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Journal of Nucleic Acids
Volume 2011, Article ID 631372, 8 pages
http://dx.doi.org/10.4061/2011/631372
Research Article

The Stability of a Model Substrate for Topoisomerase 1-Mediated DNA Religation Depends on the Presence of Mismatched Base Pairs

1Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
2Department of Physics, Wake Forest University, Winston-Salem, NC 27109, USA
3Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA

Received 9 May 2011; Revised 7 June 2011; Accepted 11 June 2011

Academic Editor: Daisuke Miyoshi

Copyright © 2011 William H. Gmeiner et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. Y. Pommier, E. Leo, H. Zhang, and C. Marchand, “DNA topoisomerases and their poisoning by anticancer and antibacterial drugs,” Chemistry and Biology, vol. 17, no. 5, pp. 421–433, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. Y. Pommier, “DNA topoisomerase I Inhibitors: chemistry, biology, and interfacial inhibition,” Chemical Reviews, vol. 109, no. 7, pp. 2894–2902, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Y. Chen and L. F. Liu, “DNA topoisomerases: essential enzymes and lethal targets,” Annual Review of Pharmacology and Toxicology, vol. 34, pp. 191–218, 1994. View at Google Scholar · View at Scopus
  4. D. A. Koster, V. Croquette, C. Dekker, S. Shuman, and N. H. Dekker, “Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB,” Nature, vol. 434, no. 7033, pp. 671–674, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. L. Stewart, M. R. Redinbo, X. Qiu, W. G. J. Hol, and J. J. Champoux, “A model for the mechanism of human topoisomerase I,” Science, vol. 279, no. 5356, pp. 1534–1541, 1998. View at Publisher · View at Google Scholar · View at Scopus
  6. S. Krogh, U. H. Mortensen, O. Westergaard, and B. J. Bonven, “Eukaryotic topoisomerase I-DNA interaction is stabilized by helix curvature,” Nucleic Acids Research, vol. 19, no. 6, pp. 1235–1241, 1991. View at Google Scholar · View at Scopus
  7. P. Pourquier and Y. Pommier, “Topoisomerase I-mediated DNA damage,” Advances in Cancer Research, vol. 80, pp. 188–216, 2001. View at Google Scholar · View at Scopus
  8. Z. Y. Liao, O. Sordet, H. L. Zhang et al., “A novel polypyrimidine antitumor agent FdUMP[10] induces thymineless death with topoisomerase I-DNA complexes,” Cancer Research, vol. 65, no. 11, pp. 4844–4851, 2005. View at Publisher · View at Google Scholar · View at Scopus
  9. P. Pourquier, C. Gioffre, G. Kohlhagen et al., “Gemcitabine (2,2-difluoro-2-deoxycytidine), an antimetabolite that poisons topoisomerase I,” Clinical Cancer Research, vol. 8, no. 8, pp. 2499–2504, 2002. View at Google Scholar · View at Scopus
  10. W. H. Gmeiner, S. Yu, R. T. Pon, P. Pourquier, and Y. Pommier, “Structural basis for topoisomerase I inhibition by nucleoside analogs,” Nucleosides, Nucleotides and Nucleic Acids, vol. 22, no. 5-8, pp. 653–658, 2003. View at Publisher · View at Google Scholar · View at Scopus
  11. I. Hirao, G. Kawai, S. Yoshizawa et al., “Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGMGC) in solution: an extraordinarily stable structure resistant to nucleases and heat,” Nucleic Acids Research, vol. 22, no. 4, pp. 576–582, 1994. View at Google Scholar · View at Scopus
  12. L. A. Marky and K. J. Breslauer, “Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves,” Biopolymers, vol. 26, no. 9, pp. 1601–1620, 1987. View at Google Scholar · View at Scopus
  13. J. C. Phillips, R. Braun, W. Wang et al., “Scalable molecular dynamics with NAMD,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1781–1802, 2005. View at Publisher · View at Google Scholar · View at Scopus
  14. A. D. MacKerell, D. Bashford, M. Bellott et al., “All-atom empirical potential for molecular modeling and dynamics studies of proteins,” Journal of Physical Chemistry B, vol. 102, no. 18, pp. 3586–3616, 1998. View at Google Scholar · View at Scopus
  15. A. D. MacKerell, N. Banavali, and N. Foloppe, “Development and current status of the CHARMM force field for nucleic acids,” Biopolymers, vol. 56, no. 4, pp. 257–265, 2000. View at Publisher · View at Google Scholar · View at Scopus
  16. B. R. Brooks, R. D. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, “CHARMM: a program for macromolecular energy, minimization and dynamics calculations,” Journal of Computational Chemistry, vol. 4, pp. 187–217, 1983. View at Google Scholar
  17. J. Farwer, M. J. Packer, and C. A. Hunter, “PREDICTOR: a web-based tool for the prediction of atomic structure from sequence for double helical DNA with up to 150 base pairs,” In Silico Biology, vol. 7, no. 6, pp. 595–600, 2007. View at Google Scholar · View at Scopus
  18. N. B. Ulyanov, W. R. Bauer, and T. L. James, “High-resolution NMR structure of an AT-rich DNA sequence,” Journal of Biomolecular NMR, vol. 22, no. 3, pp. 265–280, 2002. View at Publisher · View at Google Scholar · View at Scopus
  19. S. Ghosh, F. R. Salsbury Jr., D. A. Horita, and W. H. Gmeiner, “Zn2+ selectively stabilizes FdU-substituted DNA through a unique major groove binding motif,” Nucleic Acids Research, vol. 39, no. 10, pp. 4490–4498, 2011. View at Publisher · View at Google Scholar
  20. W. Humphrey, A. Dalke, and K. Schulten, “VMD: visual molecular dynamics,” Journal of Molecular Graphics, vol. 14, no. 1, pp. 33–38, 1996. View at Publisher · View at Google Scholar · View at Scopus
  21. Y. Zhou, M. Cook, and M. Karplus, “Protein motions at zero-total angular momentum: the importance of long-range correlations,” Biophysical Journal, vol. 79, no. 6, pp. 2902–2908, 2000. View at Google Scholar · View at Scopus
  22. F. R. Salsbury, M. W. Crowder, S. F. Kingsmore, and J. J. A. Huntley, “Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor,” Journal of Molecular Modeling, vol. 15, no. 2, pp. 133–145, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. J. S. Ullman and B. J. McCarthy, “The relationship between mismatched base pairs and the thermal stability of DNA duplexes. II. Effects of deamination of cytosmine,” Biochimica et Biophysica Acta, vol. 294, no. 3, pp. 416–424, 1973. View at Google Scholar · View at Scopus
  24. L. C. Sowers, R. Eritja, B. Kaplan, M. F. Goodman, and G. V. Fazakerly, “Equilibrium between a wobble and ionized base pair formed between fluorouracil and guanine in DNA as studied by proton and fluorine NMR,” Journal of Biological Chemistry, vol. 263, no. 29, pp. 14794–14801, 1988. View at Google Scholar · View at Scopus