated.
In addition, an Embodiment discloses one where the photodegradable substance is a photodegradable protecting group modified at the terminal of the nucleic acid probe.
In addition, an Embodiment discloses one where the photodegradable protecting group is a 2-nitrobenzyl type, a decyl-phenacyl type or a coumarinylmethyl type.
In addition, an Embodiment discloses one where a metal structure that generates a fluorescence increasing field is arranged in the reaction area field, corresponding to each of the nucleic acid probes.
In addition, an Embodiment discloses one where the reagent contains 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.
In addition, an Embodiment discloses one where 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.
In addition, an Embodiment discloses one where the reaction control optical system irradiates UV light having a wavelength range of 250 nm to 400 nm.
In addition, an Embodiment discloses one where, 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.
In addition, an Embodiment discloses a reaction control device having a single molecule as a measurement target, a metal structure for retaining the single molecule, an area regularly arranged with the metal structure, a channel regularly arranged with the area, a substrate arranged with one or more channels, a reaction solution containing a chemical substance interacting with the single molecule, a photodegradable substance inhibiting a chemical reaction between the single molecule and the chemical substance in the reaction solution, a unit for removing the inhibition of the photodegradable substance to locally initiate the interaction between the single molecule and the reaction solution, a unit for transferring the substrate, and a unit for supplying the reaction solution to the channel.
In addition, an Embodiment discloses one where the single molecule is DNA or RNA, retention of the single molecule is one by hybridization with a complementary strand of the single molecule immobilized at the metal structure, the photodegradable substance is the photodegradable protecting group modified at the terminal of the complementary strand, a unit for removing inhibition of the photodegradable protecting group is one by irradiation of light, a chemical substance contained in the reaction solution is polymerase that is an enzyme for carrying out the extension reaction of four deoxynucleotides, dATP, dCTP, dTTP and dGTP, labeled with four-colored fluorescent dyes emitting each different fluorescence, and nucleic acid.
In addition, an Embodiment discloses one where a unit for measuring the extension reaction of the nucleic acid is fluorescence measurement by total reflected illumination using visible light having a wavelength range of 420 nm to 800 nm, characterized in that size of the metal structure is smaller than wavelength of the visible light, and one for enhancing electric field intensity at the vicinity of the metal structure, and enhancing fluorescence from the fluorescent dye, by generation of surface Plasmon resonance by irradiation of visible light onto the metal structure.
In addition, an Embodiment discloses one where the unit for removing inhibition of the photodegradable protecting group uses UV light having a wavelength range of 250 nm to 400 nm, and one having a unit for selectively irradiating the UV light only to an area regularly arranged with the structure.
In addition, an Embodiment discloses one where the unit for transferring the substrate by a distance equal to the interval between the adjacent areas, after completion of the extension reaction by selectively irradiating UV light only to the area regularly arranged with the structure, is by an XY stage, and one having a unit for continuously measuring the extension reaction at the area, and a unit for auto-focusing to a fluorescent molecule of the substrate.
In addition, an Embodiment discloses one where the above photodegradable substance is a photodegradable protecting group, and the protecting group is a 2-nitrobenzyl type, a decyl-phenacyl type or a coumarinylmethyl type.
In addition, an Embodiment discloses one where a sequence of the complementary strand immobilized at the metal structure is a polyT sequence that captures mRNA.
In addition, an Embodiment discloses one where the unit for carrying out the fluorescence detection is configured by an objective lens, a notch filter, a dichroic mirror, a bandpass filter, a condensing lens, and a CCD camera.
In addition, an Embodiment discloses one where the total reflected illumination is configured by a plurality of lasers, a mirror, an ND filter, λ/4 wavelength plate, a shutter, a condensing lens, a prism, and coupling oil.
In addition, an Embodiment discloses one where a unit for supplying the reaction solution to the channel is configured by a dispensing unit, a waste liquid tank and a scepter of the substrate.
In addition, an Embodiment discloses one where the deoxynucleotide is Alexa488-dCTP, Cy3-dATP, Cy5-dCTP and Cy5.5-dCTP.
Explanation will be given below on the above and other features and effects of the novel invention, with reference to drawings. It should be noted that, the drawings are only for understanding the present invention, and not for limiting a right of the right.
