(Q36538187)

14 August 2017

Predicting thymine dimerization yields from molecular dynamics simulations (English)

1 reference

14 August 2017

0 references

5

Bern Kohler

1 reference

Carlos E Crespo-Hernández

14 August 2017

Yu Kay Law

1

0 references

Eric Olmon

object named as

Eric Olmon

series ordinal

4

0 references

object named as

Carlos E Crespo-Hernández

series ordinal

3

0 references

author name string

Javad Azadi

series ordinal

2

1 reference

PMCID

2292369

14 August 2017

language of work or name

English

0 references

publication date

11 January 2008

1 reference

14 August 2017

1 reference

14 August 2017

94

1 reference

14 August 2017

9

1 reference

14 August 2017

3590-3600

1 reference

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

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Thymine dimerization in DNA is an ultrafast photoreaction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

On the mechanism of thymine photodimerization

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

The precursor of the thymine dimer in ice.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

GROMACS: fast, flexible, and free

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

DNA and its counterions: a molecular dynamics study

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

UCSF Chimera--a visualization system for exploratory research and analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Ultrafast excited-state dynamics in nucleic acids

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Crystal structure of a DNA decamer containing a cis-syn thymine dimer

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Solvent influence on base stacking

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

MOLMOL: a program for display and analysis of macromolecular structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Crystal and molecular structure of 1,1'-trimethylenebisthymine (Thy-C3-Thy). Environment of a solid state photochemical reaction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Solid state ultraviolet irradiation of 1,1'-trimethylenebisthymine and photosensitized irradiation of 1,1'-polymethylenebisthymines

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Origin of DNA helical structure and its sequence dependence

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Nuclear magnetic resonance studies of cis-syn, trans-syn, and 6-4 photodimers of thymidylyl(3'-5')thymidine monophosphate and cis-syn photodimers of thymidylyl(3'-5')thymidine cyanoethyl phosphotriester

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Structure and dynamics of poly(T) single-strand DNA: implications toward CPD formation

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Effect of denaturation on the photochemistry of pyrimidine bases in isolated DNA.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Base stacking controls excited-state dynamics in A.T DNA.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

A new [2 + 2] photodimerization of 5-chloro- and 5-methyl-2-pyridone in their inclusion complexes with 1,1'-biphenyl-2,2'-dicarboxylic acid as a model for DNA damage by photodimerization of its thymine component

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Sugar conformational effects on the photochemistry of thymidylyl(3'-5')thymidine

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Isolation and mass spectrometric characterization of dimeric adenine photoproducts in oligodeoxynucleotides

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

UV light as a footprinting agent: modulation of UV-induced DNA damage by transcription factors bound at the promoters of three human genes

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Ultrafast Deactivation Channel for Thymine Dimerization

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Low ionic strength reduces cytosine photoreactivity in UVC-irradiated isolated DNA

4 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2292369

Conformational sampling using high-temperature molecular dynamics

4 December 2018

1 reference

12 December 2020

Depopulation of highly excited singlet states of DNA model compounds: quantum yields of 193 and 245 nm photoproducts of pyrimidine monomers and dinucleoside monophosphates

1 reference

12 December 2020

Photochemical addition of amino acids and peptides to DNA

1 reference

12 December 2020

Quantum yields and secondary photoreactions of the photoproducts of dTpdT, dTpdC and dTpdU

1 reference

12 December 2020

An NMR and conformational investigation of the trans-syn cyclobutane photodimers of dTpdU

1 reference

12 December 2020

Use of light for footprinting DNA in vivo

1 reference

12 December 2020

Molecular structure of a deoxyribose-dinucleotide, sodium thymidylyl-(5' yields to 3')-thymidylate-(5') hydrate (pTpT), and a possible structural model for polythymidylate

1 reference

12 December 2020

The photochemistry of adenosine: intermediates contributing to its photodegradation mechanism in aqueous solution at 298 K and characterization of the major product

1 reference

12 December 2020

Dinucleotide TpT and its 2'-O-Me analogue possess different backbone conformations and flexibilities but similar stacked geometries

1 reference

12 December 2020

Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides

1 reference

12 December 2020

NMR studies of bipyrimidine cyclobutane photodimers

1 reference

12 December 2020

Nonaqueous solutions of DNA. Denaturation in methanol and ethanol

1 reference

12 December 2020

The excited-state precursor of the thymine dimer

1 reference

12 December 2020

Influence of polynucleotide secondary structure on thymine photodimerization

1 reference

12 December 2020

Identification and structure determination of a third cyclobutane photodimer of thymidylyl-(3'-->5')-thymidine: the trans-syn-II product

1 reference

12 December 2020

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

1 reference

12 December 2020

Far-UV-lnduced Dimeric Photoproducts in Short Oligonucleotides: Sequence Effects

1 reference

12 December 2020

Crystal structure and photochemical behavior in solution of the 3'-N-sulfamate analogue of thymidylyl(3'-5')thymidine

1 reference

12 December 2020

Conical intersections as a mechanistic feature of organic photochemistry

1 reference

20 August 2023

https://opencitations.net/index/coci/api/v1/citations/10.1351/PAC199567050783

Identifiers

DOI

10.1529/BIOPHYSJ.107.118612

1 reference

14 August 2017

1 reference

14 August 2017

1 reference

PMCID

2292369