Probing Retroviral and Retrotransposon Genome Structures: The “SHAPE” of Things to ComeReport as inadecuate

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Molecular Biology InternationalVolume 2012 2012, Article ID 530754, 12 pages

Review ArticleRT Biochemistry Section, HIV Drug Resistance Program, National Cancer Institute, Fredrick, MD 21702-1201, USA

Received 15 February 2012; Accepted 13 March 2012

Academic Editor: Abdul Waheed

Copyright © 2012 Joanna Sztuba-Solinska and Stuart F. J. Le Grice. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Understanding the nuances of RNA structure as they pertain to biological function remains a formidable challenge for retrovirus research and development of RNA-based therapeutics, an area of particular importance with respect to combating HIV infection. Although a variety of chemical and enzymatic RNA probing techniques have been successfully employed for more than 30 years, they primarily interrogate small 100–500 nt RNAs that have been removed from their biological context, potentially eliminating long-range tertiary interactions such as kissing loops and pseudoknots that may play a critical regulatory role. Selective 2′ hydroxyl acylation analyzed by primer extension SHAPE, pioneered recently by Merino and colleagues, represents a facile, user-friendly technology capable of interrogating RNA structure with a single reagent and, combined with automated capillary electrophoresis, can analyze an entire 10,000-nucleotide RNA genome in a matter of weeks. Despite these obvious advantages, SHAPE essentially provides a nucleotide “connectivity map,” conversion of which into a 3-D structure requires a variety of complementary approaches. This paper summarizes contributions from SHAPE towards our understanding of the structure of retroviral genomes, modifications to which technology that have been developed to address some of its limitations, and future challenges.

Author: Joanna Sztuba-Solinska and Stuart F. J. Le Grice



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