Explanation will be given below on a flow cell arranged with a plurality of reaction fields in one channel, as one Embodiment of the present invention, with reference to
A substrate 107 of
As the gold structure 108 to enhance fluorescence, there are present a pyramid shape, a shape where an insulating film is sandwiched between the two gold structured bodies (a laminated layer shape), a shape arranged with two triangle poles, like a bow tie, or the like. In the case of the pyramid shape, an oligo probe is arranged at the tip part thereof or the like. In the case of the laminated layer shape, the oligo probe is arranged in the insulating film or the like. In the case of the shape arranged with the two triangle poles, the oligo probe is arranged in the space sandwiched. In addition, as the metal body which is capable of generating localized-type surface Plasmon, gold, silver, platinum, aluminum and copper or the like is known, and as a material of the gold structure 108, in addition to gold, these metals may be used as well.
It should be noted that, as for phenomenon of fluorescence enhancement by surface Plasmon, one using an island structure of nanometer-order silver, as reported in Anal. Chem. Vol. 78, 6238-6245 (Non Patent Literature 5), or one using a gold spherical fine particle with a diameter of several-ten nanometer, as reported in Nanotechnology, 2007, vol. 18, pp 44017-44021 (Non Patent Literature 6), is known. It has been shown in Nano Letters. 2004, vol. 4, 957-961 (Non Patent Literature 7), that when the triangle poles come close, strong localized-type surface Plasmon generates in a space therebetween. In the present specification, these Literatures are incorporated as a part of the specification.
Explanation will be given next on control of a real time base extension reaction using UV light 209, with reference to
Inside the reaction fields 201, 202, 203 and 204, as already explained in
Explanation will be given on chemical structure of the above-described oligo probe, with reference to
In the present Embodiment, explanation was given on sequence analysis of mRNA, as an Embodiment, and to attain selective hybridization with a polyA part present at the 3′ terminal of mRNA, a base sequence of the oligo probe 301 in the present Embodiment takes a polyT sequence.
In addition, the 3′ terminal of the oligo probe 301 is modified with the photodegradative protecting group. Although various photodegradative protecting groups have been reported up to now, in the present Embodiment, a 2-nitrobenzyl type, as a typical photodegradative protecting group, was used. Optimal wavelength to activate a 2-nitrobenzyl type compound of the present Embodiment is 260 nm. After UV light irradiation, the photodegradative protecting group is deprotected, and the oligo probe 301 is converted to a molecular structure of an oligo probe 303. In the oligo probe 303, where the photodegradative protecting group is deprotected, because a substance inhibiting the extension reaction has already been dissociated, the extension reaction proceeds where the fluorescent labeled nucleotide floating in a solution is incorporated by a polymerase, occurs. By this mechanism, control of the extension reaction by light irradiation can be carried out.
Explanation will be given below on a nucleic acid analyzer suitable for the above-described extension reaction technology, with reference to
It should be noted that, in the above Embodiment, the fluorescent dye is excited using total reflected illumination, however, the fluorescent dye may be excited by installing a nano-opening smaller than wavelength of excited light at the flow cell substrate, and using evanescent light generated by irradiation of the excited light to the opening.
Control of the extension reaction is carried out by the control PC 426. The control PC 426 releases a shutter 445 of a UV laser 444. UV light illuminates a bottom surface of a substrate 432 via the same light pass as the above-described evanescent illumination. In the present Embodiment, the same optical system is used for irradiation of the UV laser 444 and excitation of the fluorescent dye. However, a illumination method itself of the UV laser is not especially limited to evanescent illumination, and it may also be an often used epi-illumination method or an oblique illumination method.
Accompanied by irradiation of UV laser, as already explained, the photo-protecting group dissociates and the extension reaction of nucleic acid proceeds automatically. When the extension reaction at a certain reaction field is completed, the control PC drives a servomotor 433 for driving the XY stage to transfer the next reaction field within a view of an objective lens 412. Still more, the control PC drives an auto focus device 427 under scattering light of the gold structure to focus on a fluorescent molecule at a flow cell wall surface. By repeating this operation, it becomes possible to repeat measurement of the real time base extension reaction sequentially, on 200 reaction fields arranged in the flow cell. In addition, it is possible to prepare a plurality of channels inside the substrate 432, and independently dispense the reaction solution for each channel using a dispensing unit 428. In addition, a waste liquid is accumulated in a waste liquid tank 429 through a scepter 431. In addition, in order to stabilize the real time base extension reaction, a temperature adjustment unit 450 is added.
It should be noted that, in the above-described Embodiment, a desired reaction field is arranged at an area irradiated with excited light, or an area irradiated with UV light, by stage drive, however, only the desired reaction field may be irradiated with the excited light or the UV light, without transferring the stage but by controlling an optical system.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2008-162667 | Jun 2008 | JP | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/JP2009/060808 | 6/8/2009 | WO | 00 | 12/23/2010 |
