Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genomic DNA
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Gene | Primary PCR | Secondary PCR | |
---|---|---|---|
oSSP | semi-oSSP | iSSP | |
gadA | I: GGATGCTGCCTTCGGTGGGTTATTT II: GGTTTAGGGTGGATCGTATGGCGT III: ACAACAATGCTGATACGCTGCCAGA | I: ACTCCAACGGCATCCTGGGTTATTT II: TAAGGTCTTCACTGCGTATGGCGT III: TACTTTCCATAACACCGCTGCCAGA | ACGGTTGACTCCATTGCCATTAACT |
gadR | I: TAGCCAACCGTAAACCTGCGTAAAA II: AACTATCACCCCACAACGTCATCTC III: GGATACTGGCTAAAATGAATTAACTCGGAT | I: AGCTGCGATACTCCACTGCGTAAAA II: GGTCCAGCATAGGGTACGTCATCTC III: CATGTAATAACCTCGCTTCATAACTCGGAT | ACCGTTCATAGGCGAAATTGTTTGT |
hyg | I: AAGACCTGCCTGAAACCGAACTGC II: AGTTTAGCGAGAGCCTGACCTATTG III: GGAAGTGCTTGACATTGGGGAGT | I: TTAGAACTGACCCGACCGAACTGC II: CCGCCTAGCCACTGATGACCTATTG III: CTTCTCAGCCTGGATTGGGGAGT | CAAGGAATCGGTCAATACATACATGGC |
Round of PCR | Thermal Parameters | Cycle Number |
---|---|---|
Primary | 94 °C, 2 min | |
94 °C, 30 s; 60 °C, 30 s; 72 °C, 3 min | 5 | |
94 °C, 30 s; 25 °C, 30 s; 72 °C, 3 min | 1 | |
94 °C, 30 s; 60 °C, 30 s; 72 °C, 3 min | 25 | |
72 °C, 10 min | ||
Secondary | 94 °C, 2 min | |
94 °C, 30 s; 65 °C, 30 s; 72 °C, 3 min | 5 | |
94 °C, 30 s; 40 °C, 30 s; 72 °C, 3 min | 1 | |
94 °C, 30 s; 65 °C, 30 s; 72 °C, 3 min | 25 | |
72 °C, 10 min |
Approach | Rationale and Process | ESGM | Walk Range | Reference |
---|---|---|---|---|
Inverse PCR | Genomic DNA is digested with an endonuclease then self-circularized. The resultant DNA undergoes PCR performed by two SSPs with opposite extension orientations. | No | 0.3–1.8 | [1,8] |
DL-PCR | DNA is digested with an endonuclease then ligated to a random oligo. The resultant DNA undergoes 2–3 consecutive PCRs by nested pairing the oligo primer with SSPs. | No | 0.3–3.0 | [1] |
TAIL-PCR | A short random oligo is used as a walking primer. One low-stringency cycle has to be performed in every three cycles to aid walking primer annealing. The amplification of a target DNA is over a non-target one due to the differential amplification efficiency. | Yes | 0.3–3.5 | [1,12] |
POP-PCR | A set of walking primers with 3′-overlaps are individually paired with nested SSPs. A walking primer can partially anneal to a DNA template only in the one relaxed-stringency cycle of each PCR, generating a pool of ssDNAs. A target ssDNA can be converted into dsDNA by the SSP in the next high-stringency cycle, but a non-target one cannot. | Yes | 0.3–3.5 | [7] |
3SP-PCR | The rationale and process are shown in the section of “3.1 Principle of 3SP-PCR” of this study. | Yes | 0.4–8.0 | This study |
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Share and Cite
Wei, C.; Lin, Z.; Pei, J.; Pan, H.; Li, H. Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool. Curr. Issues Mol. Biol. 2023, 45, 512-523. https://doi.org/10.3390/cimb45010034
Wei C, Lin Z, Pei J, Pan H, Li H. Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool. Current Issues in Molecular Biology. 2023; 45(1):512-523. https://doi.org/10.3390/cimb45010034
Chicago/Turabian StyleWei, Cheng, Zhiyu Lin, **feng Pei, Hao Pan, and Haixing Li. 2023. "Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool" Current Issues in Molecular Biology 45, no. 1: 512-523. https://doi.org/10.3390/cimb45010034