(Q37397218)

English

Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility

scientific article published on 02 July 2013

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility (English)

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

polycyclic aromatic hydrocarbons

1 reference

based on heuristic

inferred from title

11

object named as

Suse Broyde

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Europe PubMed Central

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20 August 2017

author name string

Yuqin Cai

1

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Europe PubMed Central

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20 August 2017

Han Zheng

2

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Europe PubMed Central

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20 August 2017

Shuang Ding

3

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Europe PubMed Central

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20 August 2017

Konstantin Kropachev

4

1 reference

Europe PubMed Central

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20 August 2017

Adam G Schwaid

5

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Europe PubMed Central

PMC publication ID

20 August 2017

Yijin Tang

6

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Europe PubMed Central

PMC publication ID

20 August 2017

Hong Mu

7

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Europe PubMed Central

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20 August 2017

Shenglong Wang

8

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Europe PubMed Central

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20 August 2017

Nicholas E Geacintov

9

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20 August 2017

Yingkai Zhang

10

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20 August 2017

language of work or name

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publication date

2 July 2013

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20 August 2017

Chemical Research in Toxicology

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20 August 2017

26

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Europe PubMed Central

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20 August 2017

7

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

1115-1125

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies.

1 reference

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6 September 2017

Adenine-DNA adducts derived from the highly tumorigenic Dibenzo[a,l]pyrene are resistant to nucleotide excision repair while guanine adducts are not

1 reference

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6 September 2017

Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor

1 reference

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6 September 2017

Nuclear Magnetic Resonance Solution Structure of an N 2 -Guanine DNA Adduct Derived from the Potent Tumorigen Dibenzo[ a , l ]pyrene: Intercalation from the Minor Groove with Ruptured Watson–Crick Base Pairing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3865170

6 September 2017

Exposure to polycyclic aromatic hydrocarbons: bulky DNA adducts and cellular responses

1 reference

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6 September 2017

Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni

1 reference

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6 September 2017

Damage recognition in nucleotide excision DNA repair.

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6 September 2017

Nucleotide excision repair efficiencies of bulky carcinogen-DNA adducts are governed by a balance between stabilizing and destabilizing interactions

1 reference

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6 September 2017

Structure and stability of DNA containing an aristolactam II-dA lesion: implications for the NER recognition of bulky adducts

1 reference

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6 September 2017

Chemistry and structural biology of DNA damage and biological consequences

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6 September 2017

Energetic preference of 8-oxoG eversion pathways in a DNA glycosylase.

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6 September 2017

Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions

1 reference

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6 September 2017

Probing for DNA damage with β-hairpins: similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

1 reference

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6 September 2017

The xeroderma pigmentosum pathway: decision tree analysis of DNA quality

1 reference

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6 September 2017

Intercalative conformations of the 14R (+)- and 14S (-)-trans-anti-DB[a,l]P-N⁶-dA adducts: molecular modeling and MD simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3865170

6 September 2017

Base flipping free energy profiles for damaged and undamaged DNA.

1 reference

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6 September 2017

A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure

1 reference

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6 September 2017

Base sequence context effects on nucleotide excision repair

1 reference

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6 September 2017

Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair.

1 reference

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6 September 2017

Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3865170

6 September 2017

Two-step recognition of DNA damage for mammalian nucleotide excision repair: Directional binding of the XPC complex and DNA strand scanning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3865170

6 September 2017

The sequence dependence of human nucleotide excision repair efficiencies of benzo[a]pyrene-derived DNA lesions: insights into the structural factors that favor dual incisions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3865170

6 September 2017

On the impact of the molecule structure in chemical carcinogenesis.

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6 September 2017

Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3865170

6 September 2017

Hot topics in DNA repair: the molecular basis for different disease states caused by mutations in TFIIH and XPG.

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6 September 2017

Recognition of DNA damage by the Rad4 nucleotide excision repair protein

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6 September 2017

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

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6 September 2017

NMR structures of damaged DNA.

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6 September 2017

Computational approaches for investigating base flipping in oligonucleotides

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6 September 2017

Molecular mechanisms of mammalian global genome nucleotide excision repair.

1 reference

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6 September 2017

Dynamic conformational heterogeneities of carcinogen-DNA adducts and their mutagenic relevance

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6 September 2017

Metabolic activation of polycyclic and heterocyclic aromatic hydrocarbons and DNA damage: a review

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6 September 2017

Smoking-related DNA and protein adducts in human tissues.

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6 September 2017

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

1 reference

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6 September 2017

Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery

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6 September 2017

The Protein Data Bank

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6 September 2017

Solution structure of the (+)-cis-anti-benzo[a]pyrene-dA ([BP]dA) adduct opposite dT in a DNA duplex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3865170

6 September 2017

Tobacco smoke carcinogens and lung cancer

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6 September 2017

Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair

1 reference

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6 September 2017

1 reference

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6 September 2017

Induction of microsomal enzymes by foreign chemicals and carcinogenesis by polycyclic aromatic hydrocarbons: G. H. A. Clowes Memorial Lecture.

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6 September 2017

Recognition of DNA adducts by human nucleotide excision repair. Evidence for a thermodynamic probing mechanism

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28 September 2017

NMR solution structures of stereoisometric covalent polycyclic aromatic carcinogen-DNA adduct: principles, patterns, and diversity

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28 September 2017

Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows.

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26 June 2018

Comparative dose-response tumorigenicity studies of dibenzo[alpha,l]pyrene versus 7,12-dimethylbenz[alpha]anthracene, benzo[alpha]pyrene and two dibenzo[alpha,l]pyrene dihydrodiols in mouse skin and rat mammary gland

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26 June 2018

Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS.

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2 September 2018

Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts

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2 September 2018

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

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2 September 2018

Stereochemical, structural, and thermodynamic origins of stability differences between stereoisomeric benzo[a]pyrene diol epoxide deoxyadenosine adducts in a DNA mutational hot spot sequence

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2 September 2018

Multiple conformations of an intercalated (-)-(7S,8R,9S, 10R)-N6-[10-(7,8,9,10-tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct in the N-ras codon 61 sequence.

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2 September 2018

Dibenzo[a,l]pyrene (dibenzo[def,p]chrysene): fjord-region distortions.

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2 September 2018

Sequence specific mutagenesis of the major (+)-anti-benzo[a]pyrene diol epoxide-DNA adduct at a mutational hot spot in vitro and in Escherichia coli cells.

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2 September 2018

Solution conformation of the (+)-trans-anti-[BPh]dA adduct opposite dT in a DNA duplex: intercalation of the covalently attached benzo[c]phenanthrene to the 5'-side of the adduct site without disruption of the modified base pair

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/23758590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Unrepaired fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots

1 reference

https://pubmed.ncbi.nlm.nih.gov/23758590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Achieving broad substrate specificity in damage recognition by binding accessible nondamaged DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/23758590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/TX400156A

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

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