WO2021042884A1 - 用于检测叶酸基因多态性的探针、基因芯片及试剂盒 - Google Patents
用于检测叶酸基因多态性的探针、基因芯片及试剂盒 Download PDFInfo
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- WO2021042884A1 WO2021042884A1 PCT/CN2020/102826 CN2020102826W WO2021042884A1 WO 2021042884 A1 WO2021042884 A1 WO 2021042884A1 CN 2020102826 W CN2020102826 W CN 2020102826W WO 2021042884 A1 WO2021042884 A1 WO 2021042884A1
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
- C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Definitions
- the invention belongs to the technical field of biological detection, and particularly relates to a probe, a gene chip and a kit for detecting the polymorphism of folate gene.
- Folic acid is a water-soluble B vitamin. As the most important carrier of one carbon unit in the body, its main physiological function is to participate in many cell metabolism processes in the body. Folic acid is indispensable in the metabolism of methionine. It acts in the form of 5-methyltetrahydrofolate. The lack of folic acid will cause adverse effects on the human body, especially the development of pregnant women and fetuses. Folic acid can also have a certain effect on the gene expression of cancer cells, inhibit their growth, and have certain anti-cancer effects.
- Folic acid metabolism refers to the ability of folic acid to be absorbed and utilized by the human body, and mainly refers to the mutual conversion process between homocysteine and methionine.
- other diseases are also related to folic acid metabolism abnormalities, such as cleft lip and palate, Complications in late pregnancy, different types of neurological and mental diseases, osteoporosis and colorectal cancer and other cancers.
- senile dementia and other related brain diseases are directly or indirectly related to the lack of folic acid.
- Deficiency may also cause a variety of diseases such as pregnancy toxemia, scurvy, parasitic diseases and rheumatoid arthritis, as well as other symptoms such as glossitis, diarrhea, poor growth, mental atrophy and mental deterioration.
- the more mature gene sites for folic acid metabolism are: the C677T and A1298C sites of MTHFR (methylenetetrahydrofolate reductase), and the A66G site on MTRR (methionine synthesizing reductase).
- MTHFR catalyzes 5,10-methylenetetrahydrofolate to produce 5-methyltetrahydrofolate, which is a one-carbon unit donor for HCY (homocysteine) metabolism to produce methionine.
- HCY homocysteine
- Gene polymorphism at C677T site will cause alanine to be replaced by valine, which will lead to a decrease in enzyme activity, produce moderate hyperhomocysteinemia (HHCY), and also reduce the content of folic acid in the blood .
- HHCY moderate hyperhomocysteinemia
- the Whole Genome Consortium has confirmed that the C677 locus genotype is related to the HCY level in the blood of healthy people. Further studies have shown that double mutations at the two sites A1298C and C677T will cause the enzyme activity to decrease more severely.
- MTRR is another important enzyme in HCY metabolism. It catalyzes the formation of methionine from HCY with the participation of vitamin B12.
- the most common mutation position of this gene is the mutation of A to G at 66, which leads to a decrease in enzyme activity and an increase in the risk of HHCY.
- SNP typing methods mainly include: PCR-RFLP (restriction fragment length polymorphism polymerase chain reaction), PCR-chip hybridization method, first-generation DNA sequencing method and TaqMan -MGB (dual-labeled real-time fluorescent probe) genotyping method.
- PCR-RFLP mainly relies on the restriction enzyme cleavage site of the target, which increases the difficulty of the experiment.
- subsequent electrophoresis analysis easily causes laboratory pollution and cannot be carried out on a large scale.
- the TaqMan-MGB probe technology can not only perform gene quantitative analysis, but also analyze gene mutations.
- First-generation sequencing is the gold standard for genetic testing, but its operation process is too long, the cost is too high, and the equipment is expensive and it is difficult to be suitable for large-scale development in hospitals.
- the present invention provides a probe, gene chip and kit for detecting polymorphism of folate gene.
- the invention has the advantages of high specificity, good accuracy, no nucleic acid extraction and rapid detection of multiple sites.
