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1

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

Nicholas E. Geacintov, Suse Broyde, Tonko Buterin, Hanspeter Naegeli, Min Wu, Shixiang Yan, Dinshaw J. Patel

Journal:

Year:

2002

Language:

english

File:

PDF, 371 KB

english, 2002

2

Classical potential energy calculations for ApA, CpC, GpG, and UpU. The influence of the bases on RNA subunit conformations

Suse B. Broyde, Roger M. Wartell, Steven D. Stellman, Brian Hingerty, Robert Langridge

Journal:

Year:

1975

Language:

english

File:

PDF, 798 KB

english, 1975

3

The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC

Suse B. Broyde, Steven D. Stellman, Roger M. Wartell

Journal:

Year:

1975

Language:

english

File:

PDF, 671 KB

english, 1975

4

The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC

Suse B. Broyde, Steven D. Stellman, Roger M. Wartell

Journal:

Year:

1976

File:

PDF, 23 KB

1976

5

Influence of ribose 2′-O-methylation on GpC conformation by classical potential energy calculations

Steven D. Stellman, Suse B. Broyde, Roger M. Wartell

Journal:

Year:

1976

Language:

english

File:

PDF, 716 KB

english, 1976

6

The poly(rU) coil: A minimum-energy model that matches experimental observations

Brian E. Hingerty, Suse B. Broyde, Wilma K. Olson

Journal:

Year:

1982

Language:

english

File:

PDF, 1.19 MB

english, 1982

7

Carcinogen–base stacking and base–base stacking in dCpdG modified by (+) and (−) anti-BPDE

Brian E. Hingerty, Suse Broyde

Journal:

Year:

1985

Language:

english

File:

PDF, 916 KB

english, 1985

8

Prediction of DNA structure from sequence: A build-up technique

Brian E. Hingerty, Samuel Figueroa, Thomas L. Hayden, Suse Broyde

Journal:

Year:

1989

Language:

english

File:

PDF, 1.28 MB

english, 1989

9

Absolute configurations of DNA lesions determined by comparisons of experimental ECD and ORD spectra with DFT calculations

Shuang Ding, Alexander Kolbanovskiy, Alexander Durandin, Conor Crean, Vladimir Shafirovich, Suse Broyde, Nicholas E. Geacintov

Journal:

Year:

2009

Language:

english

File:

PDF, 623 KB

english, 2009

10

An analysis of the structural and energetic properties of deoxyribose by potential energy methods

Tamar Schlick, Charles Peskin, Suse Broyde, Michael Overton

Journal:

Journal of Computational Chemistry

Year:

1987

Language:

english

File:

PDF, 2.40 MB

english, 1987

11

The molecular mechanics program DUPLEX: Computing structures of carcinogen modified DNA by surveying the potential energy surface

Brian E. Hingerty, Suse Broyde

Journal:

Molecular Engineering

Year:

1995

Language:

english

File:

PDF, 530 KB

english, 1995

12

Photochemical Properties of Water-Soluble Chlorophyll

OSTER, GERALD, BROYDE, SUSE B.

Journal:

Year:

1961

File:

PDF, 194 KB

1961

13

DNA repair: How to accurately bypass damage

Broyde, Suse, Patel, Dinshaw J.

Journal:

Year:

2010

Language:

english

File:

PDF, 244 KB

english, 2010

14

Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4

Rechkoblit, Olga, Kolbanovskiy, Alexander, Malinina, Lucy, Geacintov, Nicholas E, Broyde, Suse, Patel, Dinshaw J

Journal:

Nature Structural and Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.45 MB

english, 2010

15

The human DNA repair factor XPC-HR23B distinguishes stereoisomeric benzo[a]pyrenyl-DNA lesions

Mocquet, Vincent, Kropachev, Konstantin, Kolbanovskiy, Marina, Kolbanovskiy, Alexander, Tapias, Angels, Cai, Yuqin, Broyde, Suse, Geacintov, Nicholas E, Egly, Jean-Marc

Journal:

The EMBO Journal

Year:

2007

Language:

english

File:

PDF, 317 KB

english, 2007

16

10.1021/ja01061a011

Oster, Gerald, Bellin, Judith S., Broyde, Suse B.

