CN1272551A

CN1272551A - Method for determining DNA sequence

Info

Publication number: CN1272551A
Application number: CN 00115385
Authority: CN
Inventors: 王庆康; 刘建华; 林志新; 刘燕刚
Original assignee: Shanghai Jiaotong University
Current assignee: Shanghai Jiaotong University
Priority date: 2000-04-13
Filing date: 2000-04-13
Publication date: 2000-11-08

Abstract

A method for determination of DNA sequence is characterized by that A, C, G and T constituted complete-combined oligonucleotide fragment whose length is L is fixed on DNA chip, the DNA fragment with sequence to be tested is a random fragment whose fluorescently-labeled one group length is L and nz nucleotides at connected point are known; at the same time, said DNA fragment and DNA chip are heat-insulated together to make DNA pairing and connect with oligonucleotide fragment paired with tested DNA sequence; after reaction, the DNA chip is washed, then detected by scanning device and the frequences of various matched fragment sequences of tested DNA fragment can be obtained, so that the nucleotide sequence of tested DNA fragment can be inverse-calculated according to these frequences.

Description

Measure the method for dna sequence dna

What the present invention relates to is a kind of method of measuring dna sequence dna, belongs to the bioinformation technical field of measurement and test.

Determined dna sequence and analysis are important rings of human genome engineering.The dna sequence analysis method of using is a dideoxy method at present, ultimate principle is with special primer and DNA to be measured pairing, containing in the presence of the deoxynucleoside acid mixture of dideoxy nucleotide, archaeal dna polymerase stops to dna replication dna to be measured and in special site, separates with the denaturing polyacrylamide gel electrophoresis method then.With radio isotope or fluorescence dye spike, this method is comparatively loaded down with trivial details in the experiment.Application number 95197574.9 " is used for the method and apparatus that dna sequencing and DNA identify ", this patent is based on the DNA sample matrix on the nylon membrane, and probe is stored in porous plate, according to the method described in its claim 1, need repeat from the incomplete probe of a cover of given length, to select probe, and must repeat hybridization, to obtain the data fitting information needed, each circulation all will be carried out the probe screening, and this brings difficulty for actual user, and the step in the implementation process is complicated.

The objective of the invention is to overcome deficiency of the prior art, a kind of method of measuring dna sequence dna is provided.

Technical scheme of the present invention and performance thereof are as follows:

The length that A, C, G, T are constituted is that the oligonucleotide fragment of all combinations of L is fixed on the DNA chip, sequence dna fragmentation to be measured is that a fluorescently-labeled group length is L, the nz at a connection site place Nucleotide is known random fragment, be incubated with the DNA chip simultaneously, carry out the DNA pairing, be connected with dna sequence dna paired oligonucleotide fragment to be measured, the DNA chip is cleaned in the reaction back, detect with scanner then, the frequency that various sequences occur in the dna fragmentation to be measured can be obtained, the nucleotide sequence of dna fragmentation to be measured can be instead released.

The structure of DNA chip: total oligonucleotide probe of chip n=4 that counts ^Lxy,, can on X, Y-axis, respectively select 4 on the chip plane that a two dimension constitutes ^Nx, 4 ^NyIndividual, and satisfy following condition: 4 ^Nx* 4 ^Ny=4 ^Lxy, the DNA chip just can be realized sequence expansion and inverting.

Oligonucleotide probe is connected the known nucleotide fragment: sequence length is L, is known fluorescently-labeled oligonucleotide fragment but have only nz Nucleotide of tie point.Its known kind is by the number decision of connection site known nucleotide.When the connection site known nucleotide is 1, just have only 4 kinds.When the connection site known nucleotide is 2, just there are 16 kinds, when the connection site known nucleotide is nz, just have 4 ^NzKind.Various pairing ligations take place in DNA section to be measured and DNA chip, and informational capacity is the three-dimensional arrangement that a kind of X, Y, Z axle make up, and the sequence total amount that wherein can comprise is N=4 ^Nx* 4 ^Ny* 4 ^NzKind, and every kind of oligonucleotide fragment sequence (length of this moment is L=L _Xy+ nz) certain location arranged in this three-dimensional structure.

