CN103951724B - Specially modified nucleotide as well as application thereof in high-throughput sequencing - Google Patents
Specially modified nucleotide as well as application thereof in high-throughput sequencing Download PDFInfo
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Abstract
The invention discloses a specially modified nucleotide as well as an application thereof in high-throughput sequencing. A fluorescence marked group of the nucleotide and a nucleotide matrix are linked through a linker arm containing a vicinal diol bond; vicinal diol hydroxyl is oxidized by a strong oxidant, so that a single bond adjacent to carbon is broken off and a fluorescent group is chemically cut simply and effectively; the same template to be sequenced is subjected to sequencing reactions in two groups, each sequencing is finished by two nucleotide dNTPs cycles marked by two pairs of different fluorescences; in a mode that each nucleotide can only be used once in one cycle, a code composed of a nucleotide fragment is obtained by each sequencing reaction, and nucleotide sequence information composed of a group of codes is obtained after the first group of sequencing reaction is finished; then the second group of sequencing reaction is performed to obtain a plurality of code information ranked by the second group of sequencing reaction; the two groups of code information are encoded according to the sequencing order, and the two groups of encoded information are combined to form the specific base sequence of a nucleotide fragment to be sequenced.
Description
Technical field
The invention belongs to biological technical field, it is a kind of method realizing nucleotide sequence high throughput assay and in particular to one
Plant the nucleotide of special modification and its application in terms of high-flux sequence.
Background technology
DNA sequencing technology is the most frequently used technology in molecular biology research, and its appearance has greatly promoted biology
Development.Ripe DNA sequencing technology starts from 20 century 70 mid-terms.Maxam and Gilbert reports by changing within 1977
Learn the method that degraded measures DNA sequence.Contemporaneity, Sanger has invented dideoxy chain termination.Early 1990s go out
Existing fluorescence automated sequencing technology brings DNA sequencing the epoch of automatization's sequencing into.These technology are referred to as first generation DNA sequencing
Technology.The second filial generation DNA sequencing technology growing up recent years then so that DNA sequencing enter high flux, low cost when
Generation.High throughput sequencing technologies are that the revolution to conventional sequencing technology improves, once can be simultaneously to millions of or even thousand of
Article ten thousand, DNA sequence is sequenced, therefore also referred to as second filial generation sequencing technologies or sequencing technologies NGS of future generation, high flux simultaneously
Sequencing technologies also make the overall transcript profile to species and genome are comprehensively parsed into for possibility, so quilt again
Referred to as deep sequencing.The high throughput sequencing technologies of main flow mainly have Three Representss at present：454 sequencing technologies of Roche company,
The Solexa sequencing technologies of Illumina company and the SOLiD sequencing technologies of ABI company.
Three kinds of main flow microarray datasets have limited part, and the maximum advantage of 454 sequencing technologies is that longer reading is long, but
The cost of 454 sequencing technologies exceeds much than other several sequencing technologies, which has limited its application.The SOLiD of ABI company surveys
The accuracy of sequence technology is very high, but due to using connection method sequencing, the speed of its sequencing is all several than other with length
Sequencing technologies are inferior many.The Solexa sequencing technologies of Illumina company can be described as at present the whole world generally acknowledge flux
High, most widely used high throughput sequencing technologies.Solexa sequencing technologies employ the method being sequenced in synthesis, anti-in synthesis
Ying Zhong, adds the archaeal dna polymerase transformed and carries 4 kinds of fluorescently-labeled dNTP, after collection 4 color fluorescence, 3 ' end resistances are held back
Group is excised, and is reduced to hydroxyl, subsequently carries out second circulation, and the step repeating first circulation, until template sequence is whole
It is synthesized double-stranded DNA.Make only to extend a bit base every time because 3 ' end resistances hold back the protection of group, increased the time of sequencing,
And because 3 ' end resistances hold back the presence of group, it is very high for the requirement of polymerase, and the reading which also limits it is long, increase
Its cost.
《Two nucleotide simultaneously synthesizing DNA sequencing method》In propose a kind of simultaneously synthesizing coding of two nucleotide, decoding
The assay method of nucleotide sequence and its application, but because its nucleotide synthesis difficulty is higher, uncertainty is too big, does not have on the market
Ripe product.
Content of the invention
Goal of the invention：The problem existing for above-mentioned prior art, it is an object of the invention to provide a kind of special modification
Nucleotide and its application in terms of high-flux sequence.The present invention also with the principle of synthesis order-checking, using special modification
Nucleotide sequencing method realizes the high-flux sequence of nucleotide sequence, the invention provides a kind of new nucleoside chemically cutting
Acid, contributes to reducing sequencing cost, simplifies sequencing flow process and shorten the sequencing time.
