Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool
Genome-walking has been frequently applied to molecular biology and related areas. Herein, a simple but reliable genome-walking technique, termed semi-site-specific primer PCR (3SP-PCR), is presented. The key to 3SP-PCR is the use of a semi-site-specific primer in secondary PCR that partially overla...
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| Format: | Article |
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MDPI AG
2023-01-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/45/1/34 |
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| author | Cheng Wei Zhiyu Lin Jinfeng Pei Hao Pan Haixing Li |
| author_facet | Cheng Wei Zhiyu Lin Jinfeng Pei Hao Pan Haixing Li |
| author_sort | Cheng Wei |
| collection | DOAJ |
| description | Genome-walking has been frequently applied to molecular biology and related areas. Herein, a simple but reliable genome-walking technique, termed semi-site-specific primer PCR (3SP-PCR), is presented. The key to 3SP-PCR is the use of a semi-site-specific primer in secondary PCR that partially overlaps its corresponding primary site-specific primer. A 3SP-PCR set comprises two rounds of nested amplification reactions. In each round of reaction, any primer is allowed to partially anneal to the DNA template once only in the single relaxed-stringency cycle, creating a pool of single-stranded DNAs. The target single-stranded DNA can be converted into a double-stranded molecule directed by the site-specific primer, and thus can be exponentially amplified by the subsequent high-stringency cycles. The non-target one cannot be converted into a double-strand due to the lack of a perfect binding site to any primer, and thus fails to be amplified. We validated the 3SP-PCR method by using it to probe the unknown DNA regions of rice hygromycin genes and <i>Levilactobacillus brevis</i> CD0817 glutamic acid decarboxylase genes. |
| first_indexed | 2024-03-09T13:09:10Z |
| format | Article |
| id | doaj.art-f18f510c4d664225bfaefec353d51cc3 |
| institution | Directory Open Access Journal |
| issn | 1467-3037 1467-3045 |
| language | English |
| last_indexed | 2024-03-09T13:09:10Z |
| publishDate | 2023-01-01 |
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| spelling | doaj.art-f18f510c4d664225bfaefec353d51cc32023-11-30T21:45:25ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452023-01-0145151252310.3390/cimb45010034Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking ToolCheng Wei0Zhiyu Lin1Jinfeng Pei2Hao Pan3Haixing Li4State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, ChinaState Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, ChinaState Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, ChinaState Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, ChinaState Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, ChinaGenome-walking has been frequently applied to molecular biology and related areas. Herein, a simple but reliable genome-walking technique, termed semi-site-specific primer PCR (3SP-PCR), is presented. The key to 3SP-PCR is the use of a semi-site-specific primer in secondary PCR that partially overlaps its corresponding primary site-specific primer. A 3SP-PCR set comprises two rounds of nested amplification reactions. In each round of reaction, any primer is allowed to partially anneal to the DNA template once only in the single relaxed-stringency cycle, creating a pool of single-stranded DNAs. The target single-stranded DNA can be converted into a double-stranded molecule directed by the site-specific primer, and thus can be exponentially amplified by the subsequent high-stringency cycles. The non-target one cannot be converted into a double-strand due to the lack of a perfect binding site to any primer, and thus fails to be amplified. We validated the 3SP-PCR method by using it to probe the unknown DNA regions of rice hygromycin genes and <i>Levilactobacillus brevis</i> CD0817 glutamic acid decarboxylase genes.https://www.mdpi.com/1467-3045/45/1/34genome-walkingsemi-site-specific primerpartial annealingrice<i>Levilactobacillus brevis</i> CD0817 |
| spellingShingle | Cheng Wei Zhiyu Lin Jinfeng Pei Hao Pan Haixing Li Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool Current Issues in Molecular Biology genome-walking semi-site-specific primer partial annealing rice <i>Levilactobacillus brevis</i> CD0817 |
| title | Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool |
| title_full | Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool |
| title_fullStr | Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool |
| title_full_unstemmed | Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool |
| title_short | Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool |
| title_sort | semi site specific primer pcr a simple but reliable genome walking tool |
| topic | genome-walking semi-site-specific primer partial annealing rice <i>Levilactobacillus brevis</i> CD0817 |
| url | https://www.mdpi.com/1467-3045/45/1/34 |
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