A kind of molecular beacon strand displacement isothermal duplication gene chip detecting technique and test kit
Technical field
The invention belongs to biological technical field, be specifically related to a kind of molecular beacon strand displacement isothermal duplication gene chip detecting technique.
Background technology
Gene chip is also DNA chip, DNA microarray (DNA microarray), oligonucleotide arrays (oligonucleotide array), this technology means that a large amount of probe molecules are fixed on to sample molecule rear and mark on upholder hybridizes, by detecting the hybridization signal intensity of each probe molecule and then obtaining quantity and the sequence information of sample molecule, realize biological sample quick, parallel, detect efficiently or medical diagnosis, because conventional silicon is as solid support, and use the technology of preparing of computer chip in preparation process, so be referred to as biochip technology.
Biochip technology is owing to a large amount of probes are fixed on upholder simultaneously, so can disposablely carry out determination and analysis to a large amount of sequences of sample, thereby solve traditional mRNA blot (Southern Blotting and Northern Blotting etc.) deficiencies such as technological operation is numerous and diverse, level of automation is low, operating sequence quantity is few, detection efficiency is low.And, by designing different probe arrays, using specific analytical procedure can make this technology there is multiple different using value, as gene expression profile mensuration, consolidation detection, polymorphism analysis, genomic library mapping and sequencing by hybridization etc.
But gene chip, before detecting, need to must increase to improve to the DNA/mRNA sample obtaining from sample and read sensitivity conventionally.In pcr amplification process, must carry out sample mark simultaneously, marking method has fluorescent marker method, biotin labeling method, isotope-labelling method etc.And due to the sequence difference of DNA, the fluorescently-labeled dCTP mixing is inconsistent in amplification procedure, under similarity condition, the DNA signal that G/C content is high is obviously better than the DNA that G/C content is low.Before chip detection, the probe on PCR product and chip is hybridized, and required time is long, and the required hybridization conditions of differing molecular is inconsistent, and error is large, and because hybridization is positioned at solid phase surface, so there is steric restriction effect to a certain degree.In sample preparation, current most company all will carry out amplification to a certain degree to improve the sensitivity detecting to sample at mark with before measuring, but still have many people attempting walking around this problem, this comprises the Solid phase PCR amplification system of Mosaic Technologies company and a large amount of parallel solid phase cloning process that Lynx Therapeutics company proposes, two kinds of methods respectively have relative merits, but not yet obtain practical application at present.
Strand displacement isothermal amplification technique is the external isothermal amplification method of a kind of enzymatic DNA growing up in recent years,, there is the archaeal dna polymerase of strand displacement activity, under steady temperature, untie DNA double chain by the method for non-thermally denature, a kind of new amplification mode of in extending new chain, downstream old chain being peeled off.
Molecular beacon is that one designs fluorescent probe cleverly.The two ends that are 15-30 mer oligonucleotide probe in length add respectively the cane district of 5-8 mer sequence complementation.In the time of free state, because making probe molecule, the combination of cane district complementary sequence forms hairpin like fold, so the hairpin probe that is otherwise known as.The 5' end of probe and 3' end mark fluorescent element molecule and quencher molecules respectively.When free state, two ends of hairpin structure are close, make fluorescence molecule and quencher molecule near (being about 7-10 nm), now there is FRET (fluorescence resonance energy transfer), the fluorescence that fluorescence molecule sends is quenched molecular absorption and distributes with hot form, fluorescence is almost completely by quencher, and this sole of fluorescence is low.When molecular beacon is combined the double-stranded crossbred of formation with the target molecules of sequence complete complementary, the complementary district of beacon cane is opened, and fluorescence molecule and quencher molecule are apart from increase, and the fluorescence that fluorescence molecule produces can not be quenched molecule and absorb, emitting fluorescence.And detected fluorescence intensity and the solution target amount that hits is directly proportional.Molecular beacons technology is simple to operate, highly sensitive with it, high specificity, can nucleic acid be carried out real-time quantitative mensuration, even can not only in biological study, be had a wide range of applications for features such as in-vivo analysis, and detects in and clinical study basic with the biomedicine such as diagnosis and also will serve as important role at disease gene.
