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

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

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 straight-forward 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 PyVADesign is open source and available at https://github.com/CDDLeiden/PyVADesign/ . Contact gerard@lacdr.leidenuniv.nl

Authors 3

1. Rosan C.M. Kuin Aachen Department of Cell and Chemical Biology Medicinal Chemistry

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands

   Medicinal Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands

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, Albinusdreef 2, 2333 ZA Leiden, the Netherlands

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

   Leiden University Medical Center

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands