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

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Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures
Creator	Borodavka, Alexander Ben-Shaul, Avinoam Tuma, Roman Gelbart, William Singaram, Surendra Stockley, Peter
topic	covid:4986b7765ef8df0192f45b087cdae599a0aaf77e#this
Source	Elsevier; Medline; PMC
abstract	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.
has issue date	2016-11-01(xsd:dateTime)
bibo:doi	10.1016/j.bpj.2016.10.014
bibo:pmid	27851933
has license	hybrid-oa
sha1sum (hex)	4986b7765ef8df0192f45b087cdae599a0aaf77e
schema:url	https://doi.org/10.1016/j.bpj.2016.10.014
resource representing a document's title	Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures
has PubMed Central identifier	PMC5113152
has PubMed identifier	27851933
schema:publication	Biophysical Journal
resource representing a document's body	covid:4986b7765ef8df0192f45b087cdae599a0aaf77e#body_text
is http://vocab.deri.ie/void#inDataset of	https://covidontheweb.inria.fr:4443/about/id/http/ns.inria.fr/covid19/4986b7765ef8df0192f45b087cdae599a0aaf77e
is schema:about of	named entity 'SIZES' named entity 'ranging' named entity 'RNA' named entity 'RNAs' named entity 'sequences' named entity 'determined' named entity 'RNA' named entity 'RNA' named entity 'CATIONS' named entity 'WIDE' named entity 'RAMIFIED' named entity 'USE' named entity 'MODEL' named entity 'ORIGINAL' named entity 'LARGE' named entity 'RNA' named entity 'POLYMERS' named entity 'USUALLY' named entity 'BRANCHED' named entity 'MEASURED' named entity 'GENOMES' named entity 'SINGLE' named entity 'STRUCTURES' named entity 'ADOPT' named entity 'FORMATION' named entity 'MAXIMUM' named entity 'ACROSS' named entity 'IONIC' named entity 'LADDER' named entity 'THEORETICAL' named entity 'EMPLOYED' named entity 'TO EXAMINE' named entity 'TO TEST' named entity 'LIFE' named entity 'VIRAL' named entity 'APPROACHES' named entity 'MOLECULES' named entity 'RELATIVE' named entity 'ASSOCIATED WITH' named entity 'IONIC STRENGTH' named entity 'BIOLOGICALLY' named entity 'DETERMINED BY' named entity 'APPLIED' named entity 'HAVE' named entity 'LOW' named entity 'PROPOSED' named entity 'SECONDARY' named entity 'DETERMINED BY' named entity 'GENE REGULATION' named entity 'EFFECTIVE' named entity 'COMPUTATIONAL' named entity 'ADDITION' named entity 'GENERIC' named entity 'HYDRODYNAMIC' named entity 'FLUORESCENCE CORRELATION SPECTROSCOPY ' named entity 'BETTER' named entity 'OVERALL' named entity 'SEQUENCES' named entity 'BRANCHING' named entity 'RNA STRUCTURE PREDICTION' named entity 'SUGGEST' named entity 'METRIC' named entity 'PATTERNS' named entity 'LONG' named entity 'SECONDARY' named entity 'REGULATORY' named entity 'FOUND' named entity 'SERVING' named entity 'DISTANCE' named entity 'THESE' named entity 'DESCRIBED' named entity 'CALCULATING' named entity 'BROAD SPECTRUM' named entity 'PHYSICAL PROPERTIES'

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