Probing Viral Genomic Structure: Alternative Viewpoints and Alternative Structures for Satellite Tobacco Mosaic Virus RNA

详细信息    查看全文

• 作者：Susan J. Schroeder
• 刊名：Biochemistry
• 出版年：2014
• 出版时间：November 4, 2014
• 年：2014
• 卷：53
• 期：43
• 页码：6728-6737
• 全文大小：388K
• ISSN：1520-4995

文摘

Viral RNA structure prediction is a valuable tool for development of drugs against viral disease. This work discusses different approaches to predicting encapsidated viral RNA and highlights satellite tobacco mosaic virus (STMV) RNA as a model system with excellent crystallography data. Fundamentally important issues for debate include thermodynamic versus kinetic control of virus assembly and the possible consequences of quasi-species in the primary structure on RNA secondary structure prediction of a single structure or an ensemble of structures. Multiple computational tools and chemical reagents are now available for improved viral RNA structure prediction. Two different predicted structures for encapsidated STMV RNA result from differences in three main areas: a different approach and philosophy to studying encapsidated viral RNA, an emphasis on different RNA motifs, and technical differences in computational methods and chemical reagents. The experiments with traditional chemical probing and SHAPE reagents are compared in terms of chemistry, results, and interpretation for STMV RNA as well as other RNA protein assemblies, such as the 5鈥睻TR of HIV and the ribosome. This discussion of the challenges of viral RNA structure prediction will lead to new experiments and improved future predictions for viral RNA.