Suse Broyde

2024

Variable Inhibition of DNA Unwinding Rates Catalyzed by the SARS-CoV-2 Helicase Nsp13 by Structurally Distinct Single DNA Lesions

Sales, A. H., Fu, I., Durandin, A., Ciervo, S., Lupoli, T. J., Shafirovich, V., Broyde, S. & Geacintov, N. E., Jul 2024, In: International journal of molecular sciences. 25, 14, 7930.

Research output: Contribution to journal › Article › peer-review

Open Access

2023

Differing structures and dynamics of two photolesions portray verification differences by the human XPD helicase

Fu, I., Geacintov, N. E. & Broyde, S., Dec 11 2023, In: Nucleic acids research. 51, 22, p. 12261-12274 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2022

Inhibition of E. coli RecQ Helicase Activity by Structurally Distinct DNA Lesions: Structure—Function Relationships

Sales, A. H., Zheng, V., Kenawy, M. A., Kakembo, M., Zhang, L., Shafirovich, V., Broyde, S. & Geacintov, N. E., Dec 2022, In: International journal of molecular sciences. 23, 24, 15654.

Research output: Contribution to journal › Article › peer-review

Open Access

Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair

Fu, I., Mu, H., Geacintov, N. E. & Broyde, S., Jul 8 2022, In: Nucleic acids research. 50, 12, p. 6837-6853 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2021

Impact of DNA sequences on DNA ‘opening’ by the Rad4/XPC nucleotide excision repair complex

Paul, D., Mu, H., Tavakoli, A., Dai, Q., Chakraborty, S., He, C., Ansari, A., Broyde, S. & Min, J. H., Nov 2021, In: DNA Repair. 107, 103194.

Research output: Contribution to journal › Article › peer-review

Open Access

Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein

Tavakoli, A., Paul, D., Mu, H., Kuchlyan, J., Baral, S., Ansari, A., Broyde, S. & Min, J. H., Apr 2021, In: RSC Chemical Biology. 2, 2, p. 523-536 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Molecular dynamics simulations reveal how H3K56 acetylation impacts nucleosome structure to promote DNA exposure for lesion sensing

Fu, I., Geacintov, N. E. & Broyde, S., Nov 2021, In: DNA Repair. 107, 103201.

Research output: Contribution to journal › Article › peer-review

Open Access

Tethering-facilitated DNA 'opening' and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein

Paul, D., Mu, H., Tavakoli, A., Dai, Q., Chen, X., Chakraborty, S., He, C., Ansari, A., Broyde, S. & Min, J. H., Dec 2 2021, In: Nucleic acids research. 48, 21, p. 12348-12364 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Translesion Synthesis Past 5-Formylcytosine-Mediated DNA-Peptide Cross-Links by hPolη Is Dependent on the Local DNA Sequence

Thomforde, J., Fu, I., Rodriguez, F., Pujari, S. S., Broyde, S. & Tretyakova, N., Jun 15 2021, In: Biochemistry. 60, 23, p. 1797-1807 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2020

The DNA damage-sensing NER repair factor XPC-RAD23B does not recognize bulky DNA lesions with a missing nucleotide opposite the lesion

Feher, K. M., Kolbanovskiy, A., Durandin, A., Shim, Y., Min, J. H., Lee, Y. C., Shafirovich, V., Mu, H., Broyde, S. & Geacintov, N. E., Dec 2020, In: DNA Repair. 96, 102985.

Research output: Contribution to journal › Article › peer-review

Open Access

Variable impact of conformationally distinct DNA lesions on nucleosome structure and dynamics: Implications for nucleotide excision repair

Cai, Y., Geacintov, N. E. & Broyde, S., Mar 2020, In: DNA Repair. 87, 102768.