- a probe for detecting polymorphism of folate gene the sequence of the probe is:
- MTHFR677-C probe AAAAAAAAAACGTGATGATGAAATCGGCTC;
- MTHFR677-T probe AAAAAAAAAACGTGATGATGAAATCGACTC;
- MTHFR1298-A probe AAAAAAAAAACAAAGACACTTTCTTCACTGGTC;
- MTHFR1298-C probe AAAAAAAAAAAAGACACTTGCTTCACTGGT;
- MTRR66-A probe AAAAAAAAAACAGCTTGCTCACATATTTCTTC;
- MTRR66-G probe AAAAAAAAAACACAGCTTGCTTGCTCACACA.
- a gene chip for detecting folic acid gene polymorphism which contains the above-mentioned probe for detecting folic acid gene polymorphism.
- a method for preparing a gene chip for detecting folic acid gene polymorphism includes the following steps:
- the substrate in step (1) is a silicon wafer (Si), the thickness of the silicon wafer is 2.5 mm and the diameter is 20 cm.
- the coating in step (1) is to plate silicon nitride with a thickness of 47.5 nm and a TSPS (T structure polyamino dimethyl silane hydrocarbon) film with a thickness of 47.5 nm and 13.5 nm on the silicon wafer.
- TSPS T structure polyamino dimethyl silane hydrocarbon
- the coating in step (2) is a polyphenylalanine-lysine coating, and the thickness of the polyphenylalanine-lysine coating is 15nm; 6-hydrazinonicotinic acid succinate
- concentration of imide ester hydrochloride is 1-10 ⁇ mol/L, and the treatment time of 6-hydrazinonicotinic acid succinimidyl ester hydrochloride is 20 min.
- an aldehyde group or amino group is used to modify one end of the probe.
- a kit for detecting folic acid gene polymorphism including the gene chip, PCR reaction system, hybridization buffer, washing solution, BW reaction solution (horseradish peroxidase + sodium citrate buffer) and TMB (3,3',5,5'-Tetramethylbenzidine) color developing solution.
- the PCR reaction system includes the following components: 5 ⁇ Buffer, dUTP mix, F-primer, R-primer, Hot taq, UNG enzyme (uracil DNA glycosylase) and dd H 2 O (double steaming water).
- UNG enzyme to the PCR reaction system can remove the contamination of the amplified product and reduce false positive results.
- sequence of the F-primer is:
- MTHFR677-F 5'-TTGAGGCTGACCTGAAGCACTTGAAGGAG-3';
- MTHFR1298-F 5'-CTTTGGGGAGCTGAAGGACTACTA-3';
- MTRR66-FP 5'-CCTTGAAGTGATGAGGAGG-3'.
- sequence of the R-primer is:
- MTHFR677-R 5'-CCTGGATGGGAAAGATCCCG-3';
- MTHFR1298-R 5'-CACTTTGTGACCATTCCGGTTT-3';
- MTRR66-RP 5'-CCACTGTAACGGCTCTAACC-3'.
- the hybridization buffer includes 0.3 mol/L trisodium citrate, 3 mol/L sodium chloride, 0.3 mol/L sodium lauryl sulfate, and Triton X-100 0.1% aqueous solution.
- the washing liquid contains washing liquid A and washing liquid B
- the washing liquid A is a 0.01-0.1 mol/L NaOH solution
- the washing liquid B is a 0.1 ⁇ SSC solution.
- a method for detecting folic acid gene polymorphism, using the kit for detection includes the following steps:
- TMB color developing solution for color development. Before and after adding TMB color developing solution, the gene chip is washed and air-dried with 0.1 ⁇ SSC solution, and the detection result is read by taking photos or naked eyes.
- the test object contains DNA fragments.
- the detection performed by the kit and the test substance is a hybridization reaction.
- the test substance contains a target gene fragment that can specifically bind to the probe, the region of the gene chip corresponding to the probe appears blue.
- the amplification conditions in step (1) are: 95°C for 10 minutes; 94°C denaturation for 30s, 56°C renaturation for 30s, 72°C extension for 30s, repeating 40 cycles; 72°C for 5min extension.
