CN114085913A - STR locus fluorescence labeling multiplex amplification kit for mouse cell strain identification and application thereof - Google Patents

STR locus fluorescence labeling multiplex amplification kit for mouse cell strain identification and application thereof Download PDF

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CN114085913A
CN114085913A CN202110753366.6A CN202110753366A CN114085913A CN 114085913 A CN114085913 A CN 114085913A CN 202110753366 A CN202110753366 A CN 202110753366A CN 114085913 A CN114085913 A CN 114085913A
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赵宪坤
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Suzhou Jianda Biotechnology Co ltd
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Abstract

The invention provides an STR locus fluorescence labeling multiplex amplification kit for mouse cell strain identification and application thereof, belonging to the technical field of genetic engineering. The present invention provides the following STR locus sets: 4-2, 6-4, 1-1, 6-7, 2-1, 17-2, 11-2, 8-1, 19-2, 7-1, 1-2, 13-1, 5-5, 12-1, 18-3, 15-3, 3-2, X-1 and TH01 and corresponding primer sets for specific amplification of the above loci. Meanwhile, a kit is provided, which comprises a primer group of the STR locus set, a DNA template, a2 xPCR Mix and the like, and the kit is applied to the identification of mouse cell strains, and has the advantages of accurate and reliable data, simple operation, patterned conditions and quick identification.

Description

STR locus fluorescence labeling multiplex amplification kit for mouse cell strain identification and application thereof
Technical Field
The invention belongs to the technical field of genetic engineering, and particularly relates to an STR locus fluorescence labeling multiplex amplification kit for identifying mouse cell strains and application thereof.
Background
Short Tandem Repeats (STR), also known as microsatellite DNA, are sequences that are relatively stable in DNA inheritance formed by tandem repeats of a unit with several bases as the core. They are widely present in the genomes of human and mammals, and generally constitute a core sequence of 2-6 bases, and constitute the genetic polymorphism of STRs among individuals due to the variation in the number of core units and the difference in the number of repeats. The STR has the characteristics of multiple varieties, wide distribution, low mutation rate, high polymorphism degree, multiple alleles, strong identification capability, high sensitivity and the like, and is widely applied to the fields of genetic mapping, forensic identification, relativity analysis (particularly paternity identification), disease gene localization, species polymorphism, diagnosis of genetic diseases and the like.
In the field of cell biology research, STR typing detection is applied to cell strain identification by taking the Authority of ICLAC, ATCC and the like as a gold standard. As early as 2001, PNAS was introduced in Short distance repeat (STR) profiling protocols and international reference standards for human cell lines, indicating that STR typing technology provides an international reference standard for the identification of human cell lines. In 2009, Nature reported that many cell lines in biological laboratories between 1/5-1/3 have been mistaken, and that the only way researchers have been to identify cell lines by using STR typing techniques to confirm whether the cells used are consistent with the data in databases. An article which is published in the nature reviews cancer journal in 2010 by ATCC and is entitled Cell differentiation of the ending also confirms the technical breakthrough brought by STR typing for Cell strain identification, and the STR typing is considered to have advantages in data reliability, time and economic cost.
At present, STR typing technology for identifying human cell strains and related databases are relatively mature, but identification of animal cell strains, particularly mouse cell strains, is not widely used in identification of mouse cell strains due to lack of a multiple STR amplification system and related products. In vitro experiments in various fields of life science research, the mouse cell strain is the most applied animal cell except the human cell strain, so that the STR typing method for identifying the mouse cell strain is established, and the development of life science basic research is further promoted.
At present, various methods are used for identifying cell strains and detecting cell strain cross contamination, such as isozyme analysis, human leukocyte antigen typing, karyotyping and immunotyping. These methods can identify a certain cell line, but the respective resolution capabilities are different, and the data repeatability and reliability are poor, so that none of the methods can be used as a standard method for comparison and reference of a database. STR is widely distributed, and has the characteristics of low mutation rate, high polymorphism degree, more alleles, strong identification capability, high sensitivity and the like, so STR typing gradually becomes a standard method for identifying cell strains.