Research output: Contribution to journal › Article › peer-review

Open Access

2019

5-Formylcytosine-induced DNA–peptide cross-links reduce transcription efficiency, but do not cause transcription errors in human cells

Ji, S., Park, D., Kropachev, K., Kolbanovskiy, M., Fu, I., Broyde, S., Essawy, M., Geacintov, N. E. & Tretyakova, N. Y., Nov 29 2019, In: Journal of Biological Chemistry. 294, 48, p. 18387-18397 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Nucleotide Excision Repair and Impact of Site-Specific 5′,8-Cyclopurine and Bulky DNA Lesions on the Physical Properties of Nucleosomes

Shafirovich, V., Kolbanovskiy, M., Kropachev, K., Liu, Z., Cai, Y., Terzidis, M. A., Masi, A., Chatgilialoglu, C., Amin, S., Dadali, A., Broyde, S. & Geacintov, N. E., Feb 12 2019, In: Biochemistry. 58, 6, p. 561-574 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome

Fu, I., Smith, D. J. & Broyde, S., Jan 2019, In: DNA Repair. 73, p. 155-163 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Structure and mechanism of pyrimidine–pyrimidone (6-4) photoproduct recognition by the Rad4/XPC nucleotide excision repair complex

Paul, D., Mu, H., Zhao, H., Ouerfelli, O., Jeffrey, P. D., Broyde, S. & Min, J. H., Jul 9 2019, In: Nucleic acids research. 47, 12, p. 6015-6028 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Transcriptional Bypass of DNA-Protein and DNA-Peptide Conjugates by T7 RNA Polymerase

Ji, S., Thomforde, J., Rogers, C., Fu, I., Broyde, S. & Tretyakova, N. Y., Dec 20 2019, In: ACS Chemical Biology. 14, 12, p. 2564-2575 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2018

5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells

Ji, S., Fu, I., Naldiga, S., Shao, H., Basu, A. K., Broyde, S. & Tretyakova, N. Y., Jul 27 2018, In: Nucleic acids research. 46, 13, p. 6455-6469 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex

Chakraborty, S., Steinbach, P. J., Paul, D., Mu, H., Broyde, S., Min, J. H. & Ansari, A., Feb 16 2018, In: Nucleic acids research. 46, 3, p. 1240-1255 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Lesion Sensing during Initial Binding by Yeast XPC/Rad4: Toward Predicting Resistance to Nucleotide Excision Repair

Mu, H., Zhang, Y., Geacintov, N. E. & Broyde, S., Nov 19 2018, In: Chemical research in toxicology. 31, 11, p. 1260-1268 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition

Cai, Y., Fu, I., Geacintov, N. E., Zhang, Y. & Broyde, S., May 2018, In: DNA Repair. 65, p. 73-78 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2017

Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion

Fu, I., Cai, Y., Geacintov, N. E., Zhang, Y. & Broyde, S., Apr 11 2017, In: Biochemistry. 56, 14, p. 1963-1973 11 p.

Research output: Contribution to journal › Article › peer-review

Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo[a]pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway

Mu, H., Geacintov, N. E., Min, J. H., Zhang, Y. & Broyde, S., Jun 19 2017, In: Chemical research in toxicology. 30, 6, p. 1344-1354 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

The Nonbulky DNA Lesions Spiroiminodihydantoin and 5-Guanidinohydantoin Significantly Block Human RNA Polymerase II Elongation in Vitro

Kolbanovskiy, M., Chowdhury, M. A., Nadkarni, A., Broyde, S., Geacintov, N. E., Scicchitano, D. A. & Shafirovich, V., Jun 20 2017, In: Biochemistry. 56, 24, p. 3008-3018 11 p.

