Base flipping free energy profiles for damaged and undamaged DNA

Chemical Research in Toxicology

Volumn 23, Issue 12, 2010, Pages 1868-1870

  Zheng, Han ^a   Cai, Yuqin ^a   Ding, Shuang ^a   Tang, Yijin ^a   Kropachev, Konstantin ^a   Zhou, Yanzi ^a   Wang, Lihua ^a   Wang, Shenglong ^a   Geacintov, Nicholas E ^a   Zhang, Yingkai ^a   Broyde, Suse ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIBENZO[A,L]PYRENE; DOUBLE STRANDED DNA;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA DAMAGE; ENERGY; EXCISION REPAIR; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID STRUCTURE, METABOLISM AND FUNCTION; PARTNER BASE FLIPPING; THERMODYNAMICS;

BENZOPYRENES; DNA; DNA ADDUCTS; DNA DAMAGE; DNA REPAIR; DNA REPAIR ENZYMES; DNA-BINDING PROTEINS; HUMANS; MOLECULAR DYNAMICS SIMULATION; THERMODYNAMICS;

EID: 78650497367     PISSN: 0893228X     EISSN: 15205010     Source Type: Journal    
DOI: 10.1021/tx1003613     Document Type: Article

References (20)

1. Gillet, L. C. and Scharer, O. D. (2006) Molecular mechanisms of mammalian global genome nucleotide excision repair Chem. Rev. 106, 253-276
2. Min, J. H. and Pavletich, N. P. (2007) Recognition of DNA damage by the Rad4 nucleotide excision repair protein Nature 449, 570-575
3. Truglio, J. J., Karakas, E., Rhau, B., Wang, H., DellaVecchia, M. J., Van Houten, B., and Kisker, C. (2006) Structural basis for DNA recognition and processing by UvrB Nat. Struct. Mol. Biol. 13, 360-364
4. Jia, L., Kropachev, K., Ding, S., Van Houten, B., Geacintov, N. E., and Broyde, S. (2009) Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[ a ]pyrene-derived lesion in UvrB Biochemistry 48, 8948-8957
5. Luch, A. (2009) On the impact of the molecules structure in chemical carcinogenesis. EXS 99, 151-179.
6. Kropachev, K., Kolbanovskiy, M., Rodriguez, F. A., Cai, Y., Ding, S., Zhang, L., Amin, S., Broyde, S., and Geacintov, N. E. (2009) Dibenzo[ a, l ]pyrene diol epoxide-adenine but not -guanine adducts are resistant to nucleotide excision repair in human cell extracts, In The 238th ACS National Meeting & Exposition, Washington, DC Chem. Res. Toxicol. 23, 282
7. Tang, Y. (2008) Optical Spectroscopic and NMR Studies of Covalent Polycyclic Aromatic Hydrocarbon-DNA Adducts: Influence of Base Sequence Context and Carcinogen Topology, Ph.D. Thesis, New York University, New York.
8. Priyakumar, U. D. and MacKerell, A. D. (2006) Base flipping in a GCGC containing DNA dodecamer: A comparative study of the performance of the nucleic acid force fields, CHARMM, AMBER, and BMS J. Chem. Theory Comput. 2, 187-200
9. Priyakumar, U. D., and and MacKerell, A. D., Jr. (2006) Computational approaches for investigating base flipping in oligonucleotides Chem. Rev. 106, 489-505
10. Song, K., Campbell, A. J., Bergonzo, C., de los Santos, C., Grollman, A. P., and Simmerling, C. (2009) An improved reaction coordinate for nucleic acid base flipping studies J. Chem. Theory Comput. 5, 3105-3113
11. Varnai, P. and Lavery, R. (2002) Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations J. Am. Chem. Soc. 124, 7272-7273
12. Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Crowley, M., Walker, R. C., Zhang, W., Merz, K. M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossváry, I., Wong, K. F., Paesani, F., Vanicek, J., Wu, X., Brozell, S. R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D. H., Seetin, M. G., Sagui, C., Babin, V., and Kollman, P. A. ((2008)) AMBER 10. University of California, San Francisco.
13. Huang, N., Banavali, N. K., and MacKerell, A. D., Jr. (2003) Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase Proc. Natl. Acad. Sci. U.S.A. 100, 68-73
14. Roux, B. (1995) The calculation of the potential of mean force using computer-simulations Comput. Phys. Commun. 91, 275-282
15. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules J. Am. Chem. Soc. 117, 5179-5197
16. Cheatham, T. E., Cieplak, P., and Kollman, P. A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn. 16, 845-862
17. Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T. E., Laughton, C. A., and Orozco, M. (2007) Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers Biophys. J. 92, 3817-3829
18. Buterin, T., Hess, M. T., Luneva, N., Geacintov, N. E., Amin, S., Kroth, H., Seidel, A., and Naegeli, H. (2000) Unrepaired fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots Cancer Res. 60, 1849-1856
19. 6 -adenine adducts: unusual thermal stabilization of modified DNA duplexes Chem. Res. Toxicol. 15, 249-261
20. Friedberg, E. C., Lehmann, A. R., and Fuchs, R. P. (2005) Trading places: how do DNA polymerases switch during translesion DNA synthesis? Mol. Cell 18, 499-505