Molecular Biotechnology

, Volume 52, Issue 2, pp 123–128 | Cite as

C.U.R.R.F. (Codon Usage regarding Restriction Finder): A Free Java®-Based Tool to Detect Potential Restriction Sites in Both Coding and Non-Coding DNA Sequences

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Abstract

The synthesis of complete genes is becoming a more and more popular approach in heterologous gene expression. Reasons for this are the decreasing prices and the numerous advantages in comparison to classic molecular cloning methods. Two of these advantages are the possibility to adapt the codon usage to the host organism and the option to introduce restriction enzyme target sites of choice. C.U.R.R.F. (Codon Usage regarding Restriction Finder) is a free Java®-based software program which is able to detect possible restriction sites in both coding and non-coding DNA sequences by introducing multiple silent or non-silent mutations, respectively. The deviation of an alternative sequence containing a desired restriction motive from the sequence with the optimal codon usage is considered during the search of potential restriction sites in coding DNA and mRNA sequences as well as protein sequences. C.U.R.R.F is available at http://www.zvm.tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_mathematik_und_naturwissenschaften/fachrichtung_biologie/mikrobiologie/allgemeine_mikrobiologie/currf.

Keywords

Potential restriction sites Codon usage Codon optimization Gene synthesis Heterologous gene expression 
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Notes

Acknowledgments

We would like to thank Martina Holz for the fast and uncomplicated installation of the above named website.

Conflict of Interest

None.

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© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Institut für MikrobiologieTechnische Universität DresdenDresdenGermany
  2. 2.Technische FakultätUniversität BielefeldBielefeldGermany

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