End-to-end attraction of duplex DNA. (Q30514058)

11 August 2017

End-to-end attraction of duplex DNA. (English)

1 reference

11 August 2017

Aleksei Aksimentiev

0 references

Christopher Maffeo

1 reference

11 August 2017

Binquan Luan

series ordinal

1 reference

11 August 2017

language of work or name

English

0 references

publication date

12 January 2012

1 reference

11 August 2017

Nucleic Acids Research

1 reference

11 August 2017

1 reference

11 August 2017

1 reference

11 August 2017

3812-3821

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

11 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Physics of DNA: unravelling hidden abilities encoded in the structure of ‘the most important molecule’.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Understanding biology by stretching proteins: recent progress.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Closing the lid on DNA end-to-end stacking interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Rapid genome sequencing with short universal tiling probes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Molecular dynamics simulations of nucleic acid-protein complexes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

End-to-end stacking and liquid crystal condensation of 6 to 20 base pair DNA duplexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Ionic effects on viral DNA packaging and portal motor function in bacteriophage phi 29.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Overview of the structure of all-AT oligonucleotides: organization in helices and packing interactions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Folding DNA to create nanoscale shapes and patterns

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Scalable molecular dynamics with NAMD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Calculation of absolute protein-ligand binding free energy from computer simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

The mechanism of non-homologous end-joining: a synopsis of synapsis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Stacked-unstacked equilibrium at the nick site of DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

A synthetic DNA walker for molecular transport

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Mechanism and regulation of human non-homologous DNA end-joining

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Osmotic shock and the strength of viral capsids

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Programmable and autonomous computing machine made of biomolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Steered molecular dynamics investigations of protein function.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Thermodynamic parameters for DNA sequences with dangling ends

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

DNA flexibility studied by covalent closure of short fragments into circles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

DNA bending, flexibility, and helical repeat by cyclization kinetics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351176

Inter-DNA attraction mediated by divalent counterions

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

Colloquium: The physics of charge inversion in chemical and biological systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

DNA-DNA interactions in tight supercoils are described by a small effective charge density

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

Intrinsic rates and activation free energies from single-molecule pulling experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

Efficiency of Coaxial Stacking Depends on the DNA Duplex Structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

Nonequilibrium Equality for Free Energy Differences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

DNA-guided crystallization of colloidal nanoparticles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

DNA-programmable nanoparticle crystallization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1220

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

21 January 2018

1 reference

12 December 2020

On the mechanism of hydrophobic association of nanoscopic solutes

1 reference

12 December 2020

Osmotic properties of DNA: Critical evaluation of counterion condensation theory

1 reference

12 December 2020

Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKR1220

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

22241779

1 reference