Abstract
Codon optimization has been widely used for designing native or synthetic genes to enhance their expression in heterologous host organisms. We recently developed Codon Optimization On-Line (COOL) which is a web-based tool to provide multi-objective codon optimization functionality for synthetic gene design. COOL provides a simple and flexible interface for customizing codon optimization based on several design parameters such as individual codon usage, codon pairing, and codon adaptation index. User-defined sequences can also be compared against the COOL optimized ones to show the extent by which the user’s sequences can be evaluated and further improved. The utility of COOL is demonstrated via a case study where the codon optimized sequence of an invertase enzyme is generated for the enhanced expression in E. coli.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Elena C, Ravasi P, Castelli ME, Peiru S, Menzella HG (2014) Expression of codon optimized genes in microbial systems: current industrial applications and perspectives. Front Microbiol 5:21
Sharp PM, Li WH (1987) The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295
Makrides SC (1996) Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol Rev 60:512–538
Chung BK-S, Yusufi FNK, Mariati YY, Lee D-Y (2013) Enhanced expression of codon optimized interferon gamma in CHO cells. J Biotechnol 167:326–333
Gould N, Hendy O, Papamichail D (2014) Computational tools and algorithms for designing customized synthetic genes. Front Bioeng Biotechnol 2:41
Chung BK-S, Lee D-Y (2012) Computational codon optimization of synthetic gene for protein expression. BMC Syst Biol 6:134
Deb K, Pratap A, Agarwal S, Meyarivan T (2002) Fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Trans Evol Comput 6:182–197
Chin JX, Chung BK-S, Lee D-Y (2014) Codon Optimization On-Line (COOL): a web-based multi-objective optimization platform for synthetic gene design. Bioinformatics 30:2210–2212
Pek HB, Klement M, Ang K-S, Chung BK-S, Ow DS-W, Lee D-Y (2015) Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli. Enzyme Microb Technol 75–76:57–63
The UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res 43(D1):D204–D212
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media New York
About this protocol
Cite this protocol
Yu, K., Ang, K.S., Lee, DY. (2017). Synthetic Gene Design Using Codon Optimization On-Line (COOL). In: Hughes, R. (eds) Synthetic DNA. Methods in Molecular Biology, vol 1472. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6343-0_2
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6343-0_2
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6341-6
Online ISBN: 978-1-4939-6343-0
eBook Packages: Springer Protocols