- the amount of PCR amplification product added in step (2) is 10 ⁇ L, and the hybridization buffer is 100 ⁇ L; the reaction conditions are: reaction at 50-60°C for 30-60 minutes.
- the 0.01-0.1mol/L NaOH solution is preheated before use, the preheating temperature is 50°C, and each wash is 5-10s, and the wash is 3 times; the temperature of the 0.1 ⁇ SSC solution is 50°C, The washing time is 1 min.
- the addition amount of the BW reaction solution in step (4) is 100 ⁇ L, and the reaction time is 10 min.
- the added amount of TMB color developing solution is 100 ⁇ L, and the reaction time is 5 minutes; the 0.1 ⁇ SSC solution is used to wash 3 times before and after adding TMB color developing solution, each time is 1 minute.
- the gene chip method is used to realize the one-time multi-site determination of the folate gene, which reduces the detection time and cost;
- the present invention has the advantages of good specificity, high accuracy, rapidity and convenience through the selection of specific probes and primers, combined with the method of gene chip;
- test results can be directly read by taking pictures or naked eyes, which is simple and convenient;
- This method uses the extraction-free PCR amplification method for gene amplification, eliminating the complicated operation of nucleic acid extraction.
- Figure 1 is the detection results of the gene chip and kit prepared in Example 1-2 of the present invention on the mixed plasmids of MTHFR677-C plasmid, MTHFR1298-A plasmid and MTRR66-A plasmid;
- Figure 2 is the detection result of the gene chip and kit prepared in Example 1-2 of the present invention on the mixed plasmids of MTHFR677-T plasmid, MTHFR1298-C plasmid and MTRR66-G plasmid;
- Figure 3 shows the mixing of the gene chip and kit prepared in Example 1-2 of the present invention on MTHFR677-C plasmid, MTHFR1298-A plasmid, MTRR66-A plasmid, MTHFR677-T plasmid, MTHFR1298-C plasmid and MTRR66-G plasmid Plasmid test results.
- a probe for detecting polymorphism of folate gene the sequence of the probe is:
- MTHFR677-C probe AAAAAAAAAACGTGATGATGAAATCGGCTC;
- MTHFR677-T probe AAAAAAAAAACGTGATGATGAAATCGACTC;
- MTHFR1298-A probe AAAAAAAAAACAAAGACACTTTCTTCACTGGTC;
- MTHFR1298-C probe AAAAAAAAAAAAGACACTTGCTTCACTGGT;
- MTRR66-A probe AAAAAAAAAACAGCTTGCTCACATATTTCTTC;
- MTRR66-G probe AAAAAAAAAACACAGCTTGCTTGCTCACACA.
- a gene chip containing the above-mentioned probe for detecting polymorphism of folate gene, and its preparation process includes the following steps:
- a silicon wafer (Si) with a thickness of about 2.5mm and a diameter of 20cm is plated with a silicon nitride film of 47.5nm and a TSPS film of 13.5nm by a rotary vacuum coater and a vacuum vapor deposition method to prepare the corresponding biosensor , And covered with 15nm polyphenylalanine-lysine coating, and finally treated with 10 ⁇ mol/L 6-hydrazinonicotinic acid succinimidyl ester hydrochloride for 20 minutes, and then rinse the chip with clean water.
- the probe is spotted on the processed chip and reacted at room temperature to prepare a gene chip containing the probe.
- the spotted PolyA plays a role in positioning on the gene chip; and when the test result does not show color at the PolyA spotted spot, it proves that the color developer is invalid.
- a kit for detecting folic acid gene polymorphism including the gene chip in Example 1, PCR reaction system, hybridization buffer, washing solution, BW reaction solution and TMB color developing solution.
- the sequence of the F-primer in the PCR reaction system is:
- MTHFR677-F 5'-TTGAGGCTGACCTGAAGCACTTGAAGGAG-3';
- MTHFR1298-F 5'-CTTTGGGGAGCTGAAGGACTACTA-3';
- MTRR66-FP 5'-CCTTGAAGTGATGAGGAGG-3'.
