(Q35567471)

8 August 2017

title

Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal (English)

1 reference

8 August 2017

Song Cao

1

1 reference

8 August 2017

Shi-Jie Chen

series ordinal

2

1 reference

8 August 2017

language of work or name

English

0 references

publication date

25 October 2011

1 reference

8 August 2017

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8 August 2017

volume

17

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8 August 2017

issue

12

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8 August 2017

page(s)

2130-2143

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YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models

8 August 2017

cites work

1 reference

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12 July 2018

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Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins

12 July 2018

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Computing the conformational entropy for RNA folds.

12 July 2018

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Predicting and modeling RNA architecture

12 July 2018

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DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model

12 July 2018

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Improved free energy parameters for RNA pseudoknotted secondary structure prediction

12 July 2018

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Improved RNA secondary structure prediction by maximizing expected pair accuracy

12 July 2018

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Protein elastic network models and the ranges of cooperativity

12 July 2018

1 reference

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Predicting structures and stabilities for H-type pseudoknots with interhelix loops.

12 July 2018

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Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance

12 July 2018

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RNA folding: conformational statistics, folding kinetics, and ion electrostatics.

12 July 2018

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Riboswitches: emerging themes in RNA structure and function

12 July 2018

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How RNA unfolds and refolds

12 July 2018

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Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

12 July 2018

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The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

12 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Direct observation of hierarchical folding in single riboswitch aptamers

12 July 2018

1 reference

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Evolution of small nuclear RNAs in S. cerevisiae, C. albicans, and other hemiascomycetous yeasts

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Automated de novo prediction of native-like RNA tertiary structures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Informatics challenges in structured RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

The spliceosome: a ribozyme at heart?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Bridging the gap in RNA structure prediction.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Unusual mechanical stability of a minimal RNA kissing complex

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

CONTRAfold: RNA secondary structure prediction without physics-based models

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Partition function and base pairing probabilities of RNA heterodimers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Predicting RNA pseudoknot folding thermodynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Folding thermodynamics of pseudoknotted chain conformations.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

The Amber biomolecular simulation programs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

The role of shape in determining molecular motions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Riboswitches as versatile gene control elements

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Fast and effective prediction of microRNA/target duplexes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Is HIV-1 RNA dimerization a prerequisite for packaging? Yes, no, probably?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Prediction of hybridization and melting for double-stranded nucleic acids

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Dimerization of retroviral RNA genomes: an inseparable pair.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

The thermodynamics of DNA structural motifs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

MicroRNAs: genomics, biogenesis, mechanism, and function

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Prediction of mammalian microRNA targets

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

microRNAs: runts of the genome assert themselves

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

RNA loop-loop interactions as dynamic functional motifs.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Self-induced structural switches in RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Bulged residues promote the progression of a loop-loop interaction to a stable and inhibitory antisense-target RNA complex

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Predicting oligonucleotide affinity to nucleic acid targets

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Stepping through an RNA structure: A novel approach to conformational analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Structure of the dimer initiation complex of HIV-1 genomic RNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Dynamic RNA-RNA interactions in the spliceosome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Improved free-energy parameters for predictions of RNA duplex stability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Dominant forces in protein folding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Partition function and base pairing probabilities for RNA-RNA interaction prediction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Potent effect of target structure on microRNA function.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Predicting RNA folding thermodynamics with a reduced chain representation model.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

The kinetics of ligand binding by an adenine-sensing riboswitch

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Secondary structure prediction of interacting RNA molecules.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Global ribosome motions revealed with elastic network model

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Structural requirement for the two-step dimerization of human immunodeficiency virus type 1 genome

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

NMR structure of the mature dimer initiation complex of HIV-1 genomic RNA.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

A 19-nucleotide sequence upstream of the 5' major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Optimised parameters for RNA double-helices

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

7 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3222126

NMR analysis of intra- and inter-molecular stems in the dimerization initiation site of the HIV-1 genome

7 December 2018

1 reference

12 December 2020

fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex

1 reference

12 December 2020

NCp7 activates HIV-1Lai RNA dimerization by converting a transient loop-loop complex into a stable dimer

1 reference

12 December 2020

Four-way junctions in antisense RNA-mRNA complexes involved in plasmid replication control: a common theme?

1 reference

12 December 2020

One sequence, two ribozymes: implications for the emergence of new ribozyme folds

1 reference

12 December 2020

Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions

1 reference

12 December 2020

A kissing complex together with a stable dimer is involved in the HIV-1Lai RNA dimerization process in vitro

1 reference

12 December 2020

Identifiers

DOI

10.1261/RNA.026658.111

1 reference

8 August 2017

1 reference

8 August 2017

1 reference