Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study (Q40640527)

22 September 2017

Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study (English)

1 reference

22 September 2017

2

1 reference

22 September 2017

Elke Duchardt

1

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PMC publication ID

2475628

22 September 2017

Jürgen Schleucher

series ordinal

3

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22 September 2017

25 June 2008

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22 September 2017

9

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inferred from page(s)

published in

Nucleic Acids Research

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22 September 2017

36

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22 September 2017

12

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22 September 2017

4211-4219

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Empirical force fields for biological macromolecules: overview and issues.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

13C and (15)N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

On the truncation of long-range electrostatic interactions in DNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

13C-NMR of the deoxyribose sugars in four DNA oligonucleotide duplexes: assignment and structural features.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Crystal structure analysis of a complete turn of B-DNA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Three-state models of furanose pseudorotation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Deoxyribose ring conformation of [d(GGTATACC)]2: an analysis of vicinal proton-proton coupling constants from two-dimensional proton nuclear magnetic resonance

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Deoxyribose conformation in [d(GTATATAC)]2: evaluation of sugar pucker by simulation of double-quantum-filtered COSY cross-peaks

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Backbone dynamics of the Bacillus subtilis glucose permease IIA domain determined from 15N NMR relaxation measurements

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Residue specific ribose and nucleobase dynamics of the cUUCGg RNA tetraloop motif by MNMR 13C relaxation.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

13C NMR relaxation studies of RNA base and ribose nuclei reveal a complex pattern of motions in the RNA binding site for human U1A protein

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

A suite of 2H NMR spin relaxation experiments for the measurement of RNA dynamics

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

Modeling furanose ring dynamics in DNA.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2475628

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

20 August 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN375

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN375

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN375

Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution: Simulations of Nucleosides

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN375

The use of model selection in the model-free analysis of protein dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN375

Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN375

An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates

21 January 2018

1 reference

12 December 2020

Rotational diffusion tensor of nucleic acids from 13C NMR relaxation

1 reference

12 December 2020

13C-NMR relaxation in three DNA oligonucleotide duplexes: model-free analysis of internal and overall motion

1 reference

12 December 2020

Selectively 13C-enriched DNA: evidence from 13C1' relaxation rate measurements of an internal dynamics sequence effect in the lac operator

1 reference

12 December 2020

Dynamics in psoralen-damaged DNA by 1H-detected natural abundance 13C NMR spectroscopy

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKN375

1 reference

22 September 2017

1 reference

PMC publication ID

2475628

22 September 2017

PubMed publication ID

18579564

1 reference

PMC publication ID

2475628