Summary of the invention
The object of the present invention is to provide a kind of molecular beacon strand displacement isothermal duplication gene chip detecting technique
The technical solution adopted in the present invention is:
A kind of method that adopts molecular beacon strand displacement isothermal duplication genechip detection target dna/RNA, comprises the steps:
(1) design of molecular beacon: molecular beacon comprises ring-shaped area, 5 ' cane district and 3 ' cane district; Wherein, ring-shaped area can with target dna/RNA specific combination, the sequence in 5 ' cane district goes out 8~25 bases than 3 ' the cane head of district, is labeled as 5 ' cane district extension, the sequence of 5 ' connection ring-shaped area, cane district part and 3 ' cane region sequence complementation, make to form hairpin structure; Molecular beacon 3 ' is terminal modified fluorescence molecule;
(2) chip point sample and strand displacement isothermal amplification: molecular beacon 5 ' end is fixed to solid support surface, form molecular beacon micro-array chip, then quenching probes and sample DNA/RNA and chip are hybridized, washing, then strand displacement isothermal amplification liquid, primer are added on micro-array chip to isothermal duplication goal gene;
Or: molecular beacon is mixed with quenching probes, point sample is fixed to solid support surface, form molecular beacon micro-array chip, then strand displacement isothermal amplification liquid, primer and sample DNA/RNA are added on micro-array chip to isothermal duplication goal gene;
Described quenching probes is the 5 ' terminal modified oligonucleotide sequence that has fluorescent quenching group, has 8 bases and the extension complementation of 5 ' cane district at least, is preferably 12 bases; Described primer and 3 ' cane district complementation;
(3) amplification is carried out to fluorescence numerical analysis, according to fluorescent value, determine whether sample DNA is target dna and content thereof.
The ring-shaped area of molecular beacon is the sequence of 15~30 bases of length.
Long 5~11 bases of complementary sequence in 5 ' cane district and 3 ' cane district.
Approach chip surface very much and produce sterically hindered impact reaction for fear of molecular beacon, can connect 10~30 thymus pyrimidines or VITAMIN B4 at 5 ' end of molecular beacon.
For realizing, molecular beacon is fixed on solid support, need carry out chemically modified to 5 ' end of molecular beacon, its modification group should react with the chemical group generation covalent chemical of solid support finishing, so that by the stable molecular beacon DNA solid support surface that is connected to securely, amino as end modified in molecular beacon 5 ', solid support finishing aldehyde radical, can form Schiff base, makes the stable solid support surface that is connected to securely of molecular beacon.
The fluorescence molecule of molecular beacon 3 ' end mark is any in the inorganic dyestuffs such as organic fluorescent dye or quantum dot such as FAM, HEX, TET, FITC, Cy3, Cy5, Cy5.5, PE, TAMRA, ROX, Texas Red, AMCA, JOE, rhodamine, bodipy, Alexa dye; Fluorescent quenching group on quenching probes is P-phenylenediamine (Para-phenylene diamine, PPD), n-propyl gallate salt (propyl gallate, NPG), 1,4-bis-azo dicyclos (2,2,2)-octane (1,4-diazobicyelo (2,2,2)-octane, DABCO), any in TAMRA, BHQ-1, BHQ-2, Eclipse, Iowa Black, nm gold particles.
Solid support is any in slide, plastic sheet, microballoon, magnetic bead.
Preferably, in strand displacement isothermal duplication process, add and use fluorescently-labeled dCTP, can improve the sensitivity of its detection.
A kind of molecular beacon strand displacement isothermal duplication genechip detection test kit, comprises the molecular beacon, quenching probes, primer, the strand displacement isothermal amplification liquid that are fixed on solid support surface, wherein:
Described molecular beacon comprises ring-shaped area, 5 ' cane district and 3 ' cane district; Wherein ring-shaped area can with target dna/RNA specific combination, the sequence in 5 ' cane district goes out 8~25 Nucleotide than 3 ' the cane head of district, be labeled as 5 ' cane district extension, 5 ' cane district, near sequence and the complementation of 3 ' cane region sequence and 3 ' cane region sequence complementation of ring-shaped area part, makes to form hairpin structure; The 5 ' terminal modified have-NH of molecular beacon
2, 3 ' terminal modifiedly has a fluorescence molecule;
Described quenching probes is the 5 ' terminal modified oligonucleotide sequence that has fluorescent quenching group, at least 8 bases and the extension complementation of 5 ' cane district;
Described primer and 3 ' cane district complementation.
