UpGene: Application of a Web-Based DNA Codon Optimization Algorithm

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• 作者：Wentao Gao ; Alexis Rzewski ; Huijie Sun ; Paul D. Robbins ; and Andrea Gambotto
• 刊名：Biotechnology Progress
• 出版年：2004
• 出版时间：April 2004
• 年：2004
• 卷：20
• 期：2
• 页码：443 - 448
• 全文大小：183K
• 年卷期：v.20,no.2(April 2004)
• ISSN：1520-6033

文摘

Although DNA codon optimization is a standard molecular biology strategy to overcomepoor gene expression, to date no public software exists to facilitate this process. Amongthe uses of codon optimization, human immunodeficiency virus (HIV) vaccine development represents one of the most difficult challenges. A key obstacle to an effectiveDNA-based vaccine is the low-level expression of HIV genes in mammalian cells, whichis due primarily to the instability of HIV mRNAs resulting from AU-rich elementsand rare codon usage. In this report we describe the development of a DNAoptimization algorithm integrated with a PCR primer design program to redesignspecific coding sequences for maximal gene expression. Using this algorithm combination, together with PCR-based gene assembly, we have successfully optimized genesequences for simian immunodeficiency virus (SIV) strain mac239 structural antigenicproteins gag and env, resulting in high-level gene expression in eukaryotic cells. Ourfindings 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 genesof interest and is freely available online at http://www.vectorcore.pitt.edu/upgene.html.