Chapter title |
Novel Biochemical Tools for Probing HIV RNA Structure
|
---|---|
Chapter number | 7 |
Book title |
HIV Protocols
|
Published in |
Methods in molecular biology, January 2016
|
DOI | 10.1007/978-1-4939-3046-3_7 |
Pubmed ID | |
Book ISBNs |
978-1-4939-3045-6, 978-1-4939-3046-3
|
Authors |
Jason W. Rausch, Joanna Sztuba-Solinska, Sabrina Lusvarghi, Stuart F. J. Le Grice, Rausch, Jason W., Sztuba-Solinska, Joanna, Lusvarghi, Sabrina, Le Grice, Stuart F. J. |
Abstract |
Functional analysis of viral RNA requires knowledge of secondary structure arrangements and tertiary base interactions. Thus, high-throughput and comprehensive methods for assessing RNA structure are highly desirable. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) has proven highly useful for modeling the secondary structures of HIV and other retroviral RNAs in recent years. This technology is not without its limitations however, as SHAPE data can be severely compromised when the RNA under study is structurally heterogeneous. In addition, the method reveals little information regarding the three-dimensional (3D) organization of an RNA. This chapter outlines four detailed SHAPE-related methodologies that circumvent these limitations. "Ensemble" and "in-gel" variations of SHAPE permit structural analysis of individual conformers within structurally heterogeneous mixtures of RNA, while probing strategies that utilize "through-space" cleavage reagents such as methidiumpropyl-EDTA (MPE) and peptides appended with an ATCUN (amino terminal copper/nickel binding motif) can provide insight into 3D organization. Combinational application of these techniques provides a formidable arsenal for exploring the structures of HIV RNAs and associated nucleoprotein complexes. |
Mendeley readers
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Unknown | 13 | 100% |
Demographic breakdown
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Student > Ph. D. Student | 4 | 31% |
Professor | 2 | 15% |
Student > Bachelor | 1 | 8% |
Other | 1 | 8% |
Student > Doctoral Student | 1 | 8% |
Other | 1 | 8% |
Unknown | 3 | 23% |
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Medicine and Dentistry | 1 | 8% |
Other | 0 | 0% |
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