Dna sequence dna is the life-information sequence that is made of four codings of ATCG, is the sequence of L for length, and the sum of the full combination of its ATCG is n=4 ^LAny one dna sequence dna like this, its length is the fragment of L, must be n=4 ^LIn full arrangement the one.Like this, any dna sequence dna all length available is that the ATCG of L makes up fragment entirely and describes, and is referred to as sequence and launches.When length be the full composite set of ATCG of sequence of L as probe stationary in the DNA chip, realize that with regard to available DNA chip sequence launches.By reverse process, can extrapolate the sequence of testing sample, be referred to as the sequence inverting.

A length be the full composite set of ATCG of L as probe stationary on the DNA chip, by the DNA pair principle (A-T, C-G), the fragment of DNA sample sequence to be measured and the coupling of the dna probe on the chip, and carry fluorescent mark.Then, the DNA chip of crossing with scanning device pair and sample effect scans detection.Just can obtain the distribution pattern of the phosphor dot on the DNA chip, this distribution pattern is encoded at the enterprising line position of chip by quaternary mode.But because the information of DNA chip is parallel processing, can not determine and the position of fragment the entire sample sequence of probe coupling, so just must use the method for recursion from the fluorescence distribution pattern that the DNA chip records.From known nucleotide fragments, fragment recursion one by one.Because there are four possibilities in each segmental next recursion fragment, so the result of recursion is not unique.Recursion result's number depends on the length of probe and the length of sample sequence, and sample sequence intrinsic degeneracy.But recursion result must have one to be actual testing sample sequence.The Realization of Simulation is as follows:

Launch and inversion technique according to above-mentioned sequence, adopting length is the dna probe of the full combination of ATCG of 11 oligonucleotide sequence as the DNA chip.According to n=4 ^L, then have 4194304 dna probes, adopt 3 D stereo arrayed method, arrange dna probe as follows: the dna probe array chip of 64 256 * 256 dot matrix is made in 256 (directions X) * 256 (Y direction) * 64 (Z direction).With Computer Simulation length be 2～5Kb testing sample sequence results.Verified technical scheme of the present invention.The present invention has substantive distinguishing features and marked improvement than existing method, and the present invention has tangible advantage.As:

1. simple to operate.This method only needs simple molecular hybridization, dna fragmentation attended operation, and remaining work all is to finish with scanner and computer.

2. save time.Molecular hybridization is connected required condition with dna fragmentation very flexible, and a people can operate a lot of samples simultaneously.Only need several minutes to finish and scan the required time.The backstepping inverting of sample sequence is finished by computer fully.On the 133MHz Personal Computer, use the given backstepping inversion technique of the present invention program, can in 1～2 hour, provide the result.

3. contain much information.Length is L _XyThe oligonucleotide kind of+nz is 4 ^Lxy+nzKind.When Lxy+nz=11, can determine the sequence about 5Kb quickly.And conventional DNA analysis method once can only be determined 1Kb left and right sides dna sequence dna.

4. cost saving.The use of a large amount of chips will make the price of chip reduce significantly.Because the disposable nucleotide sequence that can determine than long segment of chip, therefore the required expense of average single Nucleotide will reduce greatly.

Claims

1, a kind of method of measuring dna sequence dna, it is characterized in that A, C, G, the length that T constitutes is that the full combination oligonucleotide fragment of L is fixed on the DNA chip, sequence dna fragmentation to be measured is that a fluorescently-labeled group length is L, nz the Nucleotide at point to be connected place is known random fragment, be incubated with the DNA chip simultaneously, carry out the DNA pairing, be connected with dna sequence dna paired oligonucleotide fragment to be measured, the DNA chip is cleaned in the reaction back, detect with scanner then, the frequency of the various coupling fragment sequences appearance of dna fragmentation to be measured can be obtained, the nucleotide sequence of dna fragmentation to be measured can be instead released according to this frequency.

2, mensuration dna sequence dna method according to claim 1, its feature also are total oligonucleotide probe of chip n=4 that counts ^Lxy,, can on X, Y-axis, respectively select 4 on the chip plane that a two dimension constitutes ^Nx, 4 ^NyIndividual, and satisfy following condition: 4 ^Nx* 4 ^Ny=4 ^Lxy, the DNA chip just can be realized sequence expansion and inverting.