Areas of Interest

 We are focused on delineating the molecular mechanisms underlying the mutagenic and carcinogenic properties of certain environmental and endogenous carcinogens. These include polycyclic aromatic carcinogens, present in automobile exhaust, tobacco smoke and cooked foods, as well as reactive oxygen species and estrogen derivatives. These can cause reaction with DNA. This damaged DNA may initiate cancer by producing mutations during DNA replication. Our research centers on investigating replication and repair of the damaged DNA using computational approaches. We employ computer modeling, molecular mechanics and dynamics simulations and quantum mechanical calculations for structural and thermodynamic analyses, to connect structure and thermodynamics with biological function. We work in close collaboration with Professor Nicholas E. Geacintov of the NYU Chemistry Department who provides the experimental data that anchors our computational studies.

         


PI: Dr. Suse Broyde
(Click to view research interests)

 

 

 

List of Publications from PubMed

 

 

 

The Broyde Group Members

NYU Biology Department

NYU Chemistry Department

New York University

 

 

 


Cover image courtesy of Cancer Research
Cancer Research May 1, 1999, Volume 59, Number 9, PP.2023-2257. ISSN 0008-5472

 

 


Cover image courtesy of Chemical Research in Toxicology
Nuclear magnetic resonance solution structures of covalent aromatic amine-DNA adducts and their mutagenic relevance. Patel DJ, Mao B, Gu Z, Hingerty BE, Gorin A, Basu AK, Broyde S. Chem Res Toxicol. 1998 May;11(5):391-407. Invited Review Article

 

 


Cover image courtesy of Chemical Research in Toxicology
NMR solution structures of stereoisometric covalent polycyclic aromatic carcinogen-DNA adduct: principles, patterns, and diversity. Geacintov NE, Cosman M, Hingerty BE, Amin S, Broyde S, Patel DJ. Chem Res Toxicol. 1997 Feb;10(2):111-46.

 

 


Cover image courtesy of Nucleic Acids Research
Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context. Rodríguez FA, Cai Y, Lin C, Tang Y, Kolbanovskiy A, Amin S, Patel DJ, Broyde S, Geacintov NE. Nucleic Acids Res. 2007;35(5):1555-68.

 

 


Cover image courtesy of Nucleic Acids Research
A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4).Wang L, Broyde S.Nucleic Acids Res. 2006 Feb 1;34(3):785-95.

 

 


Courtesy of Dr. Shuang Ding
G*CT* Cross-link

S. Ding, K. Kropachev, Y. Cai, M. Kolbanovskiy, S. Durandina, Z. Liu, V. Shafirovich, S. Broyde and N. Geacintov (2011). Nucleic Acids Res. 2012 Mar 40(6)2506-17.

 

 


Courtesy of Dr. Lei Jia
Human DNA pol k in complex with B[a]P
(Click to download movie)

L. Jia, N. Geacintov and S. Broyde. Nucleic Acides Res. 2008 46(20):6571-84.

 

 




Courtesy of Hong Mu
Nucleotide excision repair of 2-acetylaminofluorene- and 2-aminofluorene-(C8)-guanine adducts: molecular dynamics simulations elucidate how lesion structure and base sequence context impact repair efficiencies
Mu H, Kropachev K, Wang L, Zhang L, Kolbanovskiy A, Kolbanovskiy M, E Geacintov N, Broyde S. Nucleic Acids Res. 2012 Oct 40(19):9675-90

 

 


Courtesy of Dr. Yuqin Cai
Adenine-DNA adducts derived from the highly tumorigenic dibenzo[a,l]pyrene are resistant to nucleotide excision repair while guanine adducts are not
Kropachev K, Kolbanovskiy M, Liu Z, Cai Y, Zhang L, Schwaid AG, Kolbanovskiy A, Ding S, Broyde S, and Geacintov NE Chem. Res. Toxicol. 2013 26(5):783-93

 

 


Courtesy of Dr. Shuang Ding and Dr.Yuqin Cai
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 Y. Liu Z. Ding S. Lin CH, Cai Y. Rodriguez FA, Sayer JM, Jerina DM, Amin S. Broyde S. Geacintov NE. Biochemistry 2012 51 (48)9751-62

 

 


Courtesy of Hong Mu
The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation?

Lee YC, Cai Y, Mu H, Broyde S, Amin S, Chen X, Min JH, Geacintov NE, DNA Repair (Amst). DNA Repair (Amst). 2014 Jul;19:55-63.


