Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study (Q34452369)

2 August 2017

Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study (English)

1 reference

2 August 2017

2

Martin Zacharias

1 reference

2 August 2017

André Barthel

1

1 reference

PubMed ID

16399833

2 August 2017

language of work or name

English

0 references

publication date

6 January 2006

1 reference

2 August 2017

1 reference

2 August 2017

90

1 reference

2 August 2017

7

1 reference

2 August 2017

2450-2462

1 reference

Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy

2 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Nucleic acid crystallography: current progress

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Strategies for RNA folding and assembly

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Atomistic view of base flipping in DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Simulation and modeling of nucleic acid structure, dynamics and interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

6 July 2018

Analysis of RNA motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

6 July 2018

RNA-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Simulations of nucleic acids and their complexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Structural motifs in RNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

RNA folds: insights from recent crystal structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Role of RNA structure in arginine recognition of TAR RNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Role of a bulged A residue in a specific RNA-protein interaction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Defining the structure of irregular nucleic acids: conventions and principles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Specific interaction between RNA phage coat proteins and RNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Comparative NMR study of An-bulge loops in DNA duplexes: intrahelical stacking of A, A-A, and A-A-A bulge loops

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Energetic and conformational aspects of A:T base-pair opening within the DNA double helix.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1403169

Major groove accessibility of RNA

27 October 2018

1 reference

12 December 2020

Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA

1 reference

12 December 2020

NMR structural refinement of an extrahelical adenosine tridecamer d(CGCAGAATTCGCG)2 via a hybrid relaxation matrix procedure

1 reference

12 December 2020

Systematic and statistical error in histogram-based free energy calculations

1 reference

12 December 2020

Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy

1 reference

12 December 2020

Simulation of the structure and dynamics of nonhelical RNA motifs

1 reference

12 December 2020

Crystal structure of an RNA bacteriophage coat protein–operator complex

1 reference

12 December 2020

Continuum solvent studies of the stability of RNA hairpin loops and helices

1 reference

12 December 2020

A story: unpaired adenosine bases in ribosomal RNAs

1 reference

12 December 2020

Bulge-induced bends in RNA: quantification by transient electric birefringence

1 reference

12 December 2020

10.1529/BIOPHYSJ.105.076158

Identifiers

DOI

1 reference

release_llm546qruvcvfameokrfs6bqxu

2 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/llm546qruvcvfameokrfs6bqxu

24 November 2022

mapped directly with Wikidata item

PMCID

1403169

1 reference

2 August 2017

1 reference

PubMed ID

16399833