Title: Computationally Optimised DNA Assembly of synthetic genes

Authors: Liza S.Z. Larsen, Christopher D. Wassman, G. Wesley Hatfield, Richard H. Lathrop

Addresses: CODA Genomics Inc., Laguna Hills, CA 92653, USA. ' Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA. ' The Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA. ' Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA

Abstract: Gene synthesis is hampered by two obstacles: improper assembly of oligonucleotides; oligonucleotide defects incurred during chemical synthesis. To overcome the first problem, we describe the employment of a Computationally Optimised DNA Assembly (CODA) algorithm that uses the degeneracy of the genetic code to design overlapping oligonucleotides with thermodynamic properties for self-assembly into a single, linear, DNA product. To address the second problem, we describe a hierarchical assembly strategy that reduces the incorporation of defective oligonucleotides into full-length gene constructs. The CODA algorithm and these biological methods enable fast, simple and reliable assemblies of sequence-correct full-length genes.

Keywords: synthetic biology; computational biology; DNA self-assembly; gene synthesis; DNA assembly optmisation; CODA algorithm; bioinformatics; oligonucleotides; thermodynamics.

DOI: 10.1504/IJBRA.2008.019578

International Journal of Bioinformatics Research and Applications, 2008 Vol.4 No.3, pp.324 - 336

Published online: 17 Jul 2008 *

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