Consisting of of strand displacement isothermal amplification liquid: 50mM Tris-HCl pH 7.0 ~ 8.0,1.5 mM MgSO
4, 10 mM dithiothreitol (DTT) (DTT), every kind of dNTP of 50~400 μ M, 20 μ g/ml BSA, 25~100 U/ml archaeal dna polymerases.
The advantage of the comprehensive strand displacement isothermal amplification technique of the present invention and molecular beacons technology, DNA is increased under isothermal condition, and along with the amplification of DNA, the fluorescent signal of molecular beacon is constantly released, d/d target dna is attached to again on new molecular beacon, thereby carries out amplification and the fluorescent signal release of next round.The strand replacement reaction of dependence archaeal dna polymerase reaches the object of amplification amplifying signal, reaches the object of signal detection by the Open loop and closed loop of molecular beacon.Due to the strand replacement reaction of archaeal dna polymerase, eliminate quenching group due to the impact luminous on fluorophor of fluorescent energy resonance transfer.In the time there is no additional and DNA that ring is complementary, molecular beacon is in closure state, and fluorophor and quenching group are adjacent and not luminous, encircle and be opened and add after this DNA, between the group of mark, distance increases, and makes effectively cancellation fluorescence of quenching group, thereby sends detection signal.
beneficial effect of the present invention is:
The present invention is integrated DNA/RNA amplification and signal detection, and do not need additional markers, hybridization and washing process, both simplified operation steps, raise the efficiency, reaction can be carried out under constant temperature again, thereby avoided the use of PCR instrument.Also can survey by gene amplification edges frontier inspection, realized the real-time detection of chip, make result more accurately and reliably.Meanwhile, in sample, the hybridization of target dna and molecular beacon occurs on the ring of molecular beacon, has avoided traditional biological chip because hybridization is positioned at the sterically hindered impact that solid phase surface produces.
Therefore, molecular beacon strand displacement isothermal duplication of the present invention detects the development of gene chip in real time, combine the advantage of strand replacement reaction and molecular beacon, overcome the shortcoming of traditional gene chip, realize the real-time high-throughout detection of DNA and RNA biological expression level, for DNA and RNA correlative study in the fields such as functional genomics, proteomics, clinical diagnosis and drug screening provide novel method.
Brief description of the drawings
Fig. 1 is the structural representation (1: ring-shaped area, 2:3 ' cane district, 3:5 ' cane district, 4:5 ' cane district extension) of molecular beacon of the present invention;
Fig. 2 is the schematic diagram that is related between molecular beacon, general quenching probes and universal primer;
Fig. 3 is know-why and scheme schema;
Fig. 4 is that hepatitis C virus detects gene chip real-time fluorescence scanning result (being from left to right followed successively by: HCV RNA sample sets, hepatitis B virus DNA sample sets and HIV viral RNA sample sets);
Fig. 5 is HIV virus detection gene chip real-time fluorescence scanning result (being from left to right followed successively by HIV viral RNA sample sets 1, HIV viral RNA sample sets 2, hepatitis B virus DNA sample sets, HCV RNA sample sets).
Embodiment
Below in conjunction with embodiment, the present invention is further illustrated, but be not limited to this.
embodiment 1
The present embodiment is only taking aldehyde slide as solid support, and detection HCV RNA is example, and development of the present invention and application thereof are described.
