OneClick: A Program for Designing Focused Mutagenesis Experiments

Mark Warburton; Hossam Omar Ali; Wai Choon Liong; Arona Martin Othusitse; Amir Zaki Abdullah Zubir; Steve Maddock; Tuck Seng Wong; Mark Warburton; Hossam Omar Ali; Wai Choon Liong; Arona Martin Othusitse; Amir Zaki Abdullah Zubir; Steve Maddock; Tuck Seng Wong

doi:10.3934/bioeng.2015.3.126

AIMS Bioengineering

2015, Volume 2, Issue 3: 126-143. doi: 10.3934/bioeng.2015.3.126

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Research article

OneClick: A Program for Designing Focused Mutagenesis Experiments

1.
Department of Computer Science, The University of Sheffield, Regent Court, 211 Portobello, Sheffield S1 4DP, England;
2.
ChELSI Institute and Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, England;
3.
A*STAR Institute of Materials Research and Engineering (IMRE), 3 Research Link, Singapore 117602;
4.
School of Clinical Dentistry, The University of Sheffield, 19 Claremont Crescent, Sheffield S10 2TA, England.

Received: 08 June 2015 Accepted: 17 July 2015 Published: 23 July 2015

OneClick is a user-friendly web-based program, developed specifically for quick-and-easy design of focused mutagenesis experiments (e.g., site-directed mutagenesis and saturation mutagenesis). Written in Perl and developed into a web application using CGI programming, OneClick offers a step-by-step experimental design, from mutagenic primer design to analysis of a mutant library. Upon input of a DNA sequence encoding the protein of interest, OneClick designs the mutagenic primers according to user input, e.g., amino acid position to mutate, type of amino acid substitutions (e.g., substitution to a group of amino acids with similar chemical property) and type of mutagenic primers. OneClick has incorporated an extensive range of commercially available plasmids and DNA polymerases suitable for focused mutagenesis. Therefore, OneClick also provides information on PCR mixture preparation, thermal cycling condition, expected size of PCR product and agar plate to use during bacterial transformation. Importantly, OneClick also carries out a statistical analysis of the resultant mutant library, information of which is important for selection/screening. OneClick is a unique and invaluable tool in the field of protein engineering, allowing for systematic construction of a mutant library or a protein variant and simplifying molecular biology work. The program will be constantly updated to reflect the rapid development in the fields of molecular biology and protein engineering.
- protein engineering,
- enzyme engineering,
- directed evolution,
- biocatalysis,
- focused mutagenesis,
- site-directed mutagenesis (SDM),
- saturation mutagenesis,
- QuikChange
Citation: Mark Warburton, Hossam Omar Ali, Wai Choon Liong, Arona Martin Othusitse, Amir Zaki Abdullah Zubir, Steve Maddock, Tuck Seng Wong. OneClick: A Program for Designing Focused Mutagenesis Experiments[J]. AIMS Bioengineering, 2015, 2(3): 126-143. doi: 10.3934/bioeng.2015.3.126

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Abstract

OneClick is a user-friendly web-based program, developed specifically for quick-and-easy design of focused mutagenesis experiments (e.g., site-directed mutagenesis and saturation mutagenesis). Written in Perl and developed into a web application using CGI programming, OneClick offers a step-by-step experimental design, from mutagenic primer design to analysis of a mutant library. Upon input of a DNA sequence encoding the protein of interest, OneClick designs the mutagenic primers according to user input, e.g., amino acid position to mutate, type of amino acid substitutions (e.g., substitution to a group of amino acids with similar chemical property) and type of mutagenic primers. OneClick has incorporated an extensive range of commercially available plasmids and DNA polymerases suitable for focused mutagenesis. Therefore, OneClick also provides information on PCR mixture preparation, thermal cycling condition, expected size of PCR product and agar plate to use during bacterial transformation. Importantly, OneClick also carries out a statistical analysis of the resultant mutant library, information of which is important for selection/screening. OneClick is a unique and invaluable tool in the field of protein engineering, allowing for systematic construction of a mutant library or a protein variant and simplifying molecular biology work. The program will be constantly updated to reflect the rapid development in the fields of molecular biology and protein engineering.

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