Molecular dynamics simulations of binding modes between methylene blue and DNA with alternating GC and at sequences

Biochemistry

Volumn 53, Issue 14, 2014, Pages 2391-2412

  Nogueira, Juan J ^a   González, Leticia ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; BINDING ENERGY; DNA; DRUG PRODUCTS; IONIC STRENGTH; MOLECULAR DYNAMICS; PHOTODYNAMIC THERAPY;

GROOVE BINDING MODES; HIGH IONIC STRENGTH; INTERACTION ENERGIES; INTERCALATIVE BINDING; MOLECULAR DYNAMICS SIMULATIONS; NONCOVALENT BINDING; ROTATIONAL TRANSITION; UNSTABLE STRUCTURES;

DNA SEQUENCES;

BASE PAIRING; BINDING SITES; DNA; METHYLENE BLUE; MOLECULAR DYNAMICS SIMULATION;

EID: 84898899166     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi500068z     Document Type: Article

References (46)

1. Hurley, L. H. (2002) DNA and its associated processes as targets for cancer therapy Nat. Rev. Cancer 2 (3) 188-200
2. Gurova, K. (2009) New hopes from old drugs: Revisiting DNA-binding small molecules as anticancer agents Future Oncol. 5 (10) 1685-1704
3. David-Cordonnier, M. H., Laine, W., Lansiaux, A., Rosu, F., Colson, P., de Pauw, E., Michel, S., Tillequin, F., Koch, M., Hickman, J. A., Pierré, A., and Bailly, C. (2005) Covalent binding of antitumor benzoacronycines to double-stranded DNA induces helix opening and the formation of single-stranded DNA: Unique consequences of a novel DNA-bonding mechanism Mol. Cancer Ther. 4 (1) 71-80
4. Strekowski, L. and Wilson, B. (2007) Noncovalent interactions with DNA: An overview Mutat. Res., Fundam. Mol. Mech. Mutagen. 623 (1-2) 3-13
5. Ihmels, H. and Otto, D. (2005) Intercalation of Organic dye molecules into double-stranded DNA-General principles and recent developments Top. Curr. Chem. 258, 161-204
6. Gao, Q., Williams, L. D., Egli, M., Rabinovich, D., Chen, S. L., Quigley, G. J., and Rich, A. (1991) Drug-induced DNA repair: X-ray structure of a DNA-ditercalinium complex Proc. Natl. Acad. Sci. U.S.A. 88 (6) 2422-2426
7. Banerjee, D. and Pal, S. K. (2008) Dynamics in the DNA recognition by DAPI: Exploration of the various binding modes J. Phys. Chem. B 112 (3) 1016-1021
8. Müller, W. and Crothers, D. M. (1975) Interactions of heteroaromatic compounds with nucleic acids. I. The influence of heteroatoms and polarizability on the base specificity of intercalating ligands Eur. J. Biochem. 54 (1) 267-277
9. Nordén, B. and Tjerneld, F. (1982) Structure of methylene blue-DNA complexes studied by linear and circular dichroism spectroscopy Biopolymers 21 (9) 1713-1734
10. Tong, C., Hu, Z., and Wu, J. (2010) Interaction between methylene blue and calfthymus deoxyribonucleic acid by spectroscopic technologies J. Fluoresc. 20 (1) 261-267
11. Tuite, E. and Kelly, J. M. (1995) The interaction of methylene blue, azure B, and thionine with DNA: Formation of complexes with polynucleotides and mononucleotides as model systems Biopolymers 35 (5) 419-433
12. Tuite, E. and Nordén, B. (1994) Sequence-specific interactions of methylene blue with polynucleotides and DNA: A spectroscopic study J. Am. Chem. Soc. 116 (17) 7548-7556
13. Zhang, L. Z. and Tang, G. Q. (2004) The binding properties of photosensitizer methylene blue to herring sperm DNA: A spectroscopic study J. Photochem. Photobiol., B 74 (2-3) 119-125
14. Mellish, K. J., Cox, R. D., Vernon, D. I., Griffiths, J., and Brown, S. B. (2002) In vitro photodynamic activity of a series of methylene blue analogues Photochem. Photobiol. 75 (4) 392-397
15. Orth, K., Russ, D., Beck, G., Rück, A., and Beger, H. G. (1998) Photochemotherapy of experimental colonic tumours with intra-tumorally applied methylene blue Langenbecks Arch. Surg. 383 (3-4) 276-281
16. Orth, K., Ruck, A., Stanescu, A., and Beger, H. G. (1995) Intraluminal treatment of inoperable oesophageal tumours by intralesional photodynamic therapy with methylene blue [12] Lancet 345 (8948) 519-520
17. Zolfaghari, P. S., Packer, S., Singer, M., Nair, S. P., Bennett, J., Street, C., and Wilson, M. (2009) In vivo killing of Staphylococcus aureus using a light-activated antimicrobial agent BMC Microbiol. 9, 27
18. Ragàs, X., Dai, T., Tegos, G. P., Agut, M., Nonell, S., and Hamblin, M. R. (2010) Photodynamic inactivation of Acinetobacter baumannii using phenothiazinium dyes: In vitro and in vivo studies Lasers Surg. Med. 42 (5) 384-390
19. Phillips, D. (2011) Toward targeted photodynamic therapy Pure Appl. Chem. 83 (4) 733-748
20. O'Connor, A. E., Gallagher, W. M., and Byrne, A. T. (2009) Porphyrin and nonporphyrin photosensitizers in oncology: Preclinical and clinical advances in photodynamic therapy Photochem. Photobiol. 85 (5) 1053-1074
21. Tanielian, C. and Wolff, C. (1995) Determination of the parameters controlling singlet oxygen production via oxygen and heavy-atom enhancement of triplet yields J. Phys. Chem. 99 (24) 9831-9837