- the sequence of the R-primer in the PCR reaction system is:
- MTHFR677-R 5'-CCTGGATGGGAAAGATCCCG-3';
- MTHFR1298-R 5'-CACTTTGTGACCATTCCGGTTT-3';
- MTRR66-RP 5'-CCACTGTAACGGCTCTAACC-3'.
- the hybridization buffer includes 0.3mol/L trisodium citrate, 3mol/L sodium chloride, 0.3mol/L sodium lauryl sulfate and Triton X-100 0.1% aqueous solution.
- the washing liquid contains washing liquid A and washing liquid B, washing liquid A is 0.01-0.1 mol/L NaOH solution, and washing liquid B is 0.1 ⁇ SSC solution.
- Hot-Taq enzyme, dUTP, and UNG enzyme were purchased from Shenzhen Feipeng Biological Co., Ltd.
- the primers and probes are self-designed and synthesized by Shanghai Shenggong Biological Engineering Co., Ltd.
- the gene chips and kits prepared in Example 1-2 were used for detection.
- the object to be detected was a plasmid containing the target gene fragment.
- the above plasmids were synthesized and provided by Shanghai Shenggong Bioengineering Co., Ltd.
- the target gene fragment includes one of the MTHFR677 (C/T) site, MTHFR1298 (A/C) site and MTRR66 (A/G) site.
- the specific sequences of the target gene fragment are as follows:
- the MTHFR677-C plasmid, MTHFR1298-A plasmid and MTRR66-A plasmid were mixed to obtain a mixed plasmid, and the mixed plasmid was dissolved in 1 mL TE buffer so that the concentration of the plasmid was 2 ⁇ g/mL, that is, 2000 ng/mL. Take 5 ⁇ L of the plasmid solution as the test substance and add it to the PCR reaction system so that the total reaction volume is 50 ⁇ L to prepare a PCR reaction mixture.
- the detection results are shown in Figure 1.
- the MTHFR677-C probe, MTHFR1298-A probe and MTRR66-A probe are all blue at the spot of the gene chip (area 1, 2, and 3 respectively), and PolyA spotted The place (area 7) also showed blue color, confirming that using the gene chip and kit prepared in Example 1-2, when the MTHFR677/MTHFR1298/MTRR66 site is not mutated, accurate results can be obtained by detecting it.
- Example 4 is basically the same as Example 3, except that the test substance used is a mixed plasmid of MTHFR677-T plasmid, MTHFR1298-C plasmid and MTRR66-G plasmid.
- the analyte was detected using the gene chip and kit prepared in Example 1-2.
- the detection results are shown in Figure 2.
- the MTHFR677-T probe, MTHFR1298-C probe and MTRR66-G probe are all blue at the spot of the gene chip (area 4, 5, 6 respectively), and PolyA spotted The place (area 7) also showed blue, confirming that the gene chip and kit prepared in Example 1-2 can accurately detect the mutations at the MTHFR677/MTHFR1298/MTRR66 site.
- Example 5 is basically the same as Example 3, except that the test substances used are MTHFR677-C plasmid, MTHFR1298-A plasmid, MTRR66-A plasmid, MTHFR677-T plasmid, MTHFR1298-C plasmid and MTRR66-G plasmid The mixed plasmid.
- the analyte was detected using the gene chip and kit prepared in Example 1-2.
- MTHFR677-C probe, MTHFR1298-A probe, MTRR66-A probe, MTHFR677-T probe, MTHFR1298-C probe and MTRR66-G probe are at the spot of the gene chip (Area 1, 2, 3, 4, 5, 6 respectively) are blue, and PolyA spot (area 7) is also blue. It is confirmed that the gene chip and kit prepared in Example 1-2 are used in When the 6 types of plasmids are mixed, they also have good specificity and can also get accurate detection results.
