title: UpGene: Application of a web-based DNA codon optimization algorithm.
abstract: Although DNA codon optimization is a standard molecular biology strategy to overcome poor gene expression, to date no public software exists to facilitate this process. Among the uses of codon optimization, human immunodeficiency virus (HIV) vaccine development represents one of the most difficult challenges. A key obstacle to an effective DNA-based vaccine is the low-level expression of HIV genes in mammalian cells, which is due primarily to the instability of HIV mRNAs resulting from AU-rich elements and rare codon usage. In this report we describe the development of a DNA optimization algorithm integrated with a PCR primer design program to redesign specific coding sequences for maximal gene expression. Using this algorithm combination, together with PCR-based gene assembly, we have successfully optimized gene sequences for simian immunodeficiency virus (SIV) strain mac239 structural antigenic proteins gag and env, resulting in high-level gene expression in eukaryotic cells. Our findings demonstrate that our user-friendly algorithm is a valuable tool for DNA-based HIV vaccine development. Moreover, it can be used to optimize any other genes of interest and is freely available online at http://www.vectorcore.pitt.edu/upgene.html.
authors.affiliation: Department of Molecular Genetics and Biochemistry and Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
authors.forename: Wentao
authors.initials: W
authors.lastname: Gao
authors.forename: Alexis
authors.initials: A
authors.lastname: Rzewski
authors.forename: Huijie
authors.initials: H
authors.lastname: Sun
authors.forename: Paul D
authors.initials: PD
authors.lastname: Robbins
authors.forename: Andrea
authors.initials: A
authors.lastname: Gambotto
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002460:Cell Line; D003062:Codon / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics; D005818:Genetic Engineering / Q000379:methods; D005822:Genetic Vectors / Q000235:genetics*; D006801:Humans; D020407:Internet; D007668:Kidney / Q000196:embryology / Q000378:metabolism; D008969:Molecular Sequence Data; D009862:Online Systems; D016133:Polymerase Chain Reaction / Q000379:methods; D015202:Protein Engineering / Q000379:methods*; D011994:Recombinant Proteins / Q000096:biosynthesis*; D017422:Sequence Analysis, DNA / Q000379:methods*; D015302:Simian Immunodeficiency Virus / Q000235:genetics / Q000378:metabolism; D012984:Software; D014764:Viral Proteins / Q000096:biosynthesis / Q000235:genetics
chemical_list: D003062:Codon; D011994:Recombinant Proteins; D014764:Viral Proteins; D004247:DNA