Borodavka, A, Singaram, SW, Stockley, PG orcid.org/0000-0002-1360-2751 et al. (3 more authors) (2016) Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures. Biophysical Journal, 111 (10). pp. 2077-2085. ISSN 0006-3495
Abstract
Long RNA molecules are at the core of gene regulation across all kingdoms of life, whilst also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with non-repeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. In order 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 non-coding 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 RNAmolecules are determined by the branching pattern of their secondary structures. They 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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | ©� 2016 Biophysical Society. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds) > Bioinformatics (Leeds) The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds) > Biological Chemistry (Leeds) |
Funding Information: | Funder Grant number Wellcome Trust 103068/Z/13/Z Wellcome Trust 089310/Z/09/Z |
Depositing User: | Symplectic Publications |
Date Deposited: | 13 Oct 2016 11:43 |
Last Modified: | 23 Jun 2023 22:15 |
Published Version: | https://doi.org/10.1016/j.bpj.2016.10.014 |
Status: | Published |
Publisher: | Biophysical Society |
Identification Number: | 10.1016/j.bpj.2016.10.014 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:105942 |