Title: Synthetic gene design with a large number of hidden stops

Authors: Vinhthuy Phan, Sudip Saha, Ashutosh Pandey, Tit-Yee Wong

Addresses: The Bioinformatics Program, Department of Computer Science, The University of Memphis, Memphis, TN 38152, USA. ' Department of Computer Science, The University of Memphis, Memphis, TN 38152, USA. ' The Bioinformatics Program, The University of Memphis, Memphis, TN 38152, USA. ' Department of Biology, The University of Memphis, Memphis, TN 38152, USA

Abstract: Hidden stops are nucleotide triples TAA, TAG and TGA that appear on the second and third reading frames of a protein coding gene. Recent studies suggested the important role of hidden stops in preventing misread of mRNA. We study the problem of designing protein-encoding genes with large number of hidden stops under several biological constraints. With simple constraints, redesigned genes have provable maximal number of hidden stops. With more complex constraints, redesigned genes still have many more hidden stops than wild-type genes. We showed that redesigned genes have a distinct positional advantage in assisting early termination of frame-shifts.

Keywords: synthetic biology; hidden stops; codons; mRNA; back translation; gene design; protein coding genes; bioinformatics.

DOI: 10.1504/IJDMB.2010.034195

International Journal of Data Mining and Bioinformatics, 2010 Vol.4 No.4, pp.377 - 394

Published online: 17 Jul 2010 *

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