Experimental and computational approach to the rational monitoring of hydrogen-bonding interaction of 2-Imidazolidinethione with DNA and guanine

Food and Chemical Toxicology

Volumn 48, Issue 1, 2010, Pages 29-36

  Ahmadi, F ^a   Alizadeh, A A ^a   Bakhshandeh Saraskanrood, F ^a   Jafari, B ^a   Khodadadian, M ^b  

^a KERMANSHAH UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^b RAZI UNIVERSITY   (Iran)

Author keywords

2 Imidazolidinethione; Ab initio mechanical quantum; DNA; Guanine; H bonding

Indexed keywords

2 IMIDAZOLIDINETHIONE; ACETONITRILE; GUANINE;

AB INITIO CALCULATION; ARTICLE; BASE PAIRING; CIRCULAR DICHROISM; CONTROLLED STUDY; DENATURATION; DENSITY FUNCTIONAL THEORY; DIFFERENTIAL PULSE VOLTAMMETRY; DNA DAMAGE; HYDROGEN BOND; INTERACTIONS WITH DNA; NONHUMAN; QUANTUM MECHANICS; ULTRAVIOLET SPECTROSCOPY;

ALGORITHMS; ANIMALS; CATTLE; CIRCULAR DICHROISM; COMPUTATIONAL BIOLOGY; DNA; ETHYLENETHIOUREA; GUANINE; HOT TEMPERATURE; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID DENATURATION; QUANTUM THEORY; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 72149087430     PISSN: 02786915     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fct.2009.09.010     Document Type: Article

References (75)

