(Q36901545)

17 August 2017

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes (English)

1 reference

17 August 2017

4

Ahmed H Zewail

1 reference

17 August 2017

Milo M Lin

1

1 reference

17 August 2017

Lars Meinhold

series ordinal

2

1 reference

17 August 2017

Dmitry Shorokhov

series ordinal

3

1 reference

17 August 2017

language of work or name

English

0 references

publication date

3 June 2008

1 reference

Physical Chemistry Chemical Physics

17 August 2017

1 reference

17 August 2017

10

1 reference

17 August 2017

29

1 reference

17 August 2017

4227-4239

1 reference

Coarse-grained models of protein folding: toy models or predictive tools?

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

DNA folding and melting observed in real time redefine the energy landscape

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

The thermodynamics of DNA structural motifs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

RNA hairpin-folding kinetics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

A semiflexible polymer model applied to loop formation in DNA hairpins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

29 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Canonical dynamics: Equilibrium phase-space distributions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Kinetics of conformational fluctuations in DNA hairpin-loops

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Hierarchy and dynamics of RNA folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Exceptionally stable nucleic acid hairpins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

On loop folding in nucleic acid hairpin-type structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Analysis of melting transitions of the DNA hairpins formed from the oligomer sequences d[GGATAC(X)4GTATCC] (X = A, T, G, C).

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Tetraloops and RNA folding

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base-pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14)

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

Statistical mechanics of base stacking and pairing in DNA melting.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2548322

GROMACS 3.0: a package for molecular simulation and trajectory analysis

4 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1039%2FB804675C

Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution

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

Exploring the energy landscape of a small RNA hairpin

1 reference

12 December 2020

Hairpin formation in synthetic oligonucleotides

1 reference

12 December 2020

Collapsed but not folded: looking with advanced optical spectroscopy at protein folding

1 reference

12 December 2020

Experimental thermodynamics of the helix-random coil transition. IV. Influence of the base composition of DNA on the transition enthalpy

1 reference

12 December 2020

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

1 reference

12 December 2020

Bubble nucleation and cooperativity in DNA melting

1 reference

12 December 2020

Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp

1 reference

12 December 2020

Sequence dependent rigidity of single stranded DNA

1 reference

12 December 2020

A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy

1 reference

12 December 2020

GROMACS: A message-passing parallel molecular dynamics implementation

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

A smooth particle mesh Ewald method

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

Molecular dynamics with coupling to an external bath

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

LINCS: A linear constraint solver for molecular simulations

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

Polymorphic transitions in single crystals: A new molecular dynamics method

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

Comparison of simple potential functions for simulating liquid water

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

A molecular dynamics method for simulations in the canonical ensemble

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

Constant pressure molecular dynamics for molecular systems

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

Thermal denaturation of DNA molecules: A comparison of theory with experiment

1 reference

8 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1039/B804675C

Identifiers

DOI

10.1039/B804675C

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

18633543

1 reference