Although companies have developed a patent product for STR typing of mouse cell genomes in China (application No./patent No.: 2011104336234), it can analyze only 8 polymorphic loci: d1Mit159.1, d2Mit395.1, d4Mit170.1, D7Mit40, D11Mit4, D15Mit16, D17Mit51.1 and Jarid 1. The existing methods such as isoenzyme analysis, human leukocyte antigen typing, karyotyping and the like have different resolving power and poor data repeatability and reliability; the product analysis locus of the existing mouse cell strain STR identification in China is relatively less.
Disclosure of Invention
In order to solve the technical problems, the invention provides an STR locus fluorescence labeling multiplex amplification kit for identifying mouse cell strains and application thereof.
A set of STR loci comprising the following loci: 4-2, 6-4, 1-1, 6-7, 2-1, 17-2, 11-2, 8-1, 19-2, 7-1, 1-2, 13-1, 5-5, 12-1, 18-3, 15-3, 3-2, X-1 and TH 01.
A primer set for specifically amplifying a nucleic acid sequence in said set of STR loci.
In one embodiment of the present invention, the primers in the primer set are respectively:
the 4-2 primer pair is as follows:
Primer-F TGTGATTCCCATTGGCCTGTTC (see sequence SEQ ID.1)
Primer-R GAGTGCAGGTCACAGGGAAC (see sequence SEQ ID.2)
The 6-4 primer pair is:
Primer-F AGTGAAGTTGTTTGCAACAGCTCAG (see sequence SEQ ID.3)
Primer-R CGCTGGCAGATCTTAGGTAGTTC (see sequence SEQ ID. 4);
1-1 primer pair:
Primer-F TCCGGCTGAGCCTAAGGACCT (see sequence SEQ ID.5)
Primer-R CCCTTCACTCCTTCATTCCATCTTC (see sequence SEQ ID.6);
6-7 primer pair:
Primer-F TTTCAACTATCAGTCCACCCAGTG (see sequence SEQ ID.7)
Primer-R GGTTTTAAATAACTCAGAAAGGGGACA (see sequence SEQ ID.8);
2-1 primer pair:
Primer-F AACTTCAAACTTTGCTGGAAAGAGAAAG (see sequence SEQ ID.9)
Primer-R GTTCCTGCTTAGCTTGTCATTTCC (see sequence SEQ ID.10);
17-2 primer set:
Primer-F TCTCTACTCTTCTCCATCCGTCC (see sequence SEQ ID.11)
Primer-R CATGGCTCTTGCCACAAATCTG (see sequence SEQ ID. 12);
11-2 primer set:
Primer-F AGACAGAGTCTCACCATTGCAG (see sequence SEQ ID.13)
Primer-R CCTTCTGACCTCTGTGGATATCAG (see sequence SEQ ID.14);
8-1 primer set:
Primer-F AAGCAGCATCTAACACTCAGCTA (see sequence SEQ ID.15)
Primer-R GAATGGCCTAGAACTGGGCCTG (see sequence SEQ ID. 16);
19-2 primer set:
Primer-F TGGTTAGTTCCCTGGGAACCTCAT (see sequence SEQ ID.17)
Primer-R CTGGTGCTCACAGCACTGAGT (see sequence SEQ ID.18);
7-1 primer pair:
Primer-FACTAGGATTCCTCTCTCTCTAAGATAG (see sequence SEQ ID.19)
Primer-R CATCTTAAAGAGAGAGGAATCCTTGTCA (see sequence SEQ ID.20);
1-2 primer pairs:
Primer-F CCTTTTGCCCATATTGTATGGTTTCC (see sequence SEQ ID.21)
Primer-R GATATCTCCAACTCCCCAATTCTACA (see sequence SEQ ID.22);
13-1 primer set:
Primer-F TTCTTGGTATTAACCCAAGTCCTTGAG (see sequence SEQ ID.23)
Primer-R CTCCCTGCAAAGCAACTCTGAAC (see sequence SEQ ID.24);
5-5 primer pair:
Primer-F TCGTTTTACCTGGCTGACACACT (see sequence SEQ ID.25)
Primer-R CCTGGTGTGGTTTAAAACTCAATACC (see sequence SEQ ID. 26);
12-1 primer set:
Primer-F TTTCACCTTGAATAAGAATCATGAGGC (see sequence SEQ ID.27)
Primer-R GATAGCTACGTAAATATGAGAGGGTTTG (see sequence SEQ ID.28);
18-3 primer pair:
Primer-F TGTGTCATGCTAACTCACAGGTA (see sequence SEQ ID.29)
Primer-R CTGCTAAATAACTAAGCAAGTGAACAGA (see sequence SEQ ID.30);