(1) design of probe and synthetic
Probe related in test is synthetic by Shanghai Sheng Gong Bioisystech Co., Ltd,
For the detection of HCV RNA, design 1 molecular beacon, sequence is as follows:
MB:NH-T
20-
cATCATCATCATCAT tCTTGGACACA aCTAACGCCATGGCTAGACC tGTGTCCAAGA-FAM(SEQ ID NO:1) (T
20for connecting 20 T of molecular beacon and solid support, underscore is ring-shaped area sequence, and italic is cane region sequence, and overstriking is 5 ' cane district extension);
General quenching probes: GTAGTAGTAGTA-TAMRA(SEQ ID NO:2);
Universal primer: CTTTCTATCTTTCTATCTTGGAC(SEQ ID NO:3);
Wherein, molecular beacon structure is shown in Fig. 1, the relation between molecular beacon structure and quenching probes and primer, as shown in Figure 2.
The special complementation of 5 ' cane district extension of general quenching probes and molecular beacon, 3 ' the cane district specificity complementation of universal primer and molecular beacon.
(2) design of chip and point sample
Slide: aldehyde radical slide (purchased from Bo Ao bio tech ltd)
(i), by above-mentioned amido modified molecular beacon, with 4 × SSC dissolving, configuration concentration is 200 nM, and 95 DEG C of sex change 5 minutes, is slowly down to afterwards room temperature, keeps 1 hour, makes molecular beacon renaturation, and is folded into correct structure;
(ii) after the DMSO that gets product obtained in the previous step and equivalent volumes mixes, adopt point sample instrument, according to putting in order of design in advance, on above-mentioned aldehyde slide, start point sample;
(iii) after point sample, chip is placed in wet box, the wet box of sealing, spends the night in 42 DEG C of reactions.Then use 4 × SSC to clean, remove not in conjunction with upper molecular beacon.
(3) hybridization of sample DNA/RNA and quenching probes and chip
By sample DNA/RNA(1 nM) and quenching probes (200 nM) mixed solution join on the slide that is fixed with molecular beacon, cover solution and microarray with the cover glass of hydrophobic silane treatment, be positioned in the wet box of sealing 42 DEG C of hybridizations 1 hour; After hybridization, slide contains 0.1%SDS with 4 × SSC() solution washing twice, finally clean 2 times with ultrapure aqua sterilisa, be placed in centrifuge tube centrifugal, remove surface liquid natural drying at room temperature.
(4) the real-time detection of the reaction of the isothermal strand displacement on chip and chip
Strand displacement isothermal amplification liquid containing universal primer (10 nM) (200 μ L) is added on the micro-array chip in step (3), with cover glass covering solution and the microarray of hydrophobic silane treatment, 42 DEG C of isothermal duplication 1h, and under chip scanner, carry out real time scan, recording fluorescent signal, according to Robust Multiple-array Average(RMA) method carries out data analysis.
Strand displacement isothermal amplification liquid (200 μ L) consists of: 5 U polymerase Klenow fragment exo-(Fermentas), 50 μ M each dNTPs, 40 mM Tris-HCl pH7.8,10 mM DTT, 10 mM MgCl
2.
Three experimental group (HCV RNA sample sets, hepatitis B virus DNA sample sets and HIV viral RNA sample sets) are established in this experiment, all establish a blank (substituting molecular beacon with deionized water) for each group.Experimental result is as shown in Figure 4: only HCV RNA sample sets has fluorescent signal, fluorescence intensity is 8.27855, analyze according to RMA, its nucleic acid concentration is 1.0524nM, hepatitis B virus DNA sample sets and HIV viral RNA sample sets and each blank group all do not have fluorescent signal, the detected result of present method are described accurately and reliably.
embodiment 2
The present embodiment is only taking aldehyde slide as solid support, and detecting HIV viral RNA is example, and development of the present invention and application thereof are described.
(1) design of probe and synthetic
Probe related in test is synthetic by Shanghai Sheng Gong Bioisystech Co., Ltd,
For the detection of HIV viral RNA, design 1 molecular beacon, sequence is as follows:
MB:NH-T
20-
cATCATCATCATCAT tCTTGGACACA gAACCAAGGGGAACTGAC tGTGTCCAAGA-FAM(SEQ ID NO:4) (T
20for connecting 20 T of molecular beacon and solid support, underscore is ring-shaped area sequence, and italic is cane region sequence, and overstriking is 5 ' cane district extension);
General quenching probes: GTAGTAGTAGTA-TAMRA(SEQ ID NO:5);
Universal primer: TCATCAATCAATCTTTCTTGGAC(SEQ ID NO:6);
Wherein, the relation between molecular beacon structure and quenching probes and primer, as shown in Figure 2.