Technical scheme：For achieving the above object, the present invention is achieved through the following technical solutions：A kind of nucleoside of special modification
Acid, the chemical structural formula of described nucleotide is as follows, and this nucleotide is closed by Firebird Biomelecular Sciences company
Become：
Wherein, n=1 or 2, R represents any one in dATP, dTTP, dCTP, dGTP, as n=1, obtains Cy3-
dNTP-diol-NH2Chemical structural formula, as n=2, obtain Cy5-dNTP-diol-NH2Chemical structural formula.
The fluorescence marker groups of above-mentioned nucleotide are to be connected by the linking arm containing vicinal diamines key with nucleotide parent, and
Vicinal diamines hydroxyl can be aoxidized by the strong oxidizer such as sodium metaperiodate or potassium permanganate so that the singly-bound of adjacent carbon disconnects, simply have
Realize chemical cleavage and fluorescence marker groups are excised away to effect.
Wherein, the specific chemical structural formula of the nucleotide dNTPs-diol-NH2 of special modification is as follows：
1st, Cy5-dATP-diol-NH2 chemical structural formula：
2nd, Cy5-dUTP-diol-NH2 chemical structural formula：
3rd, Cy5-dCTP-diol-NH2 chemical structural formula：
4th, Cy5-dGTP-diol-NH2 chemical structural formula：
5th, Cy3-dATP-diol-NH2 chemical structural formula
6th, Cy3-dUTP-diol-NH2 chemical structural formula
7th, Cy3-dCTP-diol-NH2 chemical structural formula
8th, Cy3-dGTP-diol-NH2 chemical structural formula
The present invention also protects a kind of application in terms of high-flux sequence for nucleotide of special modification.
The present invention also protects a kind of high-flux sequence method of the nucleotide of special modification, comprises the following steps：Core to be measured
Acid sequence is by the above-mentioned fluorescently-labeled nucleotide Cy3-dNTP-diol-NH of two kinds of differences2And Cy5-dNTP-diol-NH2According to
Certain combination is divided into two groups or more, and the sequencing that same determined nucleic acid sequence template is carried out with two groups or more is anti-
Should, every group of sequencing reaction is made up of two groups or more different fluorescently-labeled two kinds of nucleotide cycle above-mentioned, according to every kind of
Nucleotide only expendable mode in a cycle, often carry out that once sequencing reaction obtains being made up of nucleotide fragments one
Individual coding, obtains the nucleic acid sequence information being made up of one group of some coding after sequencing reaction；After the completion of this group sequencing reaction, make
Made with denaturing soln denatured double stranded, sequencing primer extended chain is removed, then sequencing by hybridization primer again, carry out the survey of later group
Sequence is reacted, and obtains some coding informations of later group sequencing reaction arrangement；Then pass through to decode some of two groups or more
Coding information, assembles the concrete base sequence of determined nucleic acid fragment.
Wherein, the different fluorescently-labeled nucleotide of above two refers to by (Cy3-dUTP-diol-NH2+Cy5-dCTP-
diol-NH2)、(Cy3-dGTP-diol-NH2+Cy5-dATP-diol-NH2)、(Cy5-dUP-diol-NH2+Cy3-dGTP-
diol-NH2)、(Cy3-dATP-diol-NH2+Cy5-dCTP-diol-NH2)、(Cy3-dUTP-diol-NH2+Cy5-dATP-
diol-NH2)、(Cy3-dCTP-diol-NH2+Cy5-dGTP-diol-NH2) arbitrary group of two kinds of nucleotide are simultaneously in six kinds of combinations
The synthesis order-checking reaction carrying out.
Wherein, the decoding of determined nucleic acid sequence is tactic some according to being sequenced by decoding two groups or more
Alkali yl coding sequence, assembles the concrete base sequence information of determined nucleic acid fragment.Wherein, the decoding of determined nucleic acid sequence is logical
Cross and decode two groups or more according to the tactic some alkali yl coding sequences that are sequenced, assemble the tool of determined nucleic acid fragment
Body base sequence information.The decoding of determined nucleic acid sequence is to be combined into, by each, one group of coding information that sequencing obtains, by dividing
Analysis fluorescence signal species and intensity, are converted to the information such as base sequence and number.The assembling of determined nucleic acid sequence is by comparing
Two groups or more synthesis order-checking obtains the information of clear and definite base sequence fragment, and the order according to sequencing is determined specifically
Base information, concrete coding/decoding method reference《Two nucleotide simultaneously synthesizing DNA sequencing method and its application》In.