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Abstract
Description
物料名称 | 浓度 | 加入量 |
5×Buffer | 10μL | |
dUTP mix | 25μmol/L | 0.4μL |
F-引物 | 200μmol/L | 0.05μL |
R-引物 | 200μmol/L | 0.05μL |
Hot taq | 5U/μL | 0.3μL |
UNG酶 | 1U/μL | 0.2μL |
ddH 2O | 加水补到45μL |
Claims (10)
- 一种用于检测叶酸基因多态性的探针,其特征在于,所述探针的序列为:MTHFR677-C探针:AAAAAAAAAACGTGATGATGAAATCGGCTC;MTHFR677-T探针:AAAAAAAAAACGTGATGATGAAATCGACTC;MTHFR1298-A探针:AAAAAAAAAACAAAGACACTTTCTTCACTGGTC;MTHFR1298-C探针:AAAAAAAAAAAAGACACTTGCTTCACTGGT;MTRR66-A探针:AAAAAAAAAACAGCTTGCTCACATATTTCTTC;MTRR66-G探针:AAAAAAAAAACACAGCTTGCTTGCTCACACA。
- 一种用于检测叶酸基因多态性的基因芯片,其特征在于,含有权利要求1所述的用于检测叶酸基因多态性的探针。
- 一种权利要求2所述用于检测叶酸基因多态性的基因芯片的制备方法,其特征在于,包括以下步骤:(1)在衬底上镀膜,得到生物传感器;(2)在生物传感器上覆盖涂层,经6-肼基烟酸琥珀酰亚胺酯盐酸盐处理后,水洗;(3)将经修饰的探针点样在生物传感器上,制得基因芯片。
- 根据权利要求3所述的制备方法,其特征在于,步骤(3)中采用醛基或氨基对探针的一端进行修饰。
- 一种用于检测叶酸基因多态性的试剂盒,其特征在于,包括权利要求2所述的基因芯片、PCR反应体系、杂交缓冲液、洗涤液、BW反应液和TMB显色液。
- 根据权利要求5所述的试剂盒,其特征在于,所述PCR反应体系包括以下组分:5×Buffer,dUTP mix,F-引物,R-引物,Hot taq,UNG酶和dd H2O。
- 根据权利要求6所述的试剂盒,其特征在于,所述F-引物的序列为:MTHFR677-F:5'-TTGAGGCTGACCTGAAGCACTTGAAGGAG-3';MTHFR1298-F:5'-CTTTGGGGAGCTGAAGGACTACTA-3';MTRR66-FP:5'-CCTTGAAGTGATGAGGAGG-3'。
- 根据权利要求6所述的试剂盒,其特征在于,所述R-引物的序列为:MTHFR677-R:5'-CCTGGATGGGAAAGATCCCG-3';MTHFR1298-R:5'-CACTTTGTGACCATTCCGGTTT-3';MTRR66-RP:5'-CCACTGTAACGGCTCTAACC-3'。
- 根据权利要求5所述的试剂盒,其特征在于,所述杂交缓冲液包括0.3mol/L柠檬酸三 钠、3mol/L氯化钠、0.3mol/L十二烷基硫酸钠和Triton X–100 0.1%水溶液。
- 一种叶酸基因多态性的检测方法,其特征在于,采用权利要求5-9中任一项所述的试剂盒进行检测,包括以下步骤:(1)将待测物加入至PCR反应体系中进行扩增,得到PCR扩增产物;(2)在基因芯片上加入PCR扩增产物和杂交缓冲液,进行反应;(3)用0.01-0.1mol/L的NaOH溶液和0.1×SSC溶液对基因芯片进行洗涤,洗涤后风干;(4)取BW反应液于基因芯片上,在室温条件下反应;(5)加入TMB显色液进行显色,加入TMB显色液的前后均使用0.1×SSC溶液对基因芯片进行洗涤并风干,通过拍照或肉眼读取检测结果。
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CN110616259A (zh) * | 2019-09-02 | 2019-12-27 | 珠海赛乐奇生物技术股份有限公司 | 用于检测叶酸基因多态性的探针、基因芯片及试剂盒 |
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