Journal:

Journal of the American Chemical Society

Year:

1964

Language:

english

File:

PDF, 755 KB

english, 1964

17

Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase

Alexandra Dimitri, Lei Jia, Vladimir Shafirovich, Nicholas E. Geacintov, Suse Broyde, David A. Scicchitano

Journal:

Year:

2008

Language:

english

File:

PDF, 1.13 MB

english, 2008

18

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

Yang Liu, Dara Reeves, Konstantin Kropachev, Yuqin Cai, Shuang Ding, Marina Kolbanovskiy, Alexander Kolbanovskiy, Judith L. Bolton, Suse Broyde, Bennett Van Houten, Nicholas E. Geacintov

Journal:

Year:

2011

Language:

english

File:

PDF, 1.93 MB

english, 2011

19

Impact of Conformational Heterogeneity of OxoG Lesions and Their Pairing Partners on Bypass Fidelity by Y Family Polymerases

Olga Rechkoblit, Lucy Malinina, Yuan Cheng, Nicholas E. Geacintov, Suse Broyde, Dinshaw J. Patel

Journal:

Year:

2009

Language:

english

File:

PDF, 1.43 MB

english, 2009

20

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases

Suse Broyde, Lihua Wang, Olga Rechkoblit, Nicholas E. Geacintov, Dinshaw J. Patel

Journal:

Trends in Biochemical Sciences

Year:

2008

Language:

english

File:

PDF, 1.59 MB

english, 2008

21

A NEW PHOTOCHEMICAL REACTION OF CHLOROPHYLL a

Suse B. Broyde, Seymour Steven Brody

Journal:

Photochemistry and Photobiology

Year:

1964

Language:

english

File:

PDF, 124 KB

english, 1964

22

Accomodation of S-cis-tamoxifen-N2-guanine adduct within a bent and widened DNA minor groove

Sakurako Shimotakahara, Andrey Gorin, Alexander Kolbanovskiy, Abdelali Kettani, Brian E Hingerty, Shantu Amin, Suse Broyde, Nicholas Geacintov, Dinshaw J Patel

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 745 KB

english, 2000

23

Molecular topology of polycyclic aromatic carcinogens determines DNA adduct conformation: a link to tumorigenic activity

Chin H Lin, Xuanwei Huang, Alexander Kolbanovskii, Brian E Hingerty, Shantu Amin, Suse Broyde, Nicholas E Geacintov, Dinshaw J Patel

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 1.00 MB

english, 2001

24

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

Rebecca A. Perlow, Suse Broyde

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 847 KB

english, 2001

25

Polymerase β simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se

Linjing Yang, William A. Beard, Samuel H. Wilson, Suse Broyde, Tamar Schlick

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 1.50 MB

english, 2002

26

Methylation of Cytosine at C5 in a CpG Sequence Context Causes a Conformational Switch of a Benzo[a]pyrene diol epoxide-N2-guanine Adduct in DNA from a Minor Groove Alignment to Intercalation with Base Displacement

Na Zhang, Chin Lin, Xuanwei Huang, Aleksandr Kolbanovskiy, Brian E. Hingerty, Shantu Amin, Suse Broyde, Nicholas E. Geacintov, Dinshaw J. Patel

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 564 KB

english, 2005

27

Dynamics of a Benzo[a]pyrene-derived Guanine DNA Lesion in TGT and CGC Sequence Contexts: Enhanced Mobility in TGT Explains Conformational Heterogeneity, Flexible Bending, and Greater Susceptibility to Nucleotide Excision Repair