Fluorescently-labeled nucleotide and common nucleotides are by 50：1 molar ratio carries out synthesis order-checking reaction, this
Ratio is more suitable for the extension of long sequence and the detection of fluorescence signal, can obtain species and the intensity letter of fluorescence by optical detection
Number.
A kind of high-flux sequence method of the nucleotide of special modification, concretely comprises the following steps：
A) sequencing template preparation：Using ultrasonic method, genes of interest group is broken into the base fragment of 100-500bp,
In the presence of ligase, DNA fragmentation two ends are added a pair of generic linker P1, P2；Then gel electrophoresiss cutting 180-220bp
DNA fragmentation purification, and carry out 8 circulation pre- amplifications obtain DNA fragmentation；Then by these pre- DNA fragmentations having expanded with
The magnetic bead of one of connexon complementary seriess carries out emulsion-based PCR reaction, obtains the Dan Ke of purposeful genomic DNA fragment in a large number
Grand magnetic bead, and degeneration obtains gene order-checking template, finally these is augmented with the monoclonal magnetic bead of genes of interest group DNA fragmentation
It is fixed on micro-fluidic chip；
B) sequencing primer hybridization：By primer hybridization complementary with energy and 3 ' end connexons for the template strand on monoclonal magnetic bead,
Hybridized primer is as the sequencing primer of template DNA；In order to ensure that each template all can occur synthetic reaction, we connect measuring
A known base sequence on son, and it is complementary to comprise it in first dinucleotide sequencing reaction in every group of sequencing reaction
Base, as known to connexon, base is A, all comprises labelling in the first time dinucleotide sequencing reaction in every group of sequencing reaction
dUTP-diol-NH2；
P1：5’-CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT-3’
3’-TTGGTGATGCGGAGGCGAAAGGAGAGATACCCGTCAGCCACTA-5’
P2：5’-CTGCCCCGGGTTCCTCATTCTCT-3’
3’-TTGACGGGGCCCAAGGAGTAAGAGA-5’
PCR Primer1：5’-CCACTACGCCTCCGCTTTCCTCTCTATG-3’
PCR Primer2：5’-CTGCCCCGGGTTCCTCATTCT-3’
PCR Primer1, PCR Primer2 obtain adopting in DNA fragmentation in the pre- amplification carrying out 8 circulations.
C) it is sequenced：By Cy3-dNTPs-diol-NH2And Cy5-dNTPs-diol-NH2Select any two groups of following manner
Or three groups be combined two nucleoside decoding cycle sequencings：As 1 group -1,1 group -2,2 group -1,2 group -2；Or 1 group -1,1 group -2,3 groups -
1st, 3 groups -2, or 1 groups -1,1 group -2,2 groups -1,2 groups -2,3 groups -1,3 groups -2；
1 group -1：Cy3-dUTP-diol-NH2+Cy5-dCTP-diol-NH2；
1 group -2：Cy3-dGTP-diol-NH2+Cy5-dATP-diol-NH2；
2 group -1：Cy5-dUTP-diol-NH2+Cy3-dGTP-diol-NH2；
2 group -2：Cy3-dATP-diol-NH2+Cy5-dCTP-diol-NH2；
3 group -1：Cy3-dUTP-diol-NH2+Cy5-dATP-diol-NH2；
3 group -2：Cy5-dGTP-diol-NH2+Cy3-dCTP-diol-NH2；
C1) in first group of sequencing reaction, it is first according to Cy3-dUTP-diol-NH2/ dTTP=50：1、Cy5-dCTP-
diol-NH2/ dCTP=50：Four kinds of nucleotide are added by 1 molar ratio, in l9 ° of N archaeal dna polymerase (New of 0.2U/ μ
England Biolabs company buy) in the presence of react 5 minutes, then with the X-100 of Trion containing 0.01%wt, 20%wt
The buffer 1 of glycerol washs, and finally becomes phase with CCD, obtains the fluorescent species of this sequencing reaction and the coding of strength information；
C2 the sodium metaperiodate of 50mM or potassium permanganate room temperature) is used by the sequencing primer in first group of sequencing reaction and its to survey
Sequence primer synthesis chain is processed 5 minutes, and oxidation vicinal diamines hydroxyl makes the singly-bound of adjacent carbon disconnect, and removes fluorophor；
C3) according to Cy3-dGTP-diol-NH2/ dGTP=50：1、Cy5-dATP-diol-NH2/ dATP=50：1 mole
Four kinds of nucleotide are added by ratio, react 5 minutes under the effect of l9 ° of N archaeal dna polymerase of 0.2U/ μ, then with containing 0.01%
The buffer 1 of wtTrion X-100,20%wt glycerol washs, and finally becomes phase with CCD, obtains the fluorescence kind of this sequencing reaction
Class and strength information；
C4 the sodium metaperiodate of 50mM or potassium permanganate room temperature treatment 5 minutes) are used, oxidation vicinal diamines hydroxyl is so that adjacent carbon
Singly-bound disconnects, and removes fluorophor；
C5) circulation step c1) c4) several times, the sequence information that nucleic acid fragment corresponding encoded needed for obtaining is constituted；
C6) processed 10 minutes at 65 DEG C with the buffer 2 of NaOH containing 0.005M and 65%wt Methanamide, by first group
Sequencing primer in sequencing reaction and its sequencing primer synthesis chain are removed, and retrieve single-stranded DNA templates, then draw with sequencing
