Abstract
Restriction enzymes are the workhorses of molecular biology. We introduce a new problem that arises in the course of our project to design virus variants to serve as potential vaccines: we wish to modify virus-length genomes to introduce large numbers of unique restriction enzyme recognition sites while preserving wild-type function by substitution of synonymous codons. We show that the resulting problem is NP-Complete, give an exponential-time algorithm, and propose effective heuristics, which we show give excellent results for five sample viral genomes. Our resulting modified genomes have several times more unique restriction sites and reduce the maximum gap between adjacent sites by three to nine-fold.
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
Preview
Unable to display preview. Download preview PDF.
References
Bugl, H., Danner, J.P., Molinari, R.J., Mulligan, J.T., Park, H.O., Reichert, B., Roth, D.A., Wagner, R., Budowle, B., Scripp, R.M., Smith, J.A.L., Steele, S.J., Church, G., Endy, D.: Dna synthesis and biological security. Nature Biotechnology 25, 627–629 (2007)
Czar, M.J., Anderson, J.C., Bader, J.S., Peccoud, J.: Gene synthesis demystified. Trends in Biotechnology 27(2), 63–72 (2009)
Coleman, J.R., Papamichail, D., Skiena, S., Futcher, B., Wimmer, E., Mueller, S.: Virus attenuation by genome-scale changes in codon pair bias. Science 320(5884), 1784–1787 (2008)
Wimmer, E., Mueller, S., Tumpey, T., Taubenberger, J.: Synthetic viruses: a new opportunity to understand and prevent viral disease. Nature Biotech. 27(12), 1163–1172 (2009)
Roberts, R., Vincze, T., Posfai, J., Macelis, D.: Rebase–a database for dna restriction and modification: enzymes, genes and genomes. Nucl. Acids Res. 38, D234–D236 (2010)
González-Ballester, D., de Montaigu, A., Galván, A., Fernández, E.: Restriction enzyme site-directed amplification PCR: a tool to identify regions flanking a marker DNA. Anal. Biochem. 340(2), 330–335
Roberts, R.: How restriction enzymes became the workhorses of molecular biology. Proc. Natl. Acad. Sci. 102, 5905–5908 (2005)
Mens, T., Tourwe, T.: A survey of software refactoring. IEEE Transactions on Software Engineering 30(2), 126–139 (2004)
Serial Cloner, http://serialbasics.free.fr/Serial_Cloner.html
Cello, J., Paul, A., Wimmer, E.: Chemical synthesis of poliovirus cdna: generation of infectious virus in the absence of natural template. Science 297(5583), 1016–1018 (2002)
Chan, L., Kosuri, S., Endy, D.: Refactoring bacteriophage t7. Mol. Syst. Biol. 1 (2005)
Anand, I., Kosuri, S., Endy, D.: Genejax: A prototype cad tool in support of genome refactoring (2006)
Evans, P., Liu, C.: Sitefind: A software tool for introducing a restriction site as a marker for successful site-directed mutagenesis. BMC Mol. Biol. 6(22)
Richardson, S.M., Wheelan, S.J., Yarrington, R.M., Boeke, J.D.: Genedesign: Rapid, automated design of multikilobase synthetic genes. Genome Res. 16(4), 550–556 (2006)
Skiena, S.: Designing better phages. Bioinformatics 17, S253–S261 (2001)
Papadimitriou, C., Yannakakis, M.: Optimization, approximation, and complexity classes. In: STOC 1988: Proceedings of the twentieth annual ACM symposium on Theory of computing, pp. 229–234. ACM, New York (1988)
Duh, R.C., Frer, M.: Approximation of k-set cover by semi-local optimization. In: Proc. 29th STOC, pp. 256–264. ACM, New York (1997)
Hopcroft, J.E., Karp, R.M.: An n 5/2 algorithm for maximum matchings in bipartite graphs. SIAM Journal on Computing 2(4), 225–231 (1973)
Aho, A.V., Corasick, M.J.: Efficient string matching: An aid to bibliographic search. Communications of the ACM 18(6), 333–340 (1975)
Vincze, T., Posfai, J., Roberts, R.J.: NEBcutter: a program to cleave DNA with restriction enzymes. Nucl. Acids Res. 31(13), 3688–3691 (2003)
Ermolaeva, M.: Synonymous codon usage in bacteria. Curr. Issues Mol. Biol. 3(4), 91–97 (2001)
Kuhn, H.W.: The hungarian method for the assignment problem. Naval Research Logistics Quarterly 2, 83–97 (1955)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Montes, P., Memelli, H., Ward, C., Kim, J., Mitchell, J.S.B., Skiena, S. (2010). Optimizing Restriction Site Placement for Synthetic Genomes. In: Amir, A., Parida, L. (eds) Combinatorial Pattern Matching. CPM 2010. Lecture Notes in Computer Science, vol 6129. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13509-5_29
Download citation
DOI: https://doi.org/10.1007/978-3-642-13509-5_29
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-13508-8
Online ISBN: 978-3-642-13509-5
eBook Packages: Computer ScienceComputer Science (R0)