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RNA Biol. 2017 Nov 2;14(11):1466-1472. doi: 10.1080/15476286.2017.1325069. Epub 2017 Oct 11.

Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch.

Author information

1
a Department of Cell Biology and Molecular Genetics , University of Maryland - College Park , College Park , MD , USA.
2
b Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research , Frederick , MD , USA.
3
c RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute , Frederick , MD , USA.

Abstract

How plus-strand [+]RNA virus genomes transition from translation templates to replication templates is a matter of much speculation. We have previously proposed that, for Turnip crinkle virus, binding of the encoded RNA-dependent RNA polymerase (RdRp) to the 3'UTR of the [+]RNA template promotes a regional wide-spread conformational switch to an alternative structure that disassembles the cap-independent translation enhancer (CITE) in the 3'UTR. The active 3'CITE folds into a tRNA-like T-shaped structure (TSS) that binds to 80S ribosomes and 60S subunits in the P-site. In this Point-of-View, we discuss the history of our research on the TSS and our recent report combining coarse level single molecule force spectroscopy (optical tweezers) with fine-grain computer simulations of this experimental process and biochemical approaches to obtain a detailed understanding of how RdRp binding in the TSS vicinity might lead to an extensive rearrangement of the RNA structure.

KEYWORDS:

3′ CITE; RNA structural switch; dynamics simulations; optical tweezer; steered molecular; translation enhancer; turnip crinkle virus

PMID:
28548627
PMCID:
PMC5785213
DOI:
10.1080/15476286.2017.1325069
[Indexed for MEDLINE]
Free PMC Article

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