Thing carries out hybridization, then changes the combination of nucleotide, according to above-mentioned c1)-c5) step by second group of nucleotide cycle
Sequencing, obtains the sequence information that second group of nucleic acid fragment coding is constituted；If the nucleotide cycle continuing to carry out the 3rd group is surveyed
Sequence；Carry out the 3rd group of nucleotide cycle sequencing and can improve sequencing accuracy rate；
D) according to the mode of the corresponding nucleic acid fragment of coding, respectively by first, second group and/or the 3rd group nucleoside of each template
The coding information of sour cycle sequencing is converted into base fragment information；
E) by comparing the base fragment information of first, second group and/or the 3rd group of each template, and combine the suitable of sequencing
Sequence, first, second group and/or the 3rd group of base fragment information of each template is assembled the concrete base of determined nucleic acid sequence
Information.
F) by the base sequence information of all templates, it is assembled into target gene group sequence respectively.
Table 1
Table 1 is a kind of nucleotide of special modification of the present invention and its application packet method pairing in terms of high-flux sequence
Become a kind of coded system of sequencing nucleic acid fragment.5 subcode T in tablenCmOr CnTm, work as n=2, during m=2, expression TTCC,
The set of CCTT, TCCT, CTTC, TCTC, CTCT all sequences, remaining is by that analogy.
Beneficial effect：The present invention utilizes a kind of nucleotide of special modification, by Firebird Biomelecular
Sciences company synthesizes, and technology maturation is reliable, and its fluorescence marker groups and nucleotide parent are by the company containing vicinal diamines key
Connect arm to connect, directly can aoxidize vicinal diamines hydroxyl using strong oxidizers such as sodium metaperiodate or potassium permanganate so that the list of adjacent carbon
Key disconnects, and simpler be effectively realized chemical cleavage and excise fluorescence marker groups, such that it is able in high-flux sequence
Application.The nucleotide sequencing method of this special modification uses decoding sequence measurement, using the principle being sequenced in synthesis,
Rather than connect sequencing principle, primary first-order equation two kinds of nucleotide of addition, and realize the chemical cleavage of fluorophor, simpler
Easy, efficiency high, low cost.Will be by fluorescently-labeled nucleotide dNTPs-diol-NH2According to certain combination, it is divided into two groups
Or more than two two groups or more carried out to same sequence template to be measured carry out sequencing reaction, every time sequencing by two to difference
Fluorescently-labeled two kinds of nucleotide dNTPs circulation composition, according to every kind of nucleotide only expendable mode in a cycle,
Often carry out once sequencing reaction to obtain being made up of a coding nucleotide fragments, obtain after some secondary responses by one group of some coding
The nucleic acid sequence information constituting；After the completion of this group sequencing reaction, made using denaturing soln denatured double stranded, sequencing primer is extended
Chain is removed, then sequencing by hybridization primer again, carries out second group of sequencing reaction, obtains some volumes of second group of sequencing reaction arrangement
Code information；The 3rd group of sequencing reaction can be carried out if necessary to improve sequencing accuracy rate；Finally by compare each template first,
The base fragment information of second, third group, and combine the order of sequencing to decode two groups or more coding information, assemble
Go out the concrete base sequence of determined nucleic acid fragment.
Specific embodiment
The present invention is described in further detail with reference to embodiments.
Embodiment 1：The nucleotide coding sequencing of the special modification of a number genome of Yan Di and Huang Di, two legendary rulers of remote antiquity
1st, full-length genome template preparation：Using ultrasonic method, genes of interest group is broken into the base piece of 100-500bp
Section, generic linker P1, the P2 in the presence of ligase, DNA fragmentation two ends being had already known plus a pair of sequences；Then coagulate
Gel electrophoresis cutting 180-220bp DNA fragmentation purification, and carry out the pre- amplification of 8 circulations；Then these pre- have been expanded
DNA fragmentation carries out emulsion-based PCR reaction with the magnetic bead being fixed with one of connexon complementary seriess, is grown purposeful base in a large number
Because organizing the monoclonal magnetic bead of DNA fragmentation, and degeneration obtains gene order-checking template, finally these is augmented with fragmentation DNA mould
The magnetic bead of plate is fixed on micro-fluidic chip.