Yuqin Cai, Dinshaw J. Patel, Nicholas E. Geacintov, Suse Broyde

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 2.21 MB

english, 2007

28

Transcription Processing at 1,N2-Ethenoguanine by Human RNA Polymerase II and Bacteriophage T7 RNA Polymerase

Alexandra Dimitri, Angela K. Goodenough, F. Peter Guengerich, Suse Broyde, David A. Scicchitano

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.15 MB

english, 2008

29

Differential Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different Sequence Contexts: Hierarchies of Recognition Signals

Yuqin Cai, Dinshaw J. Patel, Nicholas E. Geacintov, Suse Broyde

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 2.48 MB

english, 2009

30

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

Konstantin Kropachev, Marina Kolbanovskii, Yuqin Cai, Fabian Rodríguez, Alexander Kolbanovskii, Yang Liu, Lu Zhang, Shantu Amin, Dinshaw Patel, Suse Broyde, Nicholas E. Geacintov

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.07 MB

english, 2009

31

Polymerase-Tailored Variations in the Water-Mediated and Substrate-Assisted Mechanism for Nucleotidyl Transfer: Insights from a Study of T7 DNA Polymerase

Lihua Wang, Suse Broyde, Yingkai Zhang

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 520 KB

english, 2009

32

Distant Neighbor Base Sequence Context Effects in Human Nucleotide Excision Repair of a Benzo[a]pyrene-derived DNA Lesion

Yuqin Cai, Konstantin Kropachev, Rong Xu, Yijin Tang, Marina Kolbanovskii, Alexander Kolbanovskii, Shantu Amin, Dinshaw J. Patel, Suse Broyde, Nicholas E. Geacintov

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.41 MB

english, 2010

33

DNA Adducts from a Tumorigenic Metabolite of Benzo[a]pyrene Block Human RNA Polymerase II Elongation in a Sequence- and Stereochemistry-dependent Manner

Rebecca A Perlow, Alexander Kolbanovskii, Brian E Hingerty, Nicholas E Geacintov, Suse Broyde, David A Scicchitano

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 967 KB

english, 2002

34

Local Deformations Revealed by Dynamics Simulations of DNA Polymerase β with DNA Mismatches at the Primer Terminus

Linjing Yang, William A Beard, Samuel H Wilson, Benoit Roux, Suse Broyde, Tamar Schlick

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 1.13 MB

english, 2002

35

Toward Understanding the Mutagenicity of an Environmental Carcinogen: Structural Insights into Nucleotide Incorporation Preferences

Rebecca A. Perlow, Suse Broyde

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 6.09 MB

english, 2002

36

Extending the Understanding of Mutagenicity: Structural Insights into Primer-extension Past a Benzo[a]pyrene Diol Epoxide-DNA adduct

Rebecca A. Perlow, Suse Broyde

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 7.22 MB

english, 2003

37

Spectral Properties of Chlorophyllin a

Oster, Gerald., Broyde, Suse B., Bellin, Judith S.

Journal:

Journal of the American Chemical Society

Year:

1964

Language:

english

File:

PDF, 630 KB

english, 1964

38

Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions

Wang, Lihua, Hingerty, Brian E., Srinivasan, A.R., Olson, Wilma K., Broyde, Suse

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 1.78 MB

english, 2002

39

Simulating Structural and Thermodynamic Properties of Carcinogen-Damaged DNA

Yan, Shixiang, Wu, Min, Patel, Dinshaw J., Geacintov, Nicholas E., Broyde, Suse

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 924 KB

english, 2003

40

Nucleotide Excision Repair Efficiencies of Bulky Carcinogen–DNA Adducts Are Governed by a Balance between Stabilizing and Destabilizing Interactions

Cai, Yuqin, Geacintov, Nicholas E., Broyde, Suse

Journal:

Year:

2012

Language:

english

File:

PDF, 4.29 MB

english, 2012

41

Molecular Dynamics Simulation of a Tumorigenic Benzo[a]pyrene Metabolite Bound to DNA at a Single Strand-Double Strand Junction

