title: Synthetic gene design with a large number of hidden stops.
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.
authors.affiliation: The Bioinformatics Program, Department of Computer Science, The University of Memphis, Memphis, TN 38152, USA. vphan@memphis.edu
authors.forename: Vinhthuy
authors.initials: V
authors.lastname: Phan
authors.forename: Sudip
authors.initials: S
authors.lastname: Saha
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Pandey
authors.forename: Tit-Yee
authors.initials: TY
authors.lastname: Wong
mesh_terms: D001483:Base Sequence; D018388:Codon, Terminator; D005813:Genes, Synthetic; D016366:Open Reading Frames; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D018388:Codon, Terminator; D012333:RNA, Messenger