Literature DB >> 35348613

Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.

Md Solayman1, Thomas Litfin1, Jaswinder Singh2, Kuldip Paliwal2, Yaoqi Zhou1,3,4, Jian Zhan3.   

Abstract

Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of tertiary structures an increasingly attractive feature to explore. Here, we provide a survey of these recent developments, which indicate the emergence of solvent accessibility as a simple 1D property, adding to secondary and tertiary structures for investigating complex structure-function relations of RNAs.
© The Author(s) 2022. Published by Oxford University Press.

Entities:  

Keywords:  RNA; RNA–protein interactions; SASA; probing; solvent accessibility

Mesh:

Substances:

Year:  2022        PMID: 35348613      PMCID: PMC9116373          DOI: 10.1093/bib/bbac112

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   13.994


  91 in total

1.  Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica.

Authors:  C D Bustamante; J P Townsend; D L Hartl
Journal:  Mol Biol Evol       Date:  2000-02       Impact factor: 16.240

2.  sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections.

Authors:  Md Tamjidul Hoque; Yuedong Yang; Avdesh Mishra; Yaoqi Zhou
Journal:  J Comput Chem       Date:  2016-02-05       Impact factor: 3.376

3.  UNAFold: software for nucleic acid folding and hybridization.

Authors:  Nicholas R Markham; Michael Zuker
Journal:  Methods Mol Biol       Date:  2008

4.  In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

Authors:  Yiliang Ding; Yin Tang; Chun Kit Kwok; Yu Zhang; Philip C Bevilacqua; Sarah M Assmann
Journal:  Nature       Date:  2013-11-24       Impact factor: 49.962

5.  Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq.

Authors:  Yiliang Ding; Chun Kit Kwok; Yin Tang; Philip C Bevilacqua; Sarah M Assmann
Journal:  Nat Protoc       Date:  2015-06-18       Impact factor: 13.491

6.  OH radicals and oxidizing products in the gamma radiolysis of water.

Authors:  J A LaVerne
Journal:  Radiat Res       Date:  2000-02       Impact factor: 2.841

7.  Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.

Authors:  T Ooi; M Oobatake; G Némethy; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1987-05       Impact factor: 11.205

8.  The interpretation of protein structures: estimation of static accessibility.

Authors:  B Lee; F M Richards
Journal:  J Mol Biol       Date:  1971-02-14       Impact factor: 5.469

9.  Visualizing the higher order folding of a catalytic RNA molecule.

Authors:  D W Celander; T R Cech
Journal:  Science       Date:  1991-01-25       Impact factor: 47.728

10.  Probing RNA folding by hydroxyl radical footprinting.

Authors:  Maria Costa; Dario Monachello
Journal:  Methods Mol Biol       Date:  2014
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  1 in total

1.  Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling.

Authors:  Jaswinder Singh; Kuldip Paliwal; Thomas Litfin; Jaspreet Singh; Yaoqi Zhou
Journal:  Bioinformatics       Date:  2022-06-25       Impact factor: 6.931

  1 in total

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