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Insights into Secondary and Tertiary Interactions of Dengue Virus RNA by SHAPE

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Dengue

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1138))

Abstract

Dengue virus (DENV) is a single-stranded positive-sense RNA virus belonging to the Flaviviridae family. The DENV RNA genome contains multiple cis-acting elements that continue to unravel their essential role in managing viral molecular processes. Attempts have been made to predict the secondary structure of DENV RNA using a variety of computational tools. Nevertheless, a greater degree of accuracy is achieved when these methods are complemented with structure probing experimentation. This chapter outlines detailed methodology for the structural study of DENV subgenomic minigenome RNA by applying high-throughput selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). High-throughput SHAPE combines a novel chemical probing technology with reverse transcription, capillary electrophoresis, and secondary structure prediction software to rapidly and reproducibly determine the structure of RNAs from several hundred to several thousand nucleotides at single-nucleotide resolution. This methodology investigates local structure for all positions in a sequence-independent manner and as such it is particularly useful in predicting RNA secondary and tertiary interactions.

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Acknowledgments

This work was funded by the Intramural Research Program of the National Cancer Institute, National Institutes of Health, Department of Health and Human Services.

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Authors and Affiliations

  1. RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA

    Joanna Sztuba-Solinska & Stuart F. J. Le Grice

Authors
  1. Joanna Sztuba-Solinska
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  2. Stuart F. J. Le Grice
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Corresponding author

Correspondence to Stuart F. J. Le Grice .

Editor information

Editors and Affiliations

  1. Georgetown University Medical Center Dept. of Microbiology and Immunology, Washington, District of Columbia, USA

    Radhakrishnan Padmanabhan

  2. Duke-NUS GMS Singapore Emerging Infectious Diseases, Singapore, Singapore

    Subhash G. Vasudevan

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Sztuba-Solinska, J., Le Grice, S.F.J. (2014). Insights into Secondary and Tertiary Interactions of Dengue Virus RNA by SHAPE. In: Padmanabhan, R., Vasudevan, S. (eds) Dengue. Methods in Molecular Biology, vol 1138. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0348-1_14

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  • DOI: https://doi.org/10.1007/978-1-4939-0348-1_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0347-4

  • Online ISBN: 978-1-4939-0348-1

  • eBook Packages: Springer Protocols

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