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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...

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Detalles Bibliográficos
Autores principales: Hu, Yunzhuo, Xu, Fei, Huang, Bifang, Chen, Xuanyang, Lin, Shiqiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2022
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.
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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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