15-3 primer pair:
Primer-F TTCAGATTCTGGGCGTGTCTGT (see sequence SEQ ID.31)
Primer-R CTCAGATCAAGAGGCTATCTAAACTTG (see sequence SEQ ID. 32);
3-2 primer pair:
Primer-F TACCATGTGGGTACATTGTTAAGCTGT (see sequence SEQ ID.33)
Primer-R GACATGTGATAGAGGATGGATAGATGA (see sequence SEQ ID. 34);
x-1 primer set:
Primer-F TGGGATTGTGTGGTATCCTACTC (see sequence SEQ ID.35)
Primer-R GGAAAGACAAGGAGGAGGGACAG (see sequence SEQ ID. 36); TH01 primer pair:
Primer-F TGTGATTCCCATTGGCCTGTTC (see sequence SEQ ID.37)
Primer-R GAGTGCAGGTCACAGGGAAC (see sequence SEQ ID.38).
In one embodiment of the invention, the Primer-F5' end of the Primer pair in the Primer set is fluorescently modified.
In one embodiment of the present invention, the modified fluorescent substance is at least one of FAM fluorescent dye, HEX fluorescent dye, L552 fluorescent dye and LSID fluorescent dye.
In one embodiment of the invention, the TH01 primer pair, 4-2 primer pair, 6-4 primer pair, 1-1 primer pair and 6-7 primer pair are modified with FAM fluorescent dye; the 2-1 primer pair, the 17-2 primer pair, the 11-2 primer pair, the 8-1 primer pair and the 19-2 primer pair are modified by HEX fluorescent dye; the 7-1 primer pair, the 1-2 primer pair, the 13-1 primer pair, the 5-5 primer pair and the 12-1 primer pair are modified by an L552 fluorescent dye; the 18-3 primer pair, the 15-3 primer pair, the 3-2 primer pair and the X-1 primer pair are modified by LSID fluorescent dye.
A kit comprises the primer group.
The kit also comprises a DNA template and 2x PCR Mix.
The 2 XPCR Mix comprises an amplification enzyme, a buffer solution and Mg2+And dNTPs.
The kit is applied to the identification of mouse cell strains.
According to the invention, the mouse 18 STR loci and 1 human STR locus are subjected to four-color fluorescence labeling multiplex amplification and capillary electrophoresis typing to establish a typing map of a mouse cell strain, so that the mouse cell strain can be accurately compared with a database and the identity of the cell strain can be identified; and simultaneously, whether human source cell strain cross contamination exists can be determined.
Compared with the prior art, the technical scheme of the invention has the following advantages:
1, with highly rich information: the 19 STR loci can be analyzed simultaneously, the parting map of each cell strain is established, and the cell strain identity can be accurately compared with a database and confirmed.
2, high sensitivity: the method can detect ng-grade DNA, trace samples can meet the requirements, and early pollution can be detected. The method is economical, rapid, reliable in data and easy to operate. The method has the advantages of accurate and reliable data, simple operation, condition modeling and quick identification, and the whole identification time can be completed within about 5-6 hours.
Compared with other STR identification products, the method can be used for typing more STR loci and adding one STR locus. Not only can establish STR atlas of 19 loci, more accurately identify cell identity, but also can judge whether human source cell cross contamination exists.
