(Q40042600)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

title

Moving beyond Watson-Crick models of coarse grained DNA dynamics (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

author name string

Margaret C Linak

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Richard Tourdot

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

language of work or name

English

0 references

publication date

1 November 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Physics

17 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

volume

135

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

issue

20

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

page(s)

205102

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

17 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

A coarse-grained model of DNA with explicit solvation by water and ions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Chemically accurate coarse graining of double-stranded 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=3248023

Structure, location and interactions of G‐quadruplexes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in 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=3248023

Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

A mesoscale model of DNA and its renaturation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Mesoscopic modeling for nucleic acid chain 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=3248023

Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

G-quartets 40 years later: from 5'-GMP to molecular biology and supramolecular chemistry

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Human telomeric DNA: G-quadruplex, i-motif and Watson-Crick double helix

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

A semiflexible polymer model applied to loop formation 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=3248023

22 September 2017

Cleaving DNA with DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Evidence for intramolecularly folded i-DNA structures in biologically relevant CCC-repeat sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

G . T base-pairs in a DNA helix: the crystal structure of d(G-G-G-G-T-C-C-C)

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Selection of single-stranded DNA molecules that bind and inhibit human thrombin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

In vitro selection of RNA molecules that bind specific ligands

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Stabilities of double- and triple-strand helical nucleic acids

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Transient Hoogsteen base pairs in canonical duplex 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=3248023

Coarse-Grained Brownian Dynamics Simulations of the 10-23 DNAzyme.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG).

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Very stable mismatch duplexes: structural and thermodynamic studies on tandem G.A mismatches in DNA.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Molecular origins of DNA flexibility: sequence effects on conformational and mechanical properties.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Analysis of a DNA simulation model through hairpin melting experiments.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

DNA nanotweezers studied with a coarse-grained model of 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=3248023

Development of coarse-graining DNA models for single-nucleotide resolution analysis

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Coarse-grained model of nucleic acid bases.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

Brownian dynamics of double-stranded DNA in periodic systems with discrete salt

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248023

A coarse grain model for 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=3248023

Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical 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=3248023

Electrostatic Persistence Length of a Wormlike Polyelectrolyte

20 August 2018

1 reference

The nature of .pi.-.pi. interactions

21 January 2018

1 reference

Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility

21 January 2018

1 reference

The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine

21 January 2018

1 reference

Sequence-dependent DNA structure. The role of base stacking interactions

21 January 2018

1 reference

12 December 2020

Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA)

1 reference

12 December 2020

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

1 reference

12 December 2020

Self-association and protonation of adenosine 5'-monophosphate in comparison with its 2'- and 3'-analogues and tubercidin 5'-monophosphate (7-deaza-AMP)

1 reference

12 December 2020

Wobble dG X dT pairing in right-handed DNA: solution conformation of the d(C-G-T-G-A-A-T-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra

1 reference

12 December 2020

The Enthalpy of Self-Association of Purine Derivatives in Water*

1 reference

12 December 2020

Model simulations of DNA dynamics

1 reference

12 December 2020

The self-assembly of DNA Holliday junctions studied with a minimal model

1 reference

12 December 2020

Brownian dynamics simulations of single-stranded DNA hairpins

1 reference

12 December 2020

A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties

1 reference

12 December 2020

DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures

1 reference

12 December 2020

The conformation of single‐strand polynucleotides in solution: sedimentation studies of apurinic acid

1 reference

12 December 2020

Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2

1 reference

12 December 2020

Base pairing geometry in GA mismatches depends entirely on the neighboring sequence

1 reference

12 December 2020

The interaction of nucleosides in aqueous solution

1 reference

12 December 2020

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3662137

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22128958%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

PubMed publication ID

22128958

1 reference