Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model (Q40183197)

18 September 2017

Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model (English)

1 reference

18 September 2017

Zacharias M

1

1 reference

PMC publication ID

1301424

18 September 2017

language of work or name

English

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publication date

1 May 2001

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18 September 2017

14

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based on heuristic

inferred from page(s)

published in

Biophysical Journal

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18 September 2017

80

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18 September 2017

5

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18 September 2017

2350-2363

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Conformational deformability of RNA: a harmonic mode analysis

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

22 September 2017

RNA-protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Stable sheared A.C pair in DNA hairpins.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Adaptive recognition in RNA complexes with peptides and protein modules

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Hairpin loops consisting of single adenine residues closed by sheared A.A and G.G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Occurrence, solution structure and stability of DNA hairpins stabilized by a GA/CG helix unit

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Trinucleotide repeats that expand in human disease form hairpin structures in vitro

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

The purine-rich trinucleotide repeat sequences d(CAG)15 and d(GAC)15 form hairpins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Sequence analysis of the termini of virion and replicative forms of minute virus of mice DNA suggests a modified rolling hairpin model for autonomous parvovirus DNA replication

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Force field based conformational analysis of RNA structural motifs: GNRA tetraloops and their pyrimidine relatives.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

The combination of symbolic and numerical computation for three-dimensional modeling of RNA.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Experimental and computational studies of the G[UUCG]C RNA tetraloop.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

GNRA tetraloops make a U-turn

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

Stable formation of a pyrimidine-rich loop hairpin in a cruciform promoter

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301424

The hairpin structure of a topoisomerase II site DNA strand analyzed by combined NMR and energy minimization methods

4 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976205-4

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976205-4

Definitions and nomenclature of nucleic acid structure parameters

7 January 2021

1 reference

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E. coli SSB activates N4 virion RNA polymerase promoters by stabilizing a DNA hairpin required for promoter recognition

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976205-4

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

7 January 2021

1 reference

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Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

7 January 2021

1 reference

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The trinucleotide repeat sequence d(CGG)15 forms a heat-stable hairpin containing Gsyn. Ganti base pairs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976205-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976205-4

Semianalytical treatment of solvation for molecular mechanics and dynamics

7 January 2021

1 reference

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Experimental and theoretical studies of the effects of deoxyribose substitutions on the stability of the UUCG tetraloop

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976205-4

GNA trinucleotide loop sequences producing extraordinarily stable DNA minihairpins

7 January 2021

1 reference

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Simulation of the structure and dynamics of nonhelical RNA motifs

7 January 2021

1 reference

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Comparison of molecular dynamics and harmonic mode calculations on RNA

7 January 2021

1 reference

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10.1016/S0006-3495(01)76205-4

7 January 2021

Identifiers

DOI

1 reference

18 September 2017

1 reference

PMC publication ID

1301424

18 September 2017

PubMed publication ID

11325735

1 reference

PMC publication ID

1301424