PyVADesign: a python-based cloning tool for one-step generation of large mutant libraries

Bioinformatics, vol. 41

Abstract

MOTIVATION: The generation and analysis of diverse mutants of a protein is a powerful tool for understanding protein function. However, generating such mutants can be time-consuming, while the commercial option of buying a series of mutant plasmids can be expensive. In contrast, the insertion of a synthesized double-stranded DNA (dsDNA) fragment into a plasmid is a fast and low-cost method to generate a large library of mutants with one or more point mutations, insertions, or deletions. RESULTS: To aid in the design of these DNA fragments, we have developed PyVADesign: a Python package that makes the design and ordering of dsDNA fragments straightforward and cost-effective. In PyVADesign, the mutations of interest are clustered in different cloning groups for efficient exchange into the target plasmid. Additionally, primers that prepare the target plasmid for insertion of the dsDNA fragment, as well as primers for sequencing, are automatically designed within the same program. AVAILABILITY AND IMPLEMENTATION: PyVADesign is open source and available at https://github.com/CDDLeiden/PyVADesign and archived via Zenodo (https://doi.org/10.5281/zenodo.15057525).

Authors 3

1. Rosan C.M. Kuin Aachen Computational Drug Discovery Department of Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Computational Drug Discovery, Medicinal Chemistry, Leiden University , Leiden, 2333 CC,

   Department of Cell and Chemical Biology, Leiden University Medical Center , Leiden, 2333 ZA,

   Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands

   Leiden University Medical Center Department of Cell and Chemical Biology, , Leiden, 2333 ZA, the

2. Meindert Hugo Lamers Aachen Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center , Leiden, 2333 ZA,

   Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands

3. Gerard J. P. van Westen corresponding Aachen Computational Drug Discovery Department of Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Computational Drug Discovery, Medicinal Chemistry, Leiden University , Leiden, 2333 CC,

   Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands