Studies on the Conformation of a Polyelectrolyte in Solution:  Local Conformation of Cucumber Green Mottle Mosaic Virus RNA Compared with Tobacco Mosaic Virus RNA

Muroga, Yoshio; Sano, Yoh; Tagawa, Hiroyuki; Shimizu, Shigeru

doi:10.1021/jp068944j

Cited by 4 publications

(2 citation statements)

References 33 publications

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“…To account for the conformational statistics associated with an ensemble of secondary structures, it is useful (28,(40)(41)(42)(43) to represent the RNA secondary structure as a tree graph (44), i.e., a collection of points (vertices) each of which is connected by a line (bond) to at least one other point, without any closed paths. Fig.…”

Section: Theorymentioning

confidence: 99%

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures

Borodavka

Singaram

Stockley

et al. 2016

Biophysical Journal

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Long RNA molecules are at the core of gene regulation across all kingdoms of life, while also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with nonrepeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. To test whether a branched polymer model can estimate the overall sizes of large RNAs, we employed fluorescence correlation spectroscopy to examine the hydrodynamic radii of a broad spectrum of biologically important RNAs, ranging from viral genomes to long noncoding regulatory RNAs. The relative sizes of long RNAs measured at low ionic strength correspond well to those predicted by two theoretical approaches that treat the effective branching associated with secondary structure formation-one employing the Kramers theorem for calculating radii of gyration, and the other featuring the metric of maximum ladder distance. Upon addition of multivalent cations, most RNAs are found to be compacted as compared with their original, low ionic-strength sizes. These results suggest that sizes of long RNA molecules are determined by the branching pattern of their secondary structures. We also experimentally validate the proposed computational approaches for estimating hydrodynamic radii of single-stranded RNAs, which use generic RNA structure prediction tools and thus can be universally applied to a wide range of long RNAs.

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Section: Theorymentioning

confidence: 99%

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures

Borodavka

Singaram

Stockley

et al. 2016

Biophysical Journal

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“…We are not aware of any experiments that shed light on the size and structure of viral RNA as a function of the molecular weight or length. (There is size information on much shorter tRNA structures (15) and on the size of the RNA of tobacco mosaic virus (TMV), a cylindrical virus (25)). The only relevant experimental data we are aware of are recent measurements of the radius of gyration in free solution of RNA 2 of CCMV.…”

Section: Introductionmentioning

confidence: 99%

Size Regulation of ss-RNA Viruses

Zandi

Schoot

2009

Biophysical Journal

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While a monodisperse size distribution is common within one kind of spherical virus, the size of viral shells varies from one type of virus to another. In this article, we investigate the physical mechanisms underlying the size selection among spherical viruses. In particular, we study the effect of genome length and genome and protein concentrations on the size of spherical viral capsids in the absence of spontaneous curvature and bending energy. We find that the coat proteins could well adjust the size of the shell to the size of their genome, which in turn depends on the number of charges on it. Furthermore, we find that different stoichiometric mixtures of proteins and genome can produce virus particles of various sizes, consistent with in vitro experiments.

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