1. Becke A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98 (1993) 5648-5652
2. Berger I., Winston W., Manoharan R., Schwartz T., Alfken J., Kim Y.G., Lowenhaupt K., Herbert A., and Rich A. Spectroscopic characterization of a DNA-Binding domain, Zα, from the editing enzyme, dsRNA adenosine deaminase: evidence for left-handed Z-DNA in the Zα-DNA complex. Biochemistry 37 (1998) 13313-13321
3. Berman H.M., Neidle S., Zimmer C., and Thurm H. Netropsin, a DNA-binding oligopeptide structural and binding studies. Biochim. Biophys. Acta 561 (1979) 124-131
4. Besterman J.M., Elwell L.P., Blanchard S.G., and Cory M. Amiloride intercalates into DNA and inhibits DNA topoisomerase II. J. Biol. Chem. 262 (1987) 13352-13358
5. Bray A., Lewis J., and Walter R. Essential Cell Biology. An Introduction to the Molecular Biology of the Cell (1998), Garland Publishing Inc., New York, London
6. Burrows C.J., and Muller J.G. Oxidative nucleobase modifications leading to strand scission. Chem. Rev. 98 (1998) 1109-1152
7. Cao Y., and He X.W. Studies of interaction between safarine T and double helix DNA by spectral methods. Spectrochim. Acta A 54 (1998) 883-892
8. Chabra R.S., Eustis S., Haseman J.K., Kurtz P.J., and Carlton B.D. Comparative carcinogenicity of ethylene thiourea with or without perinatal exposure in rats and mice. Fundam. Appl. Toxicol. 18 (1992) 405-417
9. Chaires J.B. Biophysical chemistry of the daunomycin-DNA interaction. Biophys. Chem. 35 (1990) 191-202
10. Chowdhury S.R., Mukherjea K.K., and Bhattacharyya R. Biophysical and biochemical investigation on the binding of a manganese-cyanonitrosyl complex with DNA. Trans. Met. Chem. 30 (2005) 601-604
11. Colosio C., Fustinoni S., Birindelli S., Bonomi I., De Paschale G., Mammone T., Tiramani M., Vercelli F., Visentin S., and Maroni M. Ethylenethiourea in urine as an indicator of exposure to mancozeb in vineyard workers. Toxicol. Lett. 134 (2002) 133-140
12. Colson P., Bailly C., and Houssier C. Electric linear dichroism as a new tool to study sequence preference in drug binding to DNA. Biophys. Chem. 58 (1996) 125-140
13. Coulocheri S.A., Pigis D.G., Papavassiliou K.A., and Papavassiliou A.G. Hydrogen bonds in protein-DNA complexes: where geometry meets plasticity. Biochimie 89 (2007) 1291-1303
14. Dearfield K.L. Ethylene thiourea (ETU). A review of the genetic toxicity studies. Mutat. Res. Gen. Toxicol. 317 (1994) 111-132
15. Diederichsen U. Charge transfer in DNA: a controversy. Angew. Chem., Int. Ed. 36 (1997) 2317
16. Dolenc J., Borstnik U., Hodoscek M., Koller J., and Janezic D. An ab initio QM/MM study of the conformational stability of complexes formed by netropsin and DNA. The importance of Van der Walse interactions and hydrogem bonding. J. Mol. Struct. 718 (2005) 77-85
17. El-Gogary T.M., and Koehler G. Interaction of psoralens with DNA-bases(I). An ab-initio quantume chemical, density functional theory and second-order Moller-Plesset perturbation study. J. Mol. Struct. 808 (2007) 97-109
18. Elia M.C., Arce G., Hurt S.S., O'Neill P.J., and Scribner H.E. The genetic toxicology of ethylenethiourea - a case-study concerning the evaluation of a chemicals genotoxic potential. Mutat. Res. Gen. Toxicol. 341 (1995) 141-149
19. Fontaine-Aupart M.P., Laguitton-Pasquier H., Pansu R., Brain L., Renault E., Marden M.C., Rivalle C., and Bisagni E.E. Proton and charge transfer in the intercalating antitumour drug pazelliptine. J. Chem. Soc., Perkin Trans. 2 (1996) 1767-1774
20. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Zakrzewski, V.G., Montgomery Jr. J.A., Stratmann, R.E., Burant, J.C., Dapprich, S., Millam, J.M., Daniels, A.D., Kudin, K.N., Strain, M.C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G.A., Ayala, P.Y., Cui, Q., Morokuma, K., Salvador, P., Dannenberg, J.J., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Cioslowski, J., Ortiz, J.V., Baboul, A.G., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Andres, J.L., Gonzalez, C., Head-Gordon, M., Replogle, E.S., Pople, J.A., Gaussian 98, Gaussian Inc., Pittsburgh, PA, 1998.
21. Ha T.K., Suleimenov O.M., and Han M.J. A theoretical study of the anionic intermolecular hydrogen bonding between dihydroxy tetrahydrfuran and phosphate ions. J. Mol. Struct. 574 (2001) 75-83
22. Han D., Wang H., and Ren N. Molecular modeling of B-DNA site recognition by Ru intercalators: molecular shape selection. J. Mol. Model. 10 (2004) 216-222
23. Hobza P., and Sponer J. Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab Initio calculations. Chem. Rev. 99 (1999) 3247-3276