Drawings
In order that the present disclosure may be more readily and clearly understood, reference is now made to the following detailed description of the embodiments of the present disclosure taken in conjunction with the accompanying drawings, in which
FIG. 1 is a diagram showing the arrangement of loci in the kit of the present invention.
FIG. 2 is a diagram of the electrophoresis conditions of the present invention.
FIGS. 3 to 6 are STR maps of mouse cells A20, EMT6, YAC-1 and CT26.WT cells of the present invention, respectively.
FIGS. 7 to 10 are graphs showing the alignment of mouse cells A20, EMT6, YAC-1 and CT26.WT cells of the present invention.
Detailed Description
The present invention is further described below in conjunction with the following figures and specific examples so that those skilled in the art may better understand the present invention and practice it, but the examples are not intended to limit the present invention.
The invention relates to a four-color fluorescence labeling composite amplification kit, which can carry out STR typing on 18 loci (4-2, 6-4, 1-1, 6-7, 2-1, 17-2, 11-2, 8-1, 19-2, 7-1, 1-2, 13-1, 5-5, 12-1, 18-3, 15-3, 3-2 and X-1) of a mouse and 1 human locus (TH 01). The 18 mouse loci are highly polymorphic and species-specific, and have no highly homologous sequences to human, rat, guinea pig, hamster, and other species.
The respective gene sequences were downloaded from the NCBI nucleic acid database according to the GeneBank serial number of the 19 loci. Primer5 software and NCBI blast were used to design the primers for each of the 19 loci, and AutoDimer software was used to analyze the interactions between Primer dimers and primers to optimize the primers.
Example 1
1, DNA extraction
Four cell mouse cells A20, EMT6, YAC-1 and CT26.WT were subjected to DNA extraction using a Chelex100 crude extraction method. Sucking cell suspension 1000 μ L, shaking, centrifuging at 10000rpm for 3min, discarding supernatant, adding 200 μ L5% Chelex100 suspension and 3 μ L PK 10mg/mL, bathing at 56 deg.C for 1h, slightly shaking, boiling in water bath for 8min, shaking for 10s, centrifuging at 10000rpm for 3min, and collecting supernatant. After the DNA extraction, the DNA was quantitated by UV spectrophotometer and diluted to 1 ng/. mu.L.
Wherein, the preparation method of 5 percent Chelex-100 comprises the following steps: (shaking thoroughly before use; effective period is 1 month)
(1) 100mL of deionized water was measured and placed in a 250mL glass beaker.
(2) 5g of Chelex100 was weighed into a wide-mouth glass bottle.
(3) Deionized water was added to the jar and stored at room temperature.
2, determination of primers
Firstly, selecting two mouse cell strains, respectively using 19 pairs of primers to perform single amplification, carrying out capillary electrophoresis on amplification products through a 3130xl genetic analyzer, and judging the amplification effect of each pair of primers according to the electrophoresis result, wherein the optimal electrophoresis result is as follows: single, no double peaks or other spurious peaks. If the amplification effect of the primer is not good, the primer is redesigned. 19 after determining the primers, adding two mouse cell strains for experiment, mixing 1uL of each pair of primer mother liquor, complementing TE buffer solution to 50 uL, carrying out capillary electrophoresis on the amplification product by using the same amplification system and amplification program (the amplification system and the amplification program special for 2X PCR Mix in Xinhai, Suzhou) as before, and adjusting the absorption amount of each pair of primer mother liquor according to the peak signal intensity (the optimal signal intensity is 2000-4000) to finally determine the conditions in the table 2.
Figure BDA0003146098890000081
b, the amplification procedure is as follows: pre-denaturation at 95 ℃ for 10 min; followed by denaturation at 95 ℃ for 10s, annealing at 58 ℃ for 1min, extension at 72 ℃ for 20s, and final extension at 60 ℃ for 30min for 28 cycles, as follows:
Figure 1
3, preparation of primer mixture
Adding the determined front and back primers (38 in total) of 19 sites into TE buffer solution (shown in Table 1) with corresponding amount respectively to prepare 100 mu M primers; 2. each pair of forward and reverse primers are mixed in equal volume to prepare a primer mother solution with the concentration of 50 mu M; 3. the corresponding amount of the primer stock solution (shown in Table 2) was mixed in each 19-tube at 50. mu.M, and TE buffer was added to 50. mu.L to prepare a primer mixture.