Research output: Contribution to journal › Article › peer-review

2016

Bypass of DNA-protein cross-links conjugated to the 7-deazaguanine position of DNA by translesion synthesis polymerases

Wickramaratne, S., Ji, S., Mukherjee, S., Su, Y., Pence, M. G., Lior-Hoffmann, L., Fu, I., Broyde, S., Guengerich, F. P., Distefano, M., Schãrer, O. D., Sham, Y. Y. & Tretyakova, N., Nov 4 2016, In: Journal of Biological Chemistry. 291, 45, p. 23589-23603 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study

Fu, I., Cai, Y., Zhang, Y., Geacintov, N. E. & Broyde, S., Jan 19 2016, In: Biochemistry. 55, 2, p. 239-242 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2015

Differences in the Access of Lesions to the Nucleotide Excision Repair Machinery in Nucleosomes

Cai, Y., Kropachev, K., Terzidis, M. A., Masi, A., Chatgilialoglu, C., Shafirovich, V., Geacintov, N. E. & Broyde, S., Jul 14 2015, In: Biochemistry. 54, 27, p. 4181-4185 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion

Mu, H., Geacintov, N. E., Zhang, Y. & Broyde, S., Sep 1 2015, In: Biochemistry. 54, 34, p. 5263-5267 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse

Perera, L., Freudenthal, B. D., Beard, W. A., Shock, D. D., Pedersen, L. G., Wilson, S. H. & Broyde, S., Sep 22 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 38, p. E5228-E5236

Research output: Contribution to journal › Article › peer-review

Open Access

Resistance to nucleotide excision repair of bulky guanine adducts opposite abasic sites in DNA duplexes and relationships between structure and function

Liu, Z., Ding, S., Kropachev, K., Lei, J., Amin, S., Broyde, S. & Geacintov, N. E., Sep 4 2015, In: PloS one. 10, 9, e0137124.

Research output: Contribution to journal › Article › peer-review

Open Access

Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)

Koch, S. C., Kuper, J., Gasteiger, K. L., Simon, N., Strasser, R., Eisen, D., Geiger, S., Schneider, S., Kisker, C., Carell, T. & Broyde, S., Jul 7 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 27, p. 8272-8277 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2014

Nuclear magnetic resonance studies of an N ²-guanine adduct derived from the tumorigen dibenzo[ a, l ]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA sequence on solution conformations

Rodríguez, F. A., Liu, Z., Lin, C. H., Ding, S., Cai, Y., Kolbanovskiy, A., Kolbanovskiy, M., Amin, S., Broyde, S. & Geacintov, N. E., Mar 25 2014, In: Biochemistry. 53, 11, p. 1827-1841 15 p.

Research output: Contribution to journal › Article › peer-review

Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity

Lior-Hoffmann, L., Ding, S., Geacintov, N. E., Zhang, Y. & Broyde, S., Sep 9 2014, In: Biochemistry. 53, 35, p. 5683-5691 9 p.

Research output: Contribution to journal › Article › peer-review

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, M. A., Masi, A., Liu, Z., Cai, Y., Kolbanovskiy, M., Chatgilialoglu, C., Broyde, S., Geacintov, N. E. & Shafirovich, V., Apr 2014, In: Nucleic acids research. 42, 8, p. 5020-5032 13 p.

Research output: Contribution to journal › Article › peer-review

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

Lee, Y. C., Cai, Y., Mu, H., Broyde, S., Amin, S., Chen, X., Min, J. H. & Geacintov, N. E., Jul 2014, In: DNA Repair. 19, p. 55-63 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2013

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, A. G., Kolbanovskiy, A., Ding, S., Amin, S., Broyde, S. & Geacintov, N. E., May 20 2013, In: Chemical research in toxicology. 26, 5, p. 783-793 11 p.

Research output: Contribution to journal › Article › peer-review

DNA cytosine methylation: Structural and thermodynamic characterization of the epigenetic marking mechanism

Yang, J., Lior-Hoffmann, L., Wang, S., Zhang, Y. & Broyde, S., Apr 23 2013, In: Biochemistry. 52, 16, p. 2828-2838 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: Energetic and structural relationships to nucleotide excision repair susceptibility

