(Q41465668)

English

Accommodation of a 1S-(-)-benzo[c]phenanthrenyl-N6-dA adduct in the Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations

scientific article published on March 2005

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

1 October 2017

Accommodation of a 1S-(-)-benzo[c]phenanthrenyl-N6-dA adduct in the Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations (English)

1 reference

Europe PubMed Central

1 October 2017

6

object named as

Suse Broyde

1 reference

Europe PubMed Central

1 October 2017

author name string

Lihua Wang

1

1 reference

Europe PubMed Central

1 October 2017

Min Wu

2

1 reference

Europe PubMed Central

1 October 2017

S Frank Yan

3

1 reference

Europe PubMed Central

1 October 2017

Dinshaw J Patel

4

1 reference

Europe PubMed Central

1 October 2017

Nicholas E Geacintov

5

1 reference

Europe PubMed Central

1 October 2017

publication date

1 March 2005

1 reference

Europe PubMed Central

1 October 2017

Chemical Research in Toxicology

1 reference

Europe PubMed Central

1 October 2017

18

1 reference

Europe PubMed Central

1 October 2017

3

1 reference

Europe PubMed Central

1 October 2017

441-456

1 reference

Europe PubMed Central

1 October 2017

Nature and nurture - lessons from chemical carcinogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Conformational searches elucidate effects of stereochemistry on structures of deoxyadenosine covalently bound to tumorigenic metabolites of benzo[C] phenanthrene.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Chemical-induced DNA damage and human cancer risk

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Efficient and error-free replication past a minor-groove N2-guanine adduct by the sequential action of yeast Rev1 and DNA polymerase zeta.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Efficient and error-free replication past a minor-groove DNA adduct by the sequential action of human DNA polymerases iota and kappa

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Replication of a cis-syn thymine dimer at atomic resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Deoxynucleotide triphosphate binding mode conserved in Y family DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Effects of base sequence context on translesion synthesis past a bulky (+)-trans-anti-B[a]P-N2-dG lesion catalyzed by the Y-family polymerase pol kappa.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Damage repair DNA polymerases Y.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

How DNA lesions are turned into mutations within cells?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Translesion replication of benzo[a]pyrene and benzo[c]phenanthrene diol epoxide adducts of deoxyadenosine and deoxyguanosine by human DNA polymerase iota

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Replication of damaged DNA in mammalian cells: new solutions to an old problem

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Active site tightness and substrate fit in DNA replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Error-prone repair DNA polymerases in prokaryotes and eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Error-prone DNA polymerases: novel structures and the benefits of infidelity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Structure of the catalytic core of S. cerevisiae DNA polymerase eta: implications for translesion DNA synthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Base sequence dependence of in vitro translesional DNA replication past a bulky lesion catalyzed by the exo- Klenow fragment of Pol I.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Effects of benzo[a]pyrene DNA adducts on Escherichia coli DNA polymerase I (Klenow fragment) primer-template interactions: evidence for inhibition of the catalytically active ternary complex formation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Response of human DNA polymerase iota to DNA lesions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Error-prone lesion bypass by human DNA polymerase eta.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Human DNA polymerase kappa synthesizes DNA with extraordinarily low fidelity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Error-free and error-prone lesion bypass by human DNA polymerase kappa in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Purification and characterization of pol kappa, a DNA polymerase encoded by the human DINB1 gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Misinsertion and bypass of thymine-thymine dimers by human DNA polymerase iota

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Eukaryotic polymerases iota and zeta act sequentially to bypass DNA lesions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase eta.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Error-prone bypass of certain DNA lesions by the human DNA polymerase kappa

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Mechanisms of accurate translesion synthesis by human DNA polymerase eta

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

The human DINB1 gene encodes the DNA polymerase Poltheta

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

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=4696753

11 June 2018

The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Replication of damaged DNA: molecular defect in xeroderma pigmentosum variant cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

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=4696753

11 June 2018

Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass DNA polymerase activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

An open and closed case for all polymerases.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

DNA adduct formation by polycyclic aromatic hydrocarbon dihydrodiol epoxides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Solution conformation of the (-)-trans-anti-benzo[c]phenanthrene-dA ([BPh]dA) adduct opposite dT in a DNA duplex: intercalation of the covalently attached benzo[c]phenanthrenyl ring to the 3'-side of the adduct site and comparison with the (+)-trans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

In vitro replication by prokaryotic and eukaryotic polymerases on DNA templates containing site-specific and stereospecific benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide adducts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Oxidative Metabolism of Polycyclic Aromatic Hydrocarbons to Ultimate Carcinogens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Lennard-Jones potential calculations of the barrier to rotation around the glycosidic C-N linkage in selected purine nucleosides and nucleotides. A direct comparison of the results of 6-12 potential calculations with results of semiempirical molecul

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

N-ras and human cancer.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

ras oncogenes in human cancer: a review

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Non-planar structure of nitrous bases and non-coplanarity of Watson-Crick pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Mutations of genes of the ras family in human and experimental tumors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

11 June 2018

Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 2018

Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 2018

Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 2018

Pre-steady-state kinetic studies of the fidelity of Sulfolobus solfataricus P2 DNA polymerase IV.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 2018

Toward understanding the mutagenicity of an environmental carcinogen: structural insights into nucleotide incorporation preferences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 2018

trans-Lesion synthesis past bulky benzo[a]pyrene diol epoxide N2-dG and N6-dA lesions catalyzed by DNA bypass polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 2018

Low fidelity DNA synthesis by a y family DNA polymerase due to misalignment in the active site.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 2018

Efficient translesion replication past oxaliplatin and cisplatin GpG adducts by human DNA polymerase eta.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 2018

Factors determining mutagenic potential for individual cis and trans opened benzo[c]phenanthrene diol epoxide-deoxyadenosine adducts.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4696753

19 August 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

1 reference

https://pubmed.ncbi.nlm.nih.gov/15777084

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effect of single benzo[a]pyrene diol epoxide-deoxyguanosine adducts on the action of DNA polymerases in vitro

1 reference

https://pubmed.ncbi.nlm.nih.gov/15777084

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/15777084

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A DNA hairpin with a single residue loop closed by a strongly distorted Watson-Crick G x C base-pair

1 reference

https://pubmed.ncbi.nlm.nih.gov/15777084

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/15777084

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Interaction and solvation energies of nonpolar DNA base analogues and their role in polymerase insertion fidelity

1 reference

https://pubmed.ncbi.nlm.nih.gov/15777084

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/15777084

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Impact of the stereochemistry of benzo[a]pyrene 7,8-dihydrodiol 9,10-epoxide-deoxyadenosine adducts on resistance to digestion by phosphodiesterases I and II and translesion synthesis with HIV-1 reverse transcriptase

1 reference

https://pubmed.ncbi.nlm.nih.gov/15777084

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stereoselective metabolism of the (+)-(S,S)- and (-)-(R,R)-enantiomers of trans-3,4-dihydroxy-3,4-dihydrobenzo[c]-phenanthrene by rat and mouse liver microsomes and by a purified and reconstituted cytochrome P-450 system

1 reference

https://pubmed.ncbi.nlm.nih.gov/15777084

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Primer Extension by Various Polymerases Using Oligonucleotide Templates Containing Stereoisomeric Benzo[a]pyrene-Deoxyadenosine Adducts

1 reference

https://pubmed.ncbi.nlm.nih.gov/15777084

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/TX049786V

1 reference

Europe PubMed Central

1 October 2017

1 reference

Europe PubMed Central

1 October 2017

1 reference

Europe PubMed Central

1 October 2017

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q41465668&oldid=1921788687"