TABLE 1
Figure BDA0003146098890000091
Figure BDA0003146098890000101
TABLE 2
Figure BDA0003146098890000102
4, PCR reaction
The PCR amplification system and the amplification program are the same as those in part 2, and the PCR products of the mouse cells A20, EMT6, YAC-1 and CT26.WT are obtained by carrying out PCR amplification on the DNA of the extracted mouse cells A20, EMT6, YAC-1 and CT26. WT.
5, detection by capillary electrophoresis
Mixing the SIZ-500 internal standard and formamide according to the proportion of 1:24, taking 10 mu L of mixture to enter a 96-well plate, respectively sucking 0.5 mu L of PCR products of 4 mouse cells, injecting, mixing and standing for several minutes, centrifuging, and then putting into a 3130xl genetic analyzer for detection. Applying the detection experiment data
Figure BDA0003146098890000103
ID v3.2 software for data analysis and generation of STR typing map of each mouse cell strain (see the attached figures 3-6).
6, results of the experiment
As can be known from STR typing maps, the typing results of 18 loci, namely 4-2, 6-4, 1-1, 6-7, 2-1, 17-2, 11-2, 8-1, 19-2, 7-1, 1-2, 13-1, 5-5, 12-1, 18-3, 15-3, 3-2 and X-1, of 4 strains of mouse cells do not have the same typing results (the results of corresponding STR maps of mouse cells A20, EMT6, YAC-1 and CT26.WT are respectively shown in figures 3-6), so that the method can be used for establishing a characteristic STR map for the 15 strains of mouse cells to identify the strains of mouse cells. The comparison of the experimental data with the database (ExPASy) confirmed that all four cell lines were correct (see FIGS. 7-10 for the details of the comparison).
It should be understood that the above examples are only for clarity of illustration and are not intended to limit the embodiments. Other variations and modifications will be apparent to persons skilled in the art in light of the above description. And are neither required nor exhaustive of all embodiments. And obvious variations or modifications of the invention may be made without departing from the spirit or scope of the invention.
SEQUENCE LISTING
<110> Sozhou Jianda Biotechnology Co., Ltd
<120> STR locus fluorescence labeling multiplex amplification kit for mouse cell strain identification and application thereof
<130> 38
<160> 38
<170> PatentIn version 3.3
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<213> (Artificial Synthesis)
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tgtgattccc attggcctgt tc 22
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<212> DNA
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<400> 4
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tccggctgag cctaaggacc t 21
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cccttcactc cttcattcca tcttc 25
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tttcaactat cagtccaccc agtg 24
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Claims (10)

1. A set of STR loci, wherein said set of STR loci comprises the following loci: 4-2, 6-4, 1-1, 6-7, 2-1, 17-2, 11-2, 8-1, 19-2, 7-1, 1-2, 13-1, 5-5, 12-1, 18-3, 15-3, 3-2, X-1 and TH 01.
