Synthetic gene design with a large number of hidden stops
by Vinhthuy Phan, Sudip Saha, Ashutosh Pandey, Tit-Yee Wong
International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 4, No. 4, 2010

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.

Online publication date: Sat, 17-Jul-2010

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