Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.

PubWeight™: 0.75‹?›

🔗 View Article (PMID 28625696)

Published in Biophys J on June 15, 2017

Authors

Chanin T Woods1, Lela Lackey2, Benfeard Williams3, Nikolay V Dokholyan3, David Gotz4, Alain Laederach5

Author Affiliations

1: Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
2: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
3: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
4: Carolina Health Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
5: Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Electronic address: alain@unc.edu.

Articles cited by this

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science (2000) 28.25

Structure of the 30S ribosomal subunit. Nature (2000) 23.11

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J (1992) 21.67

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 10.35

A new generation of homology search tools based on probabilistic inference. Genome Inform (2009) 8.93

Starting at the beginning, middle, and end: translation initiation in eukaryotes. Cell (1997) 7.15

Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics (2001) 7.07

High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell (2001) 6.97

RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc (2005) 6.46

Sequences responsible for intracellular localization of beta-actin messenger RNA also affect cell phenotype. J Cell Biol (1994) 6.33

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc (2006) 6.14

Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A (2008) 5.44

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol (2004) 5.44

Spatial regulation of beta-actin translation by Src-dependent phosphorylation of ZBP1. Nature (2005) 5.29

Characterization of a beta-actin mRNA zipcode-binding protein. Mol Cell Biol (1997) 5.21

RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res (2001) 4.96

Intracellular localization of messenger RNAs for cytoskeletal proteins. Cell (1986) 4.53

Ribosome structure and the mechanism of translation. Cell (2002) 4.53

Folding of the adenine riboswitch. Chem Biol (2006) 3.95

Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res (2004) 3.81

RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA (2005) 3.80

The stem-loop structure at the 3' end of histone mRNA is necessary and sufficient for regulation of histone mRNA stability. Mol Cell Biol (1987) 3.61

RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics (2005) 3.20

Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des (1998) 2.96

Regulation of histone mRNA in the unperturbed cell cycle: evidence suggesting control at two posttranscriptional steps. Mol Cell Biol (1991) 2.94

RNA structure: reading the ribosome. Science (2005) 2.91

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA (2008) 2.86

Exploring the folding landscape of a structured RNA. Proc Natl Acad Sci U S A (2001) 2.78

Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet (2010) 2.54

Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics (2008) 2.48

RNA and protein folding: common themes and variations. Biochemistry (2005) 2.47

RNA SHAPE analysis in living cells. Nat Chem Biol (2012) 2.02

An algorithm for comparing multiple RNA secondary structures. Comput Appl Biosci (1988) 1.94

Abstract shapes of RNA. Nucleic Acids Res (2004) 1.90

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. Biochemistry (2002) 1.80

The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J Mol Biol (2003) 1.80

Revolutions in RNA secondary structure prediction. J Mol Biol (2006) 1.74

Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting". Curr Opin Struct Biol (2002) 1.73

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods (2014) 1.72

Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature (2010) 1.69

Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. RNA (2009) 1.68

ZBP1 recognition of beta-actin zipcode induces RNA looping. Genes Dev (2010) 1.63

A two-dimensional mutate-and-map strategy for non-coding RNA structure. Nat Chem (2011) 1.58

Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature (2015) 1.53

The mechanisms of RNA SHAPE chemistry. J Am Chem Soc (2012) 1.52

The histone mRNA 3' end is required for localization of histone mRNA to polyribosomes. Nucleic Acids Res (1992) 1.50

Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet (2011) 1.46

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis. PLoS Comput Biol (2015) 1.44

Single-molecule RNA folding. Acc Chem Res (2005) 1.43

Tertiary interactions determine the accuracy of RNA folding. J Am Chem Soc (2008) 1.40

Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. Proc Natl Acad Sci U S A (2005) 1.36

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res (2006) 1.33

Core requirements of the adenine riboswitch aptamer for ligand binding. RNA (2007) 1.33

Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J Comput Chem (2010) 1.31

RNA folding pathway functional intermediates: their prediction and analysis. J Mol Biol (2001) 1.31

A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. RNA (2011) 1.29

Clustering of RNA secondary structures with application to messenger RNAs. J Mol Biol (2006) 1.27

Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control. Genes Dev (2012) 1.26

The Nucleic Acid Database: new features and capabilities. Nucleic Acids Res (2013) 1.23

Evaluation of the information content of RNA structure mapping data for secondary structure prediction. RNA (2010) 1.23

Evaluating our ability to predict the structural disruption of RNA by SNPs. BMC Genomics (2012) 1.19

An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics (2012) 1.19

Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol (2008) 1.15

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. J Phys Chem B (2012) 1.14

Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering. J Am Chem Soc (2010) 1.10

Consistent global structures of complex RNA states through multidimensional chemical mapping. Elife (2015) 1.01

The Azoarcus group I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins. J Biol Chem (2011) 1.00

Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR. RNA (2015) 0.98

Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model. J Comput Biol (2007) 0.98

Riboswitch structure: an internal residue mimicking the purine ligand. Nucleic Acids Res (2009) 0.96

Detection of RNA-Protein Interactions in Living Cells with SHAPE. Biochemistry (2015) 0.95

Polar bears, antibiotics, and the evolving ribosome (Nobel Lecture). Angew Chem Int Ed Engl (2010) 0.95

Structural effects of linkage disequilibrium on the transcriptome. RNA (2011) 0.95

In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state. Proc Natl Acad Sci U S A (2015) 0.95

From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. Curr Opin Struct Biol (2015) 0.93

RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA (2011) 0.91

Evolutionary evidence for alternative structure in RNA sequence co-variation. PLoS Comput Biol (2013) 0.91

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells. Proc Natl Acad Sci U S A (2016) 0.88

ACTB in cancer. Clin Chim Acta (2012) 0.88

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method. J Math Biol (2007) 0.88

Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches. Methods Mol Biol (2009) 0.83

Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1. Nucleic Acids Res (2015) 0.81

The potential of the riboSNitch in personalized medicine. Wiley Interdiscip Rev RNA (2015) 0.81

Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution. Wiley Interdiscip Rev RNA (2016) 0.77

RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. J Mol Biol (2016) 0.75