24. Houeto P., Bindoula G., and Hoffman J.R. Ethylenebisdithiocarbamates and ethylenethiourea: possible human health hazards. Environ. Health Perspect. 103 (1995) 568-573
25. Ibrahim M.S. Voltammetric studies of the interaction of nogalamycin antitumor drug with DNA. Anal. Chim. Acta 443 (2001) 63-72
26. International Agency for Research on Cancer, 2001. Monographs, Some Thyrotropic Agents, vol. 79. IARC, Lyon, France, pp. 659-701.
27. Joshaghani M., Gholivand M.B., and Ahmadi F. Spectrophotometric and conductometric study of complexation of salophen and some transition metal ions in nonaqueous polar solvents. Spectrochim. Acta A 70 (2008) 1073-1078
28. Karadeniz H., Alparslan L., Erdem A., and Karasulu E. Electrochemical investigation of interaction between mitomycin C and DNA in a novel drug-delivery system. J. Pharm. Biomed. Anal. 45 (2007) 322-326
29. Kashanian S., Gholivand M.B., Ahmadi F., Taravati A., and Hosseinzadeh Colagar A. DNA interaction with A1-N,N-bis(salicylidene)2,2-phenylendiamine complex. Spectrochim. Acta A 67 (2007) 472-478
30. Kashanian S., Gholivand M.B., Ahmadi F., and Ravan H. Interaction of Diazinon with DNA and the protective role of selenium in DNA damage. DNA Cell Biol. 27 (2008) 325-332
31. Kashanian S., Askari S., Ahmadi F., Omidfar K., Ghobadi S., and Tarighat F.A. In vitro study of DNA interaction with clodinafop-propargyl herbicide. DNA Cell Boil. 27 (2008) 581-585
32. Kelly T.M., Tossi A.B., McConnel D.J., and Streakas T.C. A study of the interactions of some polypyridylruthenium(II) complexes with DNA using fluorescence spectroscopy, topoisomerisation and thermal denaturation. Nucleic Acids Res. 13 (1985) 6017-6034
33. Ling X., Zhong W., Huang Q., and Ni K. Spectroscopic studies on the interaction of pazufloxacin with calf thymus DNA. J. Photochem. Photobiol. Biol. 93 (2008) 172-176
34. Liu S.Q., Cao M.L., and Dong S.L. Electrochemical and ultraviolet-visible spectroscopic studies on the interaction of deoxyribonucleic acid with vitamin B6. Bioelectrochemistry 74 (2008) 164-169
35. Luo R., Gilson H.S.R., Potter M.J., and Gilson M.K. The physical basis of nucleic acid base stacking in water. Biophys. J. 80 (2001) 140
36. Maheswari P.U., and Palaniandavar M. DNA bonding and cleavage properties of certain tetramine ruthenium(II) complexes of modified 1,10-phenantrolines - effect of hydrogen bonding on DNA binding affinity. J. Inorg. Biochem. 98 (2004) 219-230
37. Marty R., Nsoukpoe-Kossi N.Ch., Charbonneau D., Weinert C.M., Kreplak L., and Tajmir-Riahi H.A. Nucleic Acids Res. 37 (2009) 849-857
38. Mefail-Isom L., Shuiand X., and Williams L.D. Biochemistry divalent cations stabilize unstacked conformations of DNA and RNA by interacting with base Π systems. Biochemistry 37 (1998) 17105-17111
39. Meric B., Kerman K., Ozkan D., Kara P., Erdem A., Kucukoglu O., Erciyas E., and Ozsoz M. Electrochemical biosensor for the interaction of DNA with the alkylating agent 4,4′-dihydroxy chalcone based on guanine and adenine signals. J. Pharm. Biomed. Anal. 30 (2002) 1339-1346
40. Miduturu C.V., and Silverman S.K. Modulation of DNA constraints that control macromolecular folding. Angew. Chem., Int. Ed. 45 (2006) 1918-1921
41. Miehlich B.A., Savin H.S., and Preuss H. Results obtained with the correlation energy density functionals of becke and Lee, Yang and Parr. Chem. Phys. Lett. 157 (1989) 200-206
42. Minehardt T.J., Marzari N., Cooke R., Kollman E.P.A., and Car R. A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP. Biophys. J. 82 (2002) 660-675
43. Neault J.F., and Tajmir-Riahi H.A. DNA-chlorophyllin interaction. J. Phys. Chem. B 102 (1998) 1610-1614
44. Nelson S.M., Ferguson L.R., and Denny W.A. Non-covalent ligand/DNA interaction: minor groove binding agent. Mutat. Res. 623 (2007) 24-40
45. Newcomb L.F., and Gellman S.H. Aromatic stacking interactions in aqueous solution: evidence that neither classical hydrophobic effects nor dispersion forces are important. J. Am. Chem. Soc. 116 (1994) 4993-4994
46. Neyhart G.A., Grover N., Smith S.R., Kalsbeck W.A., Fairley T.A., and Thorp Cory H.H. Binding and kinetics studies of oxidation of DNA by oxoruthenium(IV). J. Am. Chem. Soc. 115 (1993) 4423-4428
47. Oliveira S.C.B., Corduneanu O., and Oliveira-Brett A.M. In situ evaluation of heavy metal-DNA interactions using an electrochemical DNA biosensor. Bioelectrochemstry 72 (2008) 53-58
48. Oliveira-Brett A.M., Piedade J.A.P., Silva L.A., and Diculescu V.C. Voltammetric determination of all DNA nucleotides. Anal. Biochem. 332 (2004) 321-329
49. Petersson G.A., and Al-Laham M.A. Complete basis set model chemistry. II. Open-shell systems and the total energies of the first-row atoms. J. Chem. Phys. 94 (1991) 6081-6090