SURESH B. SINGH, BIN LI, BRIAN E. HINGERTY, ROBERT SHAPIRO, SUSE BROYDE

Journal:

Annals of the New York Academy of Sciences

Year:

1994

Language:

english

File:

PDF, 1020 KB

english, 1994

42

Highly Organized but Pliant Active Site of DNA Polymerase β: Compensatory Mechanisms in Mutant Enzymes Revealed by Dynamics Simulations and Energy Analyses

Yang, Linjing, Beard, William A., Wilson, Samuel H., Broyde, Suse, Schlick, Tamar

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 1.53 MB

english, 2004

43

Effect of Ring Size on Conformations of Aromatic Amine−DNA Adducts: The Aniline−C8 Guanine Adduct Resides in the B-DNA Major Groove

Shapiro, Robert, Ellis, Stephen, Hingerty, Brian E., Broyde, Suse

Journal:

Chemical Research in Toxicology

Year:

1998

Language:

english

File:

PDF, 215 KB

english, 1998

44

DNA Cytosine Methylation: Structural and Thermodynamic Characterization of the Epigenetic Marking Mechanism

Yang, Jin, Lior-Hoffmann, Lee, Wang, Shenglong, Zhang, Yingkai, Broyde, Suse

Journal:

Year:

2013

Language:

english

File:

PDF, 4.84 MB

english, 2013

45

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

Tang, Yijin, Liu, Zhi, Ding, Shuang, Lin, Chin H., Cai, Yuqin, Rodriguez, Fabian A., Sayer, Jane M., Jerina, Donald M., Amin, Shantu, Broyde, Suse, Geacintov, Nicholas E.

Journal:

Year:

2012

Language:

english

File:

PDF, 3.67 MB

english, 2012

46

Absolute Configurations of Spiroiminodihydantoin and Allantoin Stereoisomers: Comparison of Computed and Measured Electronic Circular Dichroism Spectra

Ding, Shuang, Jia, Lei, Durandin, Alexander, Crean, Conor, Kolbanovskiy, Alexander, Shafirovich, Vladimir, Broyde, Suse, Geacintov, Nicholas E.

Journal:

Chemical Research in Toxicology

Year:

2009

Language:

english

File:

PDF, 191 KB

english, 2009

47

Molecular Dynamics of a Food Carcinogen−DNA Adduct in a Replicative DNA Polymerase Suggest Hindered Nucleotide Incorporation and Extension

Zhang, Ling, Shapiro, Robert, Broyde, Suse

Journal:

Chemical Research in Toxicology

Year:

2005

Language:

english

File:

PDF, 1.17 MB

english, 2005

48

Ribonucleotides as nucleotide excision repair substrates

Cai, Yuqin, Geacintov, Nicholas E., Broyde, Suse

Journal:

Year:

2014

Language:

english

File:

PDF, 1.22 MB

english, 2014

49

Structural Alignments of (+)- and (-)-trans-anti-Benzo[a]pyrene-dG Adducts Positioned at a DNA Replication Fork Junction

Cosman, Monique, Hingerty, Brian E., Geacintov, Nicholas E., Broyde, Suse, Patel, Dinshaw J.

Journal:

Year:

1995

Language:

english

File:

PDF, 2.40 MB

english, 1995

50

Solution Conformation of the (+)-cis-anti-[BP]dG Adduct Opposite a Deletion Site in a DNA Duplex: Intercalation of the Covalently Attached Benzo[a]pyrene into the Helix with Base Displacement of the Modified Deoxyguanosine into the Minor Groove

Cosman, Monique, Fiala, Radovan, Hingerty, Brian E., Amin, Shantu, Geacintov, Nicholas E., Broyde, Suse, Patel, Dinshaw J.

Journal:

Year:

1994

Language:

english

File:

PDF, 1.24 MB

english, 1994

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