Courtesy of Dr. Lee Lior-Hoffmann
Structural and Dynamic Characterization of Polymerase κ's Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity.

Lior-Hoffmann L, Ding S, Geacintov NE, Zhang Y, Broyde S. Biochemistry. 2014 Sep 9;53(35):5683-91.

 

 


Cover image courtesy of Wiley-VCH
Nucleotide Excision Repair of A PAH-Damaged Lesion

The Chemical Biology of DNA Damage. N. Geacintov, S. Broyde, eds, Wiley-VCH. ISBN: 978-3-527-32295-4

 

 


Courtesy of Dr. Yuqin Cai
Nucleotide Excision Repair of A PAH-Damaged Lesion

Y. Cai, N. E. Geacintov and S. Broyde (2010). J. Nucleic Acids. Special Issue on DNA Damage, Mutagenesis and DNA Repair, vol. 2010.

 

 


(Click to download movie)
Courtesy of Dr. Yuqin Cai
PAH-damaged Nucleosome Core Particle
Y. Cai, L.Wang, S. Ding, A. Schwaid, N.E. Geacintov and S. Broyde. Biochemistry, 2010 49(46):9943-45.


Courtesy of Hong Mu
Mobile Phenyl Ring of PhIP Distorts Neighboring Base Pairs
(Click to download movie)

D. Reeves, H. Mu, K. Kropachev, Y. Cai, S. Ding, J. Krzeminsky, A. Kolbanovskiy, J. Bolton, S. Amin, K. El-Bayoumy, S. Broyde and N. Geacintov. Nucleic Acids Res. 2011 39(20): 8752-64.

 

 


Courtesy of Dr. Han Zheng
Base flipping free energy profiles for damaged and undamaged DNA

Zheng H, Cai Y, Ding S, Tang Y, Kropachev K, Zhou Y, Wang L, Wang S, Geacintov NE, Zhang Y, Broyde S.Chem.Res.Toxicol. 2010 23(12)1868-70.

 

 


Courtesy of Dr.Lee Lior-Hoffmann
Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase k elucidates error-free bypass of a bulky DNA lesion
Lior-Hoffmann L, Wang L, Wang S. Geacintov NE, Broyde S, Zhang Y. Nucleic Acids Res. 2012 Oct 1;40(18):9193-9205

 

 


Courtesy of Dr.Yuqin Cai
Nucleotide excision repair efficiencies of bulky carcinogen-DNA adducts are governed by a balance between stabilizing and destabilizing interactions
Cai Y, Geacintov NE, Broyde S. Biochemistry. 2012 Feb 21;51(7):1486-99.

 

 


Courtesy of Jin Yang
DNA cytosine methylation: structural and thermodynamic characterization of the epigenetic marking mechanism

Yang J, Lior-HOffmann L, Wang S, Zhang Y, Broyde S. Biochemistry 2013 Apr 23;52(16):2828-38.

 

 


 


(Click to download movie)
Courtesy of Dr. Yuqin Cai
Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: Energetic and structural relationships to nucleotide excision repair
Cai Y, Zheng H, Ding S, Kropachev K,Schwaid AG,Tang Y, Mu H, Wang S, Geacintov NE, Zhang Y, Broyde S. Chem. Res. Toxicol. 2013 26(7):1115-25

 

 


Courtesy of Hong Mu
The role of structural and energetic factors in regulating repair of a bulky DNA lesion with different opposite partner bases

Mu H, Kropachev K, Chen Y, Zhang H, Cai Y. Geacintov NE, Broyde S. Biochemistry, 2013, 52 (33), pp 5517–5521

 

 


 


(Click to download movie)
Courtesy of Dr. Yuqin Cai
Ribonucleotides as nucleotide excision repair substrates
Cai Y. Geacintov NE, Broyde S. DNA Repair (Amst). 2014 Jan;13:55-60.

 

 


 


Courtesy of Dr. Yuqin Cai
Structural basis for the recognition of diastereomeric 5',8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system.

Kropachev K, Ding S, Terzidis MA, Masi A, Liu Z, Cai Y, Kolbanovskiy M, Chatgilialoglu C, Broyde S, Geacintov NE, Shafirovich V. DNA Repair (Amst). Nucleic Acids Res. 2014 Apr;42(8):5020-32.