Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool

Cheng Wei; Zhiyu Lin; Jinfeng Pei; Hao Pan; Haixing Li

doi:10.3390/cimb45010034

Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool

Curr Issues Mol Biol. 2023 Jan 5;45(1):512-523. doi: 10.3390/cimb45010034.

Authors

Cheng Wei^{1

2}, Zhiyu Lin^{1

2

3}, Jinfeng Pei^{1

2}, Hao Pan^{1

2

3}, Haixing Li^{1

2}

Affiliations

¹ State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China.
² Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China.
³ School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China.

Abstract

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 Levilactobacillus brevis CD0817 glutamic acid decarboxylase genes.

Keywords: Levilactobacillus brevis CD0817; genome-walking; partial annealing; rice; semi-site-specific primer.

Grants and funding

This work was funded by the National Natural Science Foundation of China (grant No 32160014), and the State Key Laboratory of Food Science and Technology of Nanchang University (grant No SKLF-ZZB-202118).