22. Cotes Oyaga, S., Cotua Valdes, J., Borja Paez, S., and Hurtado Marquez, K. (2013) DFT Description of Intermolecular Forces between 9-Aminoacridines and DNA Base Pairs J. Theor. Chem. 2013 526569
23. Rohs, R., Sklenar, H., Lavery, R., and Röder, B. (2000) Methylene blue binding to DNA with alternating GC base sequence: A modeling study J. Am. Chem. Soc. 122 (12) 2860-2866
24. Rohs, R. and Sklenar, H. (2004) Methylene Blue Binding to DNA with Alternating AT Base Sequence: Minor Groove Binding is Favored over Intercalation J. Biomol. Struct. Dyn. 21 (5) 699-711
25. Rohs, R. and Sklenar, H. (2001) Methylene blue binding to DNA with alternating GC base sequence: Continuum treatment of salt effects Indian J. Biochem. Biophys. 38 (1-2) 1-6
26. Rohs, R., Bloch, I., Sklenar, H., and Shakked, Z. (2005) Molecular flexibility in ab initio drug docking to DNA: Binding-site and binding-mode transitions in all-atom Monte Carlo simulations Nucleic Acids Res. 33 (22) 7048-7057
27. Spink, N., Brown, D. G., Skelly, J. V., and Neidle, S. (1994) Sequence-dependent effects in drug-DNA interaction: The crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex Nucleic Acids Res. 22 (9) 1607-1612
28. Case, D. A., Darden, T. A., Cheatham, III, T. E., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Walker, R. C., Zhang, W., Merz, K. M., Roberts, B., Hayik, S., Roitberg, A., Seabra, G., Swails, J., Götz, A. W., Kolossváry, I., Wong, K. F., Paesani, F., Vanicek, J., Wolf, R. M., Liu, J., Wu, X., Brozell, S. R., Steinbrecher, T., Gohlke, H., Cai, Q., Ye, X., Wang, J., Hsieh, M.-J., Cui, G., Roe, D. R., Mathews, D. H., Seetin, M. G., Salomon-Ferrer, R., Sagui, C., Babin, V., Luchko, T., Gusarov, S., Kovalenko, A., and Kollman, P. A. (2012) AMBER 13, University of California, San Francisco.
29. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 (2) 926-935
30. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD J. Comput. Chem. 26 (16) 1781-1802
31. Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., and Case, D. A. (2004) Development and testing of a general Amber force field J. Comput. Chem. 25 (9) 1157-1174
32. Wang, J., Cieplak, P., and Kollman, P. A. (2000) How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? J. Comput. Chem. 21 (12) 1049-1074
33. Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T. E., III, Laughton, C. A., and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers Biophys. J. 92 (11) 3817-3829
34. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A., Jr., Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, N. J., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, Ö., Foresman, J. B., Ortiz, J. V., Cioslowski, J., and Fox, D. J. (2013) Gaussian 09, Revision D.01, Gaussian, Inc., Wallingford CT.
35. Lavery, R., Moakher, M., Maddocks, J. H., Petkeviciute, D., and Zakrzewska, K. (2009) Conformational analysis of nucleic acids revisited: Curves+ Nucleic Acids Res. 37 (17) 5917-5929
36. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual molecular dynamics J. Mol. Graphics 14 (1) 33-38
37. Roe, D. R. and Cheatham, T. E. (2013) PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data J. Chem. Theory Comput. 9 (7) 3084-3095
38. Srinivasan, J., Cheatham, T. E., III, Cieplak, P., Kollman, P. A., and Case, D. A. (1998) Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices J. Am. Chem. Soc. 120 (37) 9401-9409
39. Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., and Cheatham, T. E., III (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models Acc. Chem. Res. 33 (12) 889-897
40. Miller, B. R., III, McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., and Roitberg, A. E. (2012) MMPBSA.py: An efficient program for end-state free energy calculations J. Chem. Theory Comput. 8 (9) 3314-3321
41. Tan, C., Tan, Y. H., and Luo, R. (2007) Implicit nonpolar solvent models J. Phys. Chem. B 111 (42) 12263-12274
42. Homeyer, N. and Gohlke, H. (2012) Free energy calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area method Mol. Informatics 31 (2) 114-122
43. Kabeláč, M., Zimandl, F., Fessl, T., Chval, Z., and Lankaš, F. (2010) A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: Structure and dynamics Phys. Chem. Chem. Phys. 12 (33) 9677-9684
44. Zhao, G. C., Zhu, J. J., and Chen, H. Y. (1999) Spectroscopic studies of the interactive model of methylene blue with DNA by means of β-cyclodextrin Spectrochim. Acta, Part A 55 (5) 1109-1117
45. Lei, H., Wang, X., and Wu, C. (2012) Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations J. Mol. Graph. Model. 38, 279-289
46. Ramachandran, S., Temple, B., Alexandrova, A. N., Chaney, S. G., and Dokholyan, N. V. (2012) Recognition of platinum-DNA adducts by HMGB1a Biochemistry 51 (38) 7608-7617