50. Petersson G.A., Bennett A., Tensfeldt T.G., Al-Laham M.A., Shirley W.A., and Mantzaris J.A. Complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements. J. Chem. Phys. 89 (1988) 2193-2218
51. Podolyan Y., Nowak M.J., Lapinski L., and Leszczynski J. Probing ab initio MP2 approach toward the prediction of vibrational infrared spectra DNA bas paires. J. Mol. Struct. 744-747 (2005) 19-34
52. Priem D., Ha T.K., and Bauder A. Rotational spectra and structures of three hydrogen-bonded complexes between formic acid and water. J. Chem. Phys. 113 (2000) 169-175
53. Prive G.G., Heinemann U., Chandrasegaran S., Kan L.S., Kopka M.L., and Dickerson R.E. Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. Science 238 (1987) 498-504
54. 2+ and some Schiff bases in binary ACN/DMF mixtures. J. Mol. Struct. 885 (2008) 76-81
55. Rahimi-Nasrabadi M., Ahmadi F., Pourmortazavi S.M., Ganjali M.R., and Alizadeh K. Conductometric study of complex formations between some substituted pyrimidines and some metal ions in acetonitrile and the determination of thermodynamic parameters. J. Mol. Liquid 144 (2009) 97-101
56. Rajendar B., Sato Y., Nishizawaa S., and Teramae N. Improvement of base selectivity and binding affinity by controlling hydrogen bonding motifs between uncleobases and isoxanthopterin: application to the detection of T/C mutation. Bioorg. Med. Chem. Lett. 17 (2007) 3682-3685
57. Rauf S., Gooding J.J., Akhtar K., Ghauri M.A., Rahman M., Anwar M.A., and Khalid A.M. Electrochemical approach of anticancer drugs-DNA interaction. J. Pharm. Biomed. Anal. 37 (2005) 205-217
58. Sánchez-Carrasco S., Delcros J.G., Moya-García A.A., Sánchez-Jiménez F., and Ramírez F.J. Study by optical spectroscopy and molecular dynamic of the interaction of acridine-spermine conjugate with DNA. Biophys. Chem. 133 (2008) 54-65
59. Scheiner L.S. Bent hydrogen bonds and proton transfers. ACC. Chem. Res. 27 (1994) 402-408
60. Shao Y., Morita K., Dai Q., Nishizawa S., and Teramae N. Sequence dependence of cytochrome c electrochemistry on DNA modified electrodes: Effect of hhydrogen bonding of ligand to uncleobases opposite an a basic site. Electrochem. Commun. 10 (2008) 438-442
61. Somerville L. The metabolism of fungicides. Xenobiotica 16 (1986) 1017-1030
62. Sponer J., Leszcynski J., and Hobza P. Hydrogen bonding, staking and cation binding of DNA bases. J. Mol. Struct. 573 (2001) 43-53
63. Stephanos J.J. Drug-protein interactions: two-site binding of heterocyclic ligands to a monomeric hemoglobin. J. Inorg. Biochem. 62 (1996) 155-169
64. Stephanos J.J., Farina S.A., and Adison A.W. Iron ligand recognition by monomeric hemoglobins. Biochim. Biophys. Acta 1295 (1996) 209-221
65. Tabernero L., Bella J., and Alemán C. Hydrogen bond geometry in DNA-minor groove binding drug complexes. Nucleic Acids Res. 24 (1996) 3458-3466
66. 2+ with calf thymus DNA. J. Phys. Chem. 97 (1993) 1707-1711
67. Wang A.H.J., Quigley G.J., Kolpak F.J., Grawford J.L., Van Boom J.H., Mareland G.V., and Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282 (1979) 680-686
68. Wang A.H.J., Quigley G.J., and Kolpak F.J. Left-handed double helical DNA: variations in the backbone conformation. Science 211 (1981) 171-176
69. Wang F., Xu Y., Zhao J., and Hu Sh. Electrochemical oxidation of morin and interaction with DNA. Bioelectrochemistry 70 (2007) 356-362
70. World Health Organization, 1988. Dithiocarbamate pesticides, ethylenethiourea, and propylenethiourea: a general introduction. Environ. Health Crit. 78. WHO, Geneva.
71. Yang Z., Zhang D., Long H., and Liu Y. Electrochemical behavior of gallic acid interaction with DNA and detection of damage to DNA. J. Electroanal. Chem. 624 (2008) 91-96
72. Zhang Z., Huang W., Tang J., Wang E., and Dong S. Conformational transition of DNA induced by cationic lipid vesicle in acidic solution: spectroscopy investigation. Biophys. Chem. 97 (2002) 7-16
73. Zhao G.C., Zhu J.J., Zhang J.J., and Chen H.Y. Voltammetric studies of the interaction of methylene blue with DNA by means of β-cyclodextrin. Anal. Chim. Acta 394 (1999) 337-344
74. Zhoua H., Suna Z., Hoshib T., Kashiwagib Y., Anzaib J., and Li G. Temperature effect on the structural stability, similarity, and reversibility of human serum albumin in different states. Biophys. Chem. 114 (2005) 21-26
75. Zimmer C., and Wahnert U. Nonintercalating DNA-binding ligand: speccificity of interaction and their use as tools in biophysical, biochemical and biological investigation of the genetic material. Proc. Biophys. Mol. Biol. 47 (1986) 31-112