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A Python script to design primers for overlap extension PCR to ligate two DNA fragments
Ligating two or more DNA fragments is a regular operation for the subcloning and the engineering of vectors. The overlap extension PCR serves as a straightforward method to solve this issue. However, it takes a relatively long time to design the appropriate overlapping primers and the primers for th...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9632469/ https://www.ncbi.nlm.nih.gov/pubmed/36340189 http://dx.doi.org/10.7717/peerj.14283 |
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author | Hu, Yunzhuo Xu, Fei Huang, Bifang Chen, Xuanyang Lin, Shiqiang |
author_facet | Hu, Yunzhuo Xu, Fei Huang, Bifang Chen, Xuanyang Lin, Shiqiang |
author_sort | Hu, Yunzhuo |
collection | PubMed |
description | Ligating two or more DNA fragments is a regular operation for the subcloning and the engineering of vectors. The overlap extension PCR serves as a straightforward method to solve this issue. However, it takes a relatively long time to design the appropriate overlapping primers and the primers for the full-length sequence, and there has not been a professional offline software for such kind of primer design. Here, we propose a Python script to search, calculate and sort thousands of combinations of primers for users according to the predefined parameters. The results of script running and experimental validation show that this script is capable of generating the optimal pairs of primers based on the proper melting temperatures and lengths of the primers, which facilitates gene modification in research. |
format | Online Article Text |
id | pubmed-9632469 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-96324692022-11-04 A Python script to design primers for overlap extension PCR to ligate two DNA fragments Hu, Yunzhuo Xu, Fei Huang, Bifang Chen, Xuanyang Lin, Shiqiang PeerJ Biochemistry Ligating two or more DNA fragments is a regular operation for the subcloning and the engineering of vectors. The overlap extension PCR serves as a straightforward method to solve this issue. However, it takes a relatively long time to design the appropriate overlapping primers and the primers for the full-length sequence, and there has not been a professional offline software for such kind of primer design. Here, we propose a Python script to search, calculate and sort thousands of combinations of primers for users according to the predefined parameters. The results of script running and experimental validation show that this script is capable of generating the optimal pairs of primers based on the proper melting temperatures and lengths of the primers, which facilitates gene modification in research. PeerJ Inc. 2022-10-31 /pmc/articles/PMC9632469/ /pubmed/36340189 http://dx.doi.org/10.7717/peerj.14283 Text en ©2022 Hu et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Biochemistry Hu, Yunzhuo Xu, Fei Huang, Bifang Chen, Xuanyang Lin, Shiqiang A Python script to design primers for overlap extension PCR to ligate two DNA fragments |
title | A Python script to design primers for overlap extension PCR to ligate two DNA fragments |
title_full | A Python script to design primers for overlap extension PCR to ligate two DNA fragments |
title_fullStr | A Python script to design primers for overlap extension PCR to ligate two DNA fragments |
title_full_unstemmed | A Python script to design primers for overlap extension PCR to ligate two DNA fragments |
title_short | A Python script to design primers for overlap extension PCR to ligate two DNA fragments |
title_sort | python script to design primers for overlap extension pcr to ligate two dna fragments |
topic | Biochemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9632469/ https://www.ncbi.nlm.nih.gov/pubmed/36340189 http://dx.doi.org/10.7717/peerj.14283 |
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