2. A primer set for specifically amplifying a nucleic acid sequence in the STR locus set of claim 1.
3. The primer set according to claim 2, wherein the primer pairs in the primer set are respectively: the 4-2 primer pair is as follows:
Primer-F TGTGATTCCCATTGGCCTGTTC
Primer-R GAGTGCAGGTCACAGGGAAC;
the 6-4 primer pair is:
Primer-F AGTGAAGTTGTTTGCAACAGCTCAG
Primer-R CGCTGGCAGATCTTAGGTAGTTC;
1-1 primer pair:
Primer-F TCCGGCTGAGCCTAAGGACCT
Primer-R CCCTTCACTCCTTCATTCCATCTTC;
6-7 primer pair:
Primer-F TTTCAACTATCAGTCCACCCAGTG
Primer-R GGTTTTAAATAACTCAGAAAGGGGACA;
2-1 primer pair:
Primer-F AACTTCAAACTTTGCTGGAAAGAGAAAG
Primer-R GTTCCTGCTTAGCTTGTCATTTCC;
17-2 primer set:
Primer-F TCTCTACTCTTCTCCATCCGTCC
Primer-R CATGGCTCTTGCCACAAATCTG;
11-2 primer set:
Primer-F AGACAGAGTCTCACCATTGCAG
Primer-R CCTTCTGACCTCTGTGGATATCAG;
8-1 primer set:
Primer-F AAGCAGCATCTAACACTCAGCTA
Primer-R GAATGGCCTAGAACTGGGCCTG;
19-2 primer set:
Primer-F TGGTTAGTTCCCTGGGAACCTCAT
Primer-R CTGGTGCTCACAGCACTGAGT;
7-1 primer pair:
Primer-F ACTAGGATTCCTCTCTCTCTAAGATAG
Primer-R CATCTTAAAGAGAGAGGAATCCTTGTCA;
1-2 primer pairs:
Primer-F CCTTTTGCCCATATTGTATGGTTTCC
Primer-R GATATCTCCAACTCCCCAATTCTACA;
13-1 primer set:
Primer-F TTCTTGGTATTAACCCAAGTCCTTGAG
Primer-R CTCCCTGCAAAGCAACTCTGAAC;
5-5 primer pair:
Primer-F TCGTTTTACCTGGCTGACACACT
Primer-R CCTGGTGTGGTTTAAAACTCAATACC;
12-1 primer set:
Primer-F TTTCACCTTGAATAAGAATCATGAGGC
Primer-R GATAGCTACGTAAATATGAGAGGGTTTG;
18-3 primer pair:
Primer-F TGTGTCATGCTAACTCACAGGTA
Primer-R CTGCTAAATAACTAAGCAAGTGAACAGA;
15-3 primer pair:
Primer-F TTCAGATTCTGGGCGTGTCTGT
Primer-R CTCAGATCAAGAGGCTATCTAAACTTG;
3-2 primer pair:
Primer-F TACCATGTGGGTACATTGTTAAGCTGT
Primer-R GACATGTGATAGAGGATGGATAGATGA;
x-1 primer set:
Primer-F TGGGATTGTGTGGTATCCTACTC
Primer-R GGAAAGACAAGGAGGAGGGACAG;
TH01 primer pair:
Primer-F TGTGATTCCCATTGGCCTGTTC
Primer-R GAGTGCAGGTCACAGGGAAC。
4. the Primer set according to claim 3, wherein the Primer pairs in the Primer set are fluorescently modified at the 5' ends of Primer-F.
5. The primer set as claimed in claim 4, wherein the fluorescence-modified modifier is at least one of FAM fluorochrome, HEX fluorochrome, L552 fluorochrome and LSID fluorochrome.
6. The primer set of claim 3, wherein said TH01 primer pair, 4-2 primer pair, 6-4 primer pair, 1-1 primer pair, and 6-7 primer pair are modified with FAM fluorescent dye; the 2-1 primer pair, the 17-2 primer pair, the 11-2 primer pair, the 8-1 primer pair and the 19-2 primer pair are modified by HEX fluorescent dye; the 7-1 primer pair, the 1-2 primer pair, the 13-1 primer pair, the 5-5 primer pair and the 12-1 primer pair are modified by an L552 fluorescent dye; the 18-3 primer pair, the 15-3 primer pair, the 3-2 primer pair and the X-1 primer pair are modified by LSID fluorescent dye.
7. A kit comprising the primer set according to claim 2.
8. The kit of claim 7, wherein the kit further comprises a DNA template and a2 XPCR Mix.
9. The kit of claim 8, wherein the 2x PCR Mix comprises an amplification enzyme, a buffer, Mg2 +And dNTPs.
10. The use of the kit of claim 7 for the identification of mouse cell lines.
CN202110753366.6A 2021-07-02 2021-07-02 STR locus fluorescence labeling multiplex amplification kit for mouse cell strain identification and application thereof Pending CN114085913A (en)

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