(Q38339825)

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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

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scholarly article

1 reference

Europe PubMed Central

2 September 2017

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 (English)

1 reference

Europe PubMed Central

2 September 2017

computational biology

1 reference

based on heuristic

inferred from title

5

object named as

Suse Broyde

1 reference

Europe PubMed Central

2 September 2017

author name string

Rebecca A Perlow-Poehnelt

1

1 reference

Europe PubMed Central

2 September 2017

Ilya Likhterov

2

1 reference

Europe PubMed Central

2 September 2017

David A Scicchitano

3

1 reference

Europe PubMed Central

2 September 2017

Nicholas E Geacintov

4

1 reference

Europe PubMed Central

2 September 2017

language of work or name

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publication date

21 June 2004

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Europe PubMed Central

2 September 2017

number of pages

11

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inferred from page(s)

Journal of Biological Chemistry

1 reference

Europe PubMed Central

2 September 2017

279

1 reference

Europe PubMed Central

2 September 2017

36951-36961

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Europe PubMed Central

2 September 2017

35

1 reference

Europe PubMed Central

2 September 2017

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

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Translesion synthesis by human DNA polymerase kappa on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-N(2)-BPDE (7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene).

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 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://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Lesion bypass in yeast cells: Pol eta participates in a multi-DNA polymerase process

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II, IV and V) deal with lesion/sequence context diversity

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Efficiency and accuracy of SOS-induced DNA polymerases replicating benzo[a]pyrene-7,8-diol 9,10-epoxide A and G adducts

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

How DNA lesions are turned into mutations within cells?

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Active site tightness and substrate fit in DNA replication

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

DNA polymerases: structural diversity and common mechanisms

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

DNA replication fidelity

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

An open and closed case for all polymerases.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

poliota-dependent lesion bypass in vitro

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

The "tale" of UmuD and its role in SOS mutagenesis

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 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://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Human DNA polymerase mu (Pol mu) exhibits an unusual replication slippage ability at AAF lesion

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Unique misinsertion specificity of poliota may decrease the mutagenic potential of deaminated cytosines

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Lesions in DNA: hurdles for polymerases

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

A plethora of lesion-replicating DNA polymerases

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Polkappa protects mammalian cells against the lethal and mutagenic effects of benzo[a]pyrene

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Error-prone repair DNA polymerases in prokaryotes and eukaryotes

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

The Y-family of DNA polymerases

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

The expanding polymerase universe

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Functions of eukaryotic DNA polymerases

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Determination of urinary metabolites of polycyclic aromatic hydrocarbons (PAH) for the risk assessment of PAH-exposed workers

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

106. The isolation of a cancer-producing hydrocarbon from coal tar. Parts I, II, and III

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Polycyclic aromatic hydrocarbons in the diet.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in P53.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Slow repair of bulky DNA adducts along the nontranscribed strand of the human p53 gene may explain the strand bias of transversion mutations in cancers.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Tumorigenicity of the optical enantiomers of the diastereomeric benzo[a]pyrene 7,8-diol-9,10-epoxides in newborn mice: exceptional activity of (+)-7beta,8alpha-dihydroxy-9alpha,10alpha-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Solution conformation of the major adduct between the carcinogen (+)-anti-benzo[a]pyrene diol epoxide and DNA

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template-primer junction

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 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://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 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.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

The major, N2-dG adduct of (+)-anti-B[a]PDE induces G-->A mutations in a 5'-AGA-3' sequence context.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

The major, N2-dG adduct of (+)-anti-B[a]PDE shows a dramatically different mutagenic specificity (predominantly, G --> A) in a 5'-CGT-3' sequence context.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Mutational specificity of the (+)-anti-diol epoxide of benzo[a]pyrene in a supF gene of an Escherichia coli plasmid: DNA sequence context influences hotspots, mutagenic specificity and the extent of SOS enhancement of mutagenesis.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Mutagenesis by the (+)-anti-diol epoxide of benzo[a]pyrene: what controls mutagenic specificity?

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Are base substitution and frameshift mutagenesis pathways interrelated? An analysis based upon studies of the frequencies and specificities of mutations induced by the (+)-anti diol epoxide of benzo[a]pyrene

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

DNA polymerase action on benzo[a]pyrene-DNA adducts

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

The major, N2-Gua adduct of the (+)-anti-benzo[a]pyrene diol epoxide is capable of inducing G-->A and G-->C, in addition to G-->T, mutations.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Mutagenic potential of stereoisomeric bay region (+)- and (-)-cis-anti-benzo[a]pyrene diol epoxide-N2-2'-deoxyguanosine adducts in Escherichia coli and simian kidney cells

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Preferential misincorporation of purine nucleotides by human DNA polymerase eta opposite benzo[a]pyrene 7,8-diol 9,10-epoxide deoxyguanosine adducts

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Benzo[a]pyrene diol epoxide-deoxyguanosine adducts are accurately bypassed by yeast DNA polymerase zeta in vitro

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Mutagenesis by (+)-anti-B[a]P-N2-Gua, the major adduct of activated benzo[a]pyrene, when studied in an Escherichia coli plasmid using site-directed methods.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

A role for DNA polymerase V in G --> T mutations from the major benzo[a]pyrene N2-dG adduct when studied in a 5'-TGT sequence in E. coli

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 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://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Effects of benzo[a]pyrene adduct stereochemistry on downstream DNA replication in vitro: evidence for different adduct conformations within the active site of DNA polymerase I (Klenow fragment).

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 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://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Extending the understanding of mutagenicity: structural insights into primer-extension past a benzo[a]pyrene diol epoxide-DNA adduct

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Replication of a cis-syn thymine dimer at atomic resolution

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Damage repair DNA polymerases Y.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Structure of the replicating complex of a pol alpha family DNA polymerase

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Structure of Taq polymerase with DNA at the polymerase active site

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Minor Groove Interactions between Polymerase and DNA: More Essential to Replication than Watson-Crick Hydrogen Bonds?

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Spectroscopic characteristics and site I/site II classification of cis and trans benzo[a]pyrene diolepoxide enantiomer-guanosine adducts in oligonucleotides and polynucleotides

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Role of hydrophobic effects in the reaction of a polynuclear aromatic diol epoxide with oligodeoxynucleotides in aqueous solutions

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Synthesis and characterization of covalent adducts derived from the binding of benzo[a]pyrene diol expoxide to a -GGG- sequence in a deoxyoligonucleotide

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Stereochemical origin of opposite orientations in DNA adducts derived from enantiomeric anti-benzo[a]pyrene diol epoxides with different tumorigenic potentials.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Comparison of simple potential functions for simulating liquid water

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

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21 January 2018

Solvent-accessible surfaces of proteins and nucleic acids

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Localization of DNA polymerases eta and iota to the replication machinery is tightly co-ordinated in human cells.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Solution structure of a cis-opened (10R)-N6-deoxyadenosine adduct of (9S,10R)-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA duplex

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Conformational determinants of structures in stereoisomeric cis-opened anti-benzo[a]pyrene diol epoxide adducts to adenine in DNA.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1 reference

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21 January 2018

Double-stranded DNA stereoselectively binds benzo(a)pyrene diol epoxides

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M404332200

21 January 2018

Identifiers

10.1074/JBC.M404332200

1 reference

Europe PubMed Central

2 September 2017

1 reference

Europe PubMed Central

2 September 2017

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