2nd, sequencing primer hybridization：By primer hybridization complementary with energy and 3 ' end connexons for the template strand on monoclonal magnetic bead,
As the sequencing primer of template DNA, (in order to ensure that each template all can occur synthetic reaction, we connect measuring hybridized primer
A known base sequence on son, and it is complementary to comprise it in first dinucleotide sequencing reaction in every group of sequencing reaction
Base, as known to connexon, base is A, all comprises labelling in the first time dinucleotide sequencing reaction in every group of sequencing reaction
dUTP-diol-NH2).
3rd, by Cy3-dNTPs-diol-NH2And Cy5-dNTPs-diol-NH2Mode according to table 2 carries out two kinds of nucleotide
Simultaneously synthesizing cycle sequencing：
Table 2
1), in first group of sequencing reaction, it is first according to Cy3-dUTP-diol-NH2/ dTTP=50：1(1μM∶0.02μ
M)、Cy5-dCTP-diol-NH2/ dCTP=50：Two kinds of nucleotide are added by the molar ratio of 1 (1 μm of M: 0.02 μm of M),
React 5 minutes in the presence of l9 ° of N archaeal dna polymerase of 0.2U/ μ, then with the X-100 of Trion containing 0.01%wt, 20%wt glycerol
Buffer 1 wash, finally become phase with CCD, obtain the coding of the fluorescent species of this sequencing reaction and strength information (wherein
Cy3 represents that base T, Cy5 represents base C, and fluorescence intensity is finally by the sequencing intensity comparing different number of times in same template
It is finally translated into base number).
2) use the sodium metaperiodate room temperature treatment 5 minutes of 50mM, oxidation vicinal diamines hydroxyl is so that the singly-bound of adjacent carbon disconnects, clearly
Except fluorophor；
3) according to Cy3-dGTP-diol-NH2/ dGTP=50：1(1μM∶0.02μM)、Cy5-dATP-diol-NH2/dATP
=50：Four kinds of nucleotide are added by the molar ratio of 1 (1 μM: 0.02 μM), react under l9 ° of N archaeal dna polymerase effect of 0.2U/ μ
5 minutes, then washed with the buffer 1 of the X-100 of Trion containing 0.01%wt, 20%wt glycerol, finally become phase with CCD, obtain
(wherein Cy3 represents that bases G, Cy5 represent base A, and fluorescence intensity is last for the fluorescent species of this sequencing reaction and strength information
Base number is finally translated into by the sequencing intensity comparing different number of times in same template, for example：Analysis draws a base
Baseline fluorescence intensity be 8000, the baseline fluorescence intensity of two bases is 12000, according to fluorescence intensity level draw base
Number)；
4) use the sodium metaperiodate room temperature treatment 5 minutes of 50mM, oxidation vicinal diamines hydroxyl is so that the singly-bound of adjacent carbon disconnects, clearly
Except fluorophor；
5) circulation step 1)～4) several times, such as carry out the simultaneously synthesizing cycle sequencing of 40 two nucleotide, then at least can obtain
The sequence information constituting to 40 nucleic acid fragment corresponding encoded.
6) processed 10 minutes at 65 DEG C with the buffer 2 of NaOH containing 0.005M and 65%wt Methanamide, first group is surveyed
Sequencing primer in sequence reaction and its sequencing primer synthesis chain are removed, and retrieve single-stranded DNA templates；
7) then change nucleotide combination, according to above-mentioned 1) -5) step second group of nucleotide cycle is sequenced, obtain
The sequence information that second group of nucleic acid fragment coding is constituted；
8) according to the mode of the corresponding nucleic acid fragment of coding, respectively by the first, second group of nucleotide cycle sequencing of each template
Coding information be converted into base fragment information；
9) by comparing the base fragment information of first, second group of each template, and combine the order being sequenced, by each mould
The base fragment information of first, second group of plate assembles the concrete base information of determined nucleic acid sequence.
By the base sequence information of all templates, it is assembled into number genome sequence of Yan Di and Huang Di, two legendary rulers of remote antiquity respectively.