The special complementation of 5 ' cane district extension of general quenching probes and molecular beacon, 3 ' the cane district specificity complementation of universal primer and molecular beacon.
(2) design of chip, quenching probes hybridization and point sample
Slide: aldehyde radical slide (purchased from Bo Ao bio tech ltd)
(i) by above-mentioned amido modified molecular beacon and quenching probes, with 4 × SSC mixed dissolution, configuration concentration is 200 nM, and 95 DEG C of sex change 5 minutes, slowly be down to afterwards room temperature, keep 1 hour, make molecular beacon renaturation, and being folded into correct structure, quenching probes is attached on molecular beacon simultaneously;
(ii) after the DMSO that gets product obtained in the previous step and equivalent volumes mixes, adopt point sample instrument, according to putting in order of design in advance, on above-mentioned aldehyde slide, start point sample;
(iii) after point sample, chip is placed in wet box, the wet box of sealing, spends the night in 42 DEG C of reactions.Then use 4 × SSC to clean, remove not in conjunction with upper molecular beacon and probe.
(3) hybridization of sample RNA and chip
By sample RNA(1 nM) join on the slide that is fixed with molecular beacon, cover solution and microarray with the cover glass of hydrophobic silane treatment, be positioned in the wet box of sealing 42 DEG C of hybridizations 1 hour; After hybridization, slide contains 0.1%SDS with 4 × SSC() solution washing twice, finally clean 2 times with ultrapure aqua sterilisa, be placed in centrifuge tube centrifugal, remove surface liquid natural drying at room temperature.
(4) the real-time detection of the reaction of the isothermal strand displacement on chip and chip
Strand displacement isothermal amplification liquid containing universal primer (10 nM) (200 μ L) is added on the micro-array chip in step (3), with cover glass covering solution and the microarray of hydrophobic silane treatment, 42 DEG C of isothermal duplication 1h, and under chip scanner, carry out real time scan, recording fluorescent signal, according to Robust Multiple-array Average(RMA) method carries out data analysis.
Strand displacement isothermal amplification liquid (200 μ L) consists of: 5 U polymerase Klenow fragment exo-(Fermentas), 50 μ M dNTPs, 40 mM Tris-HCl pH7.8,10 mM DTT, 10 mM MgCl
2.
Four experimental group (dCTP in HIV viral RNA sample sets 1, HIV viral RNA sample sets 2(strand displacement isothermal amplification liquid replaces with isocyatic FAM-11-dCTP) are established in this experiment), hepatitis B virus DNA sample sets, HCV RNA sample sets, all establish a blank (substituting molecular beacon with deionized water) for each group.Experimental result is as shown in Figure 5: hepatitis B virus DNA sample sets and HCV RNA sample sets, and each blank group does not all have fluorescent signal, only HIV viral RNA sample sets and HIV viral RNA sample sets 2 have fluorescent signal, HIV viral RNA sample sets fluorescence intensity is respectively 7.7218, analyze according to RMA, its nucleic acid concentration is 0.9986nM, HIV viral RNA sample sets 2 fluorescence intensities are 10.63853, the fluorescent value of HIV viral RNA sample sets 2 is higher than the fluorescent value of HIV viral RNA sample sets, prove that FAM-11-dUTP can play the effect that improves fluorescent signal to the replacement of dCTP, the detected result of present method is described accurately and reliably.
Above embodiment is only for introducing preferred case of the present invention, and to those skilled in the art, any apparent changes and improvements of carrying out in the scope that does not deviate from spirit of the present invention, all should be regarded as a part of the present invention.
<110> Jiangyin Tianrui Biotech LLC
<120> molecular beacon strand displacement isothermal duplication gene chip detecting technique and test kit
<130>
<160> 6
<170> PatentIn version 3.5
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