Cai, Y., Zheng, H., Ding, S., Kropachev, K., Schwaid, A. G., Tang, Y., Mu, H., Wang, S., Geacintov, N. E., Zhang, Y. & Broyde, S., Jul 15 2013, In: Chemical research in toxicology. 26, 7, p. 1115-1125 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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, N. E. & Broyde, S., Aug 20 2013, In: Biochemistry. 52, 33, p. 5517-5521 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2012

Nuclear magnetic resonance solution structure of an N²-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, C. H., Cai, Y., Rodriguez, F. A., Sayer, J. M., Jerina, D. M., Amin, S., Broyde, S. & Geacintov, N. E., Dec 4 2012, In: Biochemistry. 51, 48, p. 9751-9762 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Nucleotide excision repair efficiencies of bulky carcinogen-DNA adducts are governed by a balance between stabilizing and destabilizing interactions

Cai, Y., Geacintov, N. E. & Broyde, S., Feb 21 2012, In: Biochemistry. 51, 7, p. 1486-1499 14 p.

Research output: Contribution to journal › Article › peer-review

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., Geacintov, N. E. & Broyde, S., Oct 2012, In: Nucleic acids research. 40, 19, p. 9675-9690 16 p.

Research output: Contribution to journal › Article › peer-review

Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion

Lior-Hoffmann, L., Wang, L., Wang, S., Geacintov, N. E., Broyde, S. & Zhang, Y., Oct 2012, In: Nucleic acids research. 40, 18, p. 9193-9205 13 p.

Research output: Contribution to journal › Article › peer-review

Structural, energetic and dynamic properties of guanine(C8)-thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair

Ding, S., Kropachev, K., Cai, Y., Kolbanovskiy, M., Durandina, S. A., Liu, Z., Shafirovich, V., Broyde, S. & Geacintov, N. E., Mar 2012, In: Nucleic acids research. 40, 6, p. 2506-2517 12 p.

Research output: Contribution to journal › Article › peer-review

2011

Intercalative conformations of the 14R(+)- and 14S(-)- trans-anti-DB[a,l]P- N⁶-dA adducts: Molecular modeling and MD simulations

Cai, Y., Ding, S., Geacintov, N. E. & Broyde, S., Apr 18 2011, In: Chemical research in toxicology. 24, 4, p. 522-531 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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

Liu, Y., Reeves, D., Kropachev, K., Cai, Y., Ding, S., Kolbanovskiy, M., Kolbanovskiy, A., Bolton, J. L., Broyde, S., Van Houten, B. & Geacintov, N. E., Jul 15 2011, In: DNA Repair. 10, 7, p. 684-696 13 p.

Research output: Contribution to journal › Article › peer-review

Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions

Reeves, D. A., Mu, H., Kropachev, K., Cai, Y., Ding, S., Kolbanovskiy, A., Kolbanovskiy, M., Chen, Y., Krzeminski, J., Amin, S., Patel, D. J., Broyde, S. & Geacintov, N. E., Nov 2011, In: Nucleic acids research. 39, 20, p. 8752-8764 13 p.

Research output: Contribution to journal › Article › peer-review

2010

A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure

Cai, Y., Wang, L., Ding, S., Schwaid, A., Geacintov, N. E. & Broyde, S., Nov 23 2010, In: Biochemistry. 49, 46, p. 9943-9945 3 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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, N. E., Zhang, Y. & Broyde, S., Dec 20 2010, In: Chemical research in toxicology. 23, 12, p. 1868-1870 3 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion

Cai, Y., Kropachev, K., Xu, R., Tang, Y., Kolbanovskii, M., Kolbanovskii, A., Amin, S., Patel, D. J., Broyde, S. & Geacintov, N. E., Jun 2010, In: Journal of Molecular Biology. 399, 3, p. 397-409 13 p.

Research output: Contribution to journal › Article › peer-review

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

Rechkoblit, O., Kolbanovskiy, A., Malinina, L., Geacintov, N. E., Broyde, S. & Patel, D. J., Mar 2010, In: Nature Structural and Molecular Biology. 17, 3, p. 379-388 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Suse Broyde

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