Embodiment 2：The nucleotide coding sequencing of the special modification of saccharomyces cerevisiae genome
1st, full-length genome template preparation：Using ultrasonic method, saccharomyces cerevisiae genome is broken into the alkali of 100-500bp
Substrate section, generic linker P1, the P2 in the presence of ligase, DNA fragmentation two ends being had already known plus a pair of sequences；So
Gel electrophoresiss cutting 180-220bp DNA fragmentation purification afterwards, and carry out the pre- amplification of 8 circulations；Then by these pre- amplifications
Good DNA fragmentation carries out emulsion-based PCR reaction with the magnetic bead being fixed with one of connexon complementary seriess, and being grown in a large number has mesh
Genomic DNA fragment monoclonal magnetic bead, and degeneration obtains gene order-checking template, finally these is augmented with fragmentation
The magnetic bead of DNA profiling is fixed on micro-fluidic chip.
2nd, sequencing primer hybridization：By primer hybridization complementary with energy and 3 ' end connexons for the template strand on monoclonal magnetic bead,
As the sequencing primer of template DNA, (in order to ensure that each template all can occur synthetic reaction, we connect measuring hybridized primer
A known base sequence on son, and it is complementary to comprise it in first dinucleotide sequencing reaction in every group of sequencing reaction
Base, as known to connexon, base is A, all comprises labelling in the first time dinucleotide sequencing reaction in every group of sequencing reaction
dUTP-diol-NH2).
3rd, by Cy3-dNTPs-diol-NH2And Cy5-dNTPs-diol-NH2Mode according to table 3 carries out two kinds of nucleotide
Simultaneously synthesizing cycle sequencing：
Table 3
1), in first group of sequencing reaction, it is first according to Cy3-dUTP-diol-NH2/ dTTP=50：1(1μM∶0.02μ
M)、Cy5-dCTP-diol-NH2/ dCTP=50：Two kinds of nucleotide are added by the molar ratio of 1 (1 μm of M: 0.02 μm of M),
React 5 minutes in the presence of l9 ° of N archaeal dna polymerase of 0.2U/ μ, then with the X-100 of Trion containing 0.01%wt, 20%wt glycerol
Buffer 1 wash, finally become phase with CCD, obtain the coding of the fluorescent species of this sequencing reaction and strength information (wherein
Cy3 represents that base T, Cy5 represents base C, and fluorescence intensity is finally by the sequencing intensity comparing different number of times in same template
It is finally translated into base number, for example：Analysis show that the baseline fluorescence intensity of a base is 8000, and the benchmark of two bases is glimmering
Light intensity is 12000, draws the number of base according to fluorescence intensity level).
2) use the potassium permanganate room temperature treatment 5 minutes of 50mM, oxidation vicinal diamines hydroxyl is so that the singly-bound of adjacent carbon disconnects, clearly
Except fluorophor；
3) according to Cy3-dGTP-diol-NH2/ dGTP=50：1(1μM∶0.02μM)、Cy5-dATP-diol-NH2/dATP
=50：Four kinds of nucleotide are added by the molar ratio of 1 (1 μM: 0.02 μM), react under l9 ° of N archaeal dna polymerase effect of 0.2U/ μ
5 minutes, then washed with the buffer 1 of the X-100 of Trion containing 0.01%wt, 20%wt glycerol, finally become phase with CCD, obtain
(wherein Cy3 represents that bases G, Cy5 represent base A, and fluorescence intensity is last for the fluorescent species of this sequencing reaction and strength information
Base number is finally translated into by the sequencing intensity comparing different number of times in same template)；
4) use the potassium permanganate room temperature treatment 5 minutes of 50mM, oxidation vicinal diamines hydroxyl is so that the singly-bound of adjacent carbon disconnects, clearly
Except fluorophor；
5) circulation step 1)～4) several times, such as carry out the simultaneously synthesizing cycle sequencing of 40 two nucleotide, then at least can obtain
The sequence information constituting to 40 nucleic acid fragment corresponding encoded.
6) processed 10 minutes at 65 DEG C with the buffer 2 of NaOH containing 0.005M and 65%wt Methanamide, first group is surveyed
Sequencing primer in sequence reaction and its sequencing primer synthesis chain are removed, and retrieve single-stranded DNA templates；
7) then change nucleotide combination, according to above-mentioned 1) -5) step second group of nucleotide cycle is sequenced, obtain
The sequence information that second group of nucleic acid fragment coding is constituted, in order to improve sequencing accuracy rate, carries out the 3rd group according to the method described above
Nucleotide cycle is sequenced；
8) according to the mode of the corresponding nucleic acid fragment of coding, respectively by first, second, third group of nucleotide cycle of each template
The coding information of sequencing is converted into base fragment information；
9) by comparing the base fragment information of first, second, third group of each template, and combine the order being sequenced, will
The base fragment information of first, second, third group of each template assembles the concrete base information of determined nucleic acid sequence.
