Molecular Dynamics Study of One-Base Deletion Duplexes Containing the Major DNA Adduct Formed by Ochratoxin A: Effects of Sequence Context and Adduct Ionization State on Lesion Site Structure and Mutagenicity

Preetleen Kathuria; Prebhleen Singh; Purshotam Sharma; Richard A. Manderville; Stacey D. Wetmore

doi:10.1021/acs.jpcb.9b06489

Molecular Dynamics Study of One-Base Deletion Duplexes Containing the Major DNA Adduct Formed by Ochratoxin A: Effects of Sequence Context and Adduct Ionization State on Lesion Site Structure and Mutagenicity

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.9b06489 ◽

2019 ◽

Vol 123 (32) ◽

pp. 6980-6989

Author(s):

Preetleen Kathuria ◽

Prebhleen Singh ◽

Purshotam Sharma ◽

Richard A. Manderville ◽

Stacey D. Wetmore

Keyword(s):

Molecular Dynamics ◽

Ochratoxin A ◽

Dna Adduct ◽

Lesion Site ◽

Ionization State ◽

Sequence Context ◽

Site Structure

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Molecular Modeling of the Major DNA Adduct Formed from Food Mutagen Ochratoxin A inNarI Two-Base Deletion Duplexes: Impact of Sequence Context and Adduct Ionization on Conformational Preference and Mutagenicity

Chemical Research in Toxicology ◽

10.1021/acs.chemrestox.7b00103 ◽

2017 ◽

Vol 30 (8) ◽

pp. 1582-1591 ◽

Cited By ~ 3

Author(s):

Preetleen Kathuria ◽

Purshotam Sharma ◽

Richard A. Manderville ◽

Stacey D. Wetmore

Keyword(s):

Molecular Modeling ◽

Ochratoxin A ◽

Dna Adduct ◽

Conformational Preference ◽

Sequence Context ◽

Food Mutagen

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Molecular Dynamics Simulations of Mismatched DNA Duplexes Associated with the Major C8-Linked 2′-Deoxyguanosine Adduct of the Food Mutagen Ochratoxin A: Influence of Opposing Base, Adduct Ionization State, and Sequence on the Structure of Damaged DNA

Chemical Research in Toxicology ◽

10.1021/acs.chemrestox.8b00064 ◽

2018 ◽

Vol 31 (8) ◽

pp. 712-720 ◽

Cited By ~ 1

Author(s):

Preetleen Kathuria ◽

Purshotam Sharma ◽

Richard A. Manderville ◽

Stacey D. Wetmore

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Ochratoxin A ◽

Dna Duplexes ◽

Ionization State ◽

Mismatched Dna ◽

Dynamics Simulations ◽

Food Mutagen ◽

Damaged Dna

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Impact of DNA Adduct Size, Number, and Relative Position on the Toxicity of Aromatic Amines: A Molecular Dynamics Case Study of ANdG- and APdG-Containing DNA Duplexes

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.1c00202 ◽

2021 ◽

Author(s):

Ryan W. Kung ◽

Trinity K. Deak ◽

Cassidy A. Griffith-Salik ◽

Nathania A. Takyi ◽

Stacey D. Wetmore

Keyword(s):

Molecular Dynamics ◽

Relative Position ◽

Aromatic Amines ◽

Dna Adduct ◽

Dna Duplexes ◽

Size Number

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Cytochrome P-450 Isoforms Implicated in Ochratoxin A Genotoxicity Determined by DNA Adduct Formation

Clinical Chemistry ◽

10.1093/clinchem/41.12.1927 ◽

1995 ◽

Vol 41 (12) ◽

pp. 1927-1929 ◽

Cited By ~ 2

Keyword(s):

Ochratoxin A ◽

Adduct Formation ◽

Dna Adduct ◽

Cytochrome P 450

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Base damage, local sequence context andTP53mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability

Nucleic Acids Research ◽

10.1093/nar/gkv910 ◽

2015 ◽

Vol 43 (19) ◽

pp. 9133-9146 ◽

Cited By ~ 9

Author(s):

Georgina E. Menzies ◽

Simon H. Reed ◽

Andrea Brancale ◽

Paul D. Lewis

Keyword(s):

Molecular Dynamics ◽

Sequence Context ◽

Base Damage ◽

Local Sequence

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The influence of ochratoxin A on DNA adduct formation by the carcinogen aristolochic acid in rats

Archives of Toxicology ◽

10.1007/s00204-014-1360-1 ◽

2014 ◽

Vol 89 (11) ◽

pp. 2141-2158 ◽

Cited By ~ 13

Author(s):

Marie Stiborová ◽

František Bárta ◽

Kateřina Levová ◽

Petr Hodek ◽

Eva Frei ◽

...

Keyword(s):

Ochratoxin A ◽

Aristolochic Acid ◽

Adduct Formation ◽

Dna Adduct

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Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.9b00751 ◽

2019 ◽

Vol 15 (11) ◽

pp. 6524-6535 ◽

Cited By ~ 5

Author(s):

Hugo Guterres ◽

Hui Sun Lee ◽

Wonpil Im

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Binding Site ◽

Structure Refinement ◽

Ligand Binding Site ◽

Site Structure ◽

Predicted Binding Site

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Molecular dynamics simulations of matrix deposition. III. Site structure analysis for porphycene in argon and xenon

The Journal of Chemical Physics ◽

10.1063/1.1997128 ◽

2005 ◽

Vol 123 (6) ◽

pp. 064706 ◽

Cited By ~ 9

Author(s):

Alexander Kyrychenko ◽

Jacek Waluk

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Structure Analysis ◽

Site Structure ◽

Matrix Deposition ◽

Dynamics Simulations

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Gilvocarcin V exhibits both equilibrium DNA binding and UV light induced DNA adduct formation which is sequence context dependent

Nucleic Acids Research ◽

10.1093/nar/20.17.4553 ◽

1992 ◽

Vol 20 (17) ◽

pp. 4553-4557 ◽

Cited By ~ 16

Author(s):

Robert M. Knobler ◽

F.Bernhard Radlwimmer ◽

Michael J. Lane

Keyword(s):

Dna Binding ◽

Uv Light ◽

Adduct Formation ◽

Dna Adduct ◽

Sequence Context ◽

Context Dependent ◽

Gilvocarcin V

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Structural insights by molecular dynamics simulations into specificity of the major human AP endonuclease toward the benzene-derived DNA adduct, pBQ-C

Nucleic Acids Research ◽

10.1093/nar/gkh594 ◽

2004 ◽

Vol 32 (9) ◽

pp. 2844-2852 ◽

Cited By ~ 27

Author(s):

A. B. Guliaev

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dna Adduct ◽

Ap Endonuclease ◽

Dynamics Simulations ◽

Structural Insights

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