Porphyrin intercalation in G4-DNA quadruplexes by molecular dynamics simulations

Journal of Physical Chemistry B

Volumn 113, Issue 40, 2009, Pages 13152-13160

  Cavallari, Manuela ^a   Garbesi, Anna ^a   Di Felice, Rosa ^a  

^a UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; MOLECULAR DYNAMICS; NUCLEIC ACIDS; OLIGOMERS; PORPHYRINS;

CLASSICAL MOLECULAR DYNAMICS; DNA OLIGOMERS; DNA QUADRUPLEXES; EDGE TERMINATION; EXPERIMENTAL EVIDENCE; HELICAL CONFORMATION; MOLECULAR DYNAMICS SIMULATIONS; PORPHYRIN DERIVATIVES; QUADRUPLEXES; STACKING DISTANCES; STOICHIOMETRIC RATIO;

POSITIVE IONS;

GUANINE QUADRUPLEX; PORPHYRIN; TETRA(4 N METHYLPYRIDYL)PORPHINE; TETRA(4-N-METHYLPYRIDYL)PORPHINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; HYDROGEN BOND;

COMPUTER SIMULATION; G-QUADRUPLEXES; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; PORPHYRINS;

EID: 70349687552     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9039226     Document Type: Article

References (41)

1. Izbicka, E.; Wheelhouse, R. T.; Raymond, E.; Davidson, K. K.; Lawrence, R. A.; Sun, D.; Windle, B. E.; Hurley, L. H.; Von Hoff, D. D. Cancer Res. 1999, 59, 639-644.
2. Kim, M.-Y.; Gleason-Guzman, M.; Izbicka, E.; Nishioka, D.; Hurley, L. H. Cancer Res. 2003, 63, 3247-3256.
3. Grand, C. L.; Han, H.; Munoz, R. M.; Weitman, S.; Von Hoff, D. D.; Hurley, L. H.; Bearss, D. J. Mol. Cancer Ther. 2002, 1, 565-573.
4. Kotlyar, A. B.; Borovok, N.; Molotsky, T.; Fadeev, L.; Gozin, M. Nucleic Acids Res. 2005, 33, 525-535.
5. Kotlyar, A. B.; Borovok, N.; Molotsky, T.; Cohen, H.; Shapir, E.; Porath, D. Adv. Mater. 2005, 17, 1901-1905.
6. Cohen, H.; Sapir, T.; Borovok, N.; Molotsky, T.; Di Felice, R.; Kotlyar, A. B.; Porath, D. Nano Lett. 2007, 7, 981.
7. Porath, D.; Cuniberti, G.; Di Felice, R. Top. Curr. Chem. 2004, 237, 183-227.
8. TMPyP4 = meso-tetrakis(4-W-methylpyridyl)porphyrin.
9. Wheelhouse, R. T.; Sun, D.; Han, H.; Han, F. X.; Hurley, L. H. J. Am. Chem. Soc. 1998, 120, 3261-3262.
10. Han, F. X.; Wheelhouse, R. T.; Hurley, L. H. J. Am. Chem. Soc. 1999, 121, 3561-3570.
11. Han, H.; Langley, D. R.; Rangan, A.; Hurley, L. H. J. Am. Chem. Soc. 2001, 123, 8902-8913.
12. Wei, C; Jia, G.; Yuan, J.; Feng, Z.; Li, C. Biochemistry 2006, 45, 6681-6691.
13. Parkinson, G. N.; Ghosh, R.; Neidle, S. Biochemistry 2007, 46, 2390-2397.
14. Anantha, N. V.; Azam, M.; Sheardy, R. D. Biochemistry 1998, 37, 2709-2714.
15. Haq, I.; Trent, J. O.; Chowdhry, B. Z.; Jenkins, T. C. J. Am. Chem. Soc. 1999, 121, 1768-1779.
16. Lubitz, I.; Borovok, N.; Kotlyar, A. B. Biochemistry 2007, 46, 12925-12929.
17. Phillips, J. C; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.
18. Foloppe, N.; MacKerell, A. D., Jr. J. Comput. Chem. 2000, 21, 86-104.
19. MacKerell, A. D., Jr.; Banavali, N. J. Comput. Chem. 2000, 21, 105-120.
20. Cavallari, M.; Calzolari, A.; Garbesi, A.; Di Felice, R. J. Phys. Chem. B 2006, 110, 26337.
21. http://accelrys.com/products/quanta/.
22. Stewart, J. J. P. J. Mol. Model. 2004, 10, 155-164.
23. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
24. Fletcher, R.; Reeves, C. M. Comput. J. 1964, 7, 149.
25. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 237.
26. Berendsen, H. J. C; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
27. Kolb, A.; Dünweg, B. J. Chem. Phys. 1999, 111, 4453.
28. Nosé, S. J. Chem. Phys. 1984, 81, 511.
29. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
30. Phillips, K.; Dauter, Z.; Murchie, A. I. H.; Lilley, D. M. J.; Luisi, B. J. Mol. Biol. 1997, 273, 171.
31. Borovok, N.; Iram, N.; Zikich, D.; Ghabboun, J.; Livshits, G. I.; Porath, D.; Kotlyar, A. B. Nucleic Acids Res. 2008, 36, 5050-5060.
32. Kotlyar, A. B. Private communication.
33. Borovok, N.; Molotsky, T.; Ghabboun, J.; Porath, D.; Kotlyar, A. B. Anal. Biochem. 2008, 374, 71-78.
34. Fadrna, E.; Špackova, N.; Šfl, R.; Koèa, J.; Cheatham, T. E., Ill; Sponer, J. Biophys. J. 2004, 87, 227-242.
35. Yamashita, T.; Uno, T.; Ishikawa, Y. Bioorg. Med. Chem. 2005, 13, 2423-2430.
36. Hardin, C. C; Watson, T.; Corregan, M.; Bailey, C. Biochemistry 1992, 31, 833.
37. Xu, Q.; Deng, H.; Braunlin, W. Biochemistry 1993, 32, 13130.
38. Guschlbauer, W.; Chantot, J. F.; Thiele, D. J. Biomol. Struct. Dyn. 1990, 8, 491.
39. In this work the represented probability density distributions of the quantities of interest are obtained as linear convolutions of the computed normalized histograms collecting all the values of each quantity found in the production runs. We used Scott's choice (Scott, David W. (1979). "On optimal and data-based histograms". Biometrika 66 (3)) to compute the histogram bin with h, that is: h = 3.5s/n1/3, where s is the sample standard deviation and n is the number of collected values.
40. Maragliano, L.; Cottone, G.; Cordone, L.; Ciccotti, G. Biophys. J. 2004, 86, 2765-2772.
41. Our results and our main conclusions essentially derive from the stacking interactions between the porphyrins and the bases, and are thus unlikely to be dependent on the ribonucleic backbone.