By the base sequence information of all templates, it is assembled into saccharomyces cerevisiae genome sequence respectively.
Claims (3)
1. a kind of high-flux sequence method of the nucleotide using special modification, the chemical structural formula of the nucleotide of this special modification
As follows：
Wherein, n=1 or 2, R represents any one in dATP, dTTP, dCTP, dGTP, as n=1, obtains Cy3 dNTP
diol‐NH2Chemical structural formula, as n=2, obtain Cy5 dNTP diol NH2Chemical structural formula it is characterised in that profit
Comprised the following steps with the high-flux sequence method of the nucleotide of this special modification：Determined nucleic acid sequence is by two kinds of different fluorescence marks
The nucleotide Cy3 dNTP diol NH of note2With Cy5 dNTP diol NH2According to certain combination be divided into two groups or two groups with
On, same determined nucleic acid sequence template is carried out with two groups or more sequencing reaction, every group of sequencing reaction is by above-mentioned two groups
Or difference more than two fluorescently-labeled two kinds of nucleotide cycle composition, according to every kind of nucleotide in a cycle only using one
Secondary mode, often carries out the coding that once sequencing reaction obtains being made up of nucleotide fragments, obtains by one after sequencing reaction
The nucleic acid sequence information that some codings of group are constituted；After the completion of this group sequencing reaction, made using denaturing soln denatured double stranded, will survey
Sequence primer extension chain is removed, then sequencing by hybridization primer again, carries out the sequencing reaction of later group, obtains later group sequencing reaction
Some coding informations of arrangement；Then pass through to decode two groups or more some coding informations, assemble determined nucleic acid piece
The concrete base sequence of section；
The concretely comprising the following steps of this sequencing：
A) sequencing template preparation：Using ultrasonic method, genes of interest group is broken into the base fragment of 100 500bp, is connecting
In the presence of enzyme, DNA fragmentation two ends are added a pair of generic linker P1, P2；Then gel electrophoresiss cut 180 220bp DNA
Fragment purification, and carry out 8 circulation pre- amplifications obtain DNA fragmentation；Then by these pre- DNA fragmentations having expanded with wherein
The magnetic bead of one connexon complementary series carries out emulsion-based PCR reaction, obtains the monoclonal magnetic of purposeful genomic DNA fragment in a large number
Pearl, and degeneration obtains gene order-checking template, finally fixes these monoclonal magnetic beads being augmented with genes of interest group DNA fragmentation
On micro-fluidic chip；
B) sequencing primer hybridization：By primer hybridization complementary with energy and 3 ' end connexons for the template strand on monoclonal magnetic bead, hybridization
Primer is as the sequencing primer of template DNA；
C) it is sequenced：By Cy3 dNTPs diol NH2With Cy5 dNTPs diol NH2Select any two groups or three of following manner
Group is combined two nucleoside decoding cycle sequencings：
1 group 1：Cy3‐dUTP‐diol‐NH2+Cy5‐dCTP‐diol‐NH2；
1 group 2：Cy3‐dGTP‐diol‐NH2+Cy5‐dATP‐diol‐NH2；
2 group 1：Cy5‐dUTP‐diol‐NH2+Cy3‐dGTP‐diol‐NH2；
2 group 2：Cy3‐dATP‐diol‐NH2+Cy5‐dCTP‐diol‐NH2；
3 group 1：Cy3‐dUTP‐diol‐NH2+Cy5‐dATP‐diol‐NH2；
3 group 2：Cy5‐dGTP‐diol‐NH2+Cy3‐dCTP‐diol‐NH2；
C1) in first group of sequencing reaction, it is first according to Cy3 dUTP diol NH2/ dTTP=50：1、Cy5‐dCTP‐diol‐
NH2/ dCTP=50：Four kinds of nucleotide are added by 1 molar ratio, react 5 in the presence of 9 ° of N archaeal dna polymerases of 0.2U/ μ l
Minute, then washed with the buffer 1 of the X of Trion containing 0.01%wt 100,20%wt glycerol, finally become phase with CCD, obtain
This time fluorescent species of sequencing reaction and the coding of strength information；
C2) with the sodium metaperiodate or potassium permanganate room temperature of 50mM, the sequencing primer in first group of sequencing reaction and its sequencing are drawn
Thing synthesis chain is processed 5 minutes, and oxidation vicinal diamines hydroxyl makes the singly-bound of adjacent carbon disconnect, and removes fluorophor；
C3) according to Cy3 dGTP diol NH2/ dGTP=50：1、Cy5‐dATP‐diol‐NH2/ dATP=50：1 molar ratio
Four kinds of nucleotide are added, reacts 5 minutes under 9 ° of N archaeal dna polymerase effects of 0.2U/ μ l, then with containing 0.01%wt
Trion X 100, the buffer 1 of 20%wt glycerol wash, and finally become phase with CCD, obtain the fluorescent species of this sequencing reaction
And strength information；
C4 the sodium metaperiodate of 50mM or potassium permanganate room temperature treatment 5 minutes) are used, oxidation vicinal diamines hydroxyl is so that the singly-bound of adjacent carbon
Disconnect, remove fluorophor；
C5) circulation step c1) c4) several times, the sequence information that nucleic acid fragment corresponding encoded needed for obtaining is constituted；
C6) processed 10 minutes at 65 DEG C with the buffer 2 of NaOH containing 0.005M and 65%wt Methanamide, first group is sequenced
Sequencing primer in reaction and its sequencing primer synthesis chain are removed, and retrieve single-stranded DNA templates, then enter with sequencing primer
Row hybridization, then changes the combination of nucleotide, according to above-mentioned c1)-c5) step second group of nucleotide cycle is surveyed
Sequence, obtains the sequence information that second group of nucleic acid fragment coding is constituted；If continuing to carry out the 3rd group of nucleotide cycle sequencing；
D) according to the mode of the corresponding nucleic acid fragment of coding, respectively first, second group and/or the 3rd group nucleotide of each template is followed
The coding information of ring sequencing is converted into base fragment information；
E) by comparing the base fragment information of first, second group and/or the 3rd group of each template, and combine the order being sequenced,
First, second group and/or the 3rd group of base fragment information of each template is assembled the concrete base letter of determined nucleic acid sequence
Breath；
F) by the base sequence information of all templates, it is assembled into target gene group sequence respectively.
2. a kind of high-flux sequence method of the nucleotide of special modification according to claim 1 is it is characterised in that described
The fluorescently-labeled nucleotide of two kinds of differences refers to by (Cy3 dUTP diol NH2+Cy5‐dCTP‐diol‐NH2)、(Cy3‐dGTP‐
diol‐NH2+Cy5‐dATP‐diol‐NH2)、(Cy5‐dUP‐diol‐NH2+Cy3‐dGTP‐diol‐NH2)、(Cy3‐dATP‐
diol‐NH2+Cy5‐dCTP‐diol‐NH2)、(Cy3‐dUTP‐diol‐NH2+Cy5‐dATP‐diol‐NH2)、(Cy3‐dCTP‐
diol‐NH2+Cy5‐dGTP‐diol‐NH2) arbitrary group of two kinds of nucleotide are carried out simultaneously in six kinds of combinations synthesis order-checking reaction.
3. a kind of high-flux sequence method of the nucleotide of special modification according to claim 1 is it is characterised in that to be measured
The decoding of nucleotide sequence is by decoding two groups or more according to the tactic some alkali yl coding sequences that are sequenced, assembling
Go out the concrete base sequence information of determined nucleic acid fragment.
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| CN102329884A (en) * | 2011-10-20 | 2012-01-25 | 东南大学 | Synchronous synthesis and DNA sequencing method for two nucleotides and application thereof |
| CN102634586A (en) * | 2012-04-27 | 2012-08-15 | 东南大学 | Decoding and sequencing method by real-time synthesis of two nucleotides into deoxyribonucleic acid (DNA) |
| CN102971335A (en) * | 2009-03-23 | 2013-03-13 | 史蒂芬·阿尔伯特·本纳 | Reagents for reversibly terminating primer extension |
| WO2013173844A1 (en) * | 2012-05-18 | 2013-11-21 | Pacific Biosciences Of California, Inc. | Heteroarylcyanine dyes |
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| CN102971335A (en) * | 2009-03-23 | 2013-03-13 | 史蒂芬·阿尔伯特·本纳 | Reagents for reversibly terminating primer extension |
| CN102329884A (en) * | 2011-10-20 | 2012-01-25 | 东南大学 | Synchronous synthesis and DNA sequencing method for two nucleotides and application thereof |
| CN102634586A (en) * | 2012-04-27 | 2012-08-15 | 东南大学 | Decoding and sequencing method by real-time synthesis of two nucleotides into deoxyribonucleic acid (DNA) |
| WO2013173844A1 (en) * | 2012-05-18 | 2013-11-21 | Pacific Biosciences Of California, Inc. | Heteroarylcyanine dyes |
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