Drug-DNA Interaction: A Theoretical Study of the Stability of CP-DNA Binding with Thionine

Ghazala Yunus, Seema Srivastava, Vishwambhar Dayal Gupta

Department of Physics, Integral University, Lucknow, India.

DOI: 10.4236/ojapps.2012.22013                

Abstract

The recent study on binding of small molecules to double stranded DNA suggested that the intercalation of a tricyclic heteroaromatic molecule, thionine, with natural DNA provided thermal stabilization to the complex. In the present study, we reported theoretical analysis of thionine binding with Clostridium perfringenes DNA duplex (CP-DNA) by using an amended Zimm and Bragg theory, to explain the melting behaviour and heat capacity of CP-DNA with and without thionine binding. The experimental models of Paul et al. (2010) have been used for the study. The sharpness of transition has been examined in terms of half width and sensitivity parameter (?H/σ). The results of theoretical approach suggested that the various parameters such as transition profile, sharpness of the transition, heat capacity curve and half widths are in good agreement with the experimental measurements for binding of thionine. Therefore, the proposed theoretical analysis may be useful in order to understand interaction of small molecules to DNA that may be applied in the process of drug development and for designing more potential DNA binding therapeutic molecules.

Keywords

Thionine; DNA Binding; Transition Profile; Heat Capacity; Drug Design

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	M. J. Waring, “DNA Modification and Cancer,” Annual Reviews Biochemistry, Vol. 50, 1981, pp. 159-192. doi:10.1146/annurev.bi.50.070181.001111
[2]	L. H. Hurley, “Secondary DNA Structures as Molecular Targets for Cancer Therapeutics,” Biochemical Society Transactions, Vol. 29, No. 6, 2001, pp. 692-696.
[3]	L. H. Hurley, “DNA and Its Associated Processes as Targets for Cancer Therapy,” Nature Reviews Cancer, Vol. 2, No. 3, 2002, pp. 188-200. doi:10.1038/nrc749
[4]	R. Martinez and L. Chacon-Garcia, “The Search of DNAIntercalators as Antitumoral Drugs: What It Worked and What Did Not Work,” Current Medicinal Chemistry, Vol. 12, No. 2, 2005, pp. 127-151.
[5]	R. Palchaudhuri and P. J. Hergenrother, “DNA as a Target for Anticancer Compounds: Methods to Determine the Mode of Binding and the Mechanism of Action,” Current Opinion in Biotechnololy, Vol. 18, No. 6, 2007, pp. 497-503. doi:10.1016/j.copbio.2007.09.006
[6]	M. Maiti and G. S. Kumar, “Molecular Aspects on the Interaction of Protoberberine, Benzophenanthridine, and Aristolochia Group of Alkaloids with Nucleic Acid Structures and Biological Perspectives,” Medicinal Research Reviews, Vol. 27, No. 5, 2007, pp. 649-695. doi:10.1002/med.20087
[7]	P. Paul, M. Hossain, R. C. Yadav and G. S. Kumar, “Biophysical Studies on the Base Specificity and Energetics of the DNA Interaction of Photoactive Dye Thionine: Spectroscopic and Calorimetric Approach,” Biophysical Chemistry, Vol. 148, No. 1-3, 2010, pp. 93-103. doi:10.1016/j.bpc.2010.02.015
[8]	K. Bhadra and G. S. Kumar, “Therapeutic Potential of Nucleic Acid-Binding Isoquinoline Alkaloids: Binding Aspects and Implications for Drug Design,” Medicinal Research Reviews, Vol. 31, No. 6, 2011, pp. 821-862. doi:10.1002/med.20202
[9]	J. Y. Du, X. H. Huang, F. Xu, Y. Y. Feng, W. Xing and T. H. Lu, “Spectral Study on the Interaction Mechanism between Thionine and Calf Thymus DNA,” Guang Pu Xue Yu Guang Pu Fen Xi, Vol. 25, No. 9, 2005, 14351448.
[10]	S. Jockusch, D. Lee, N. J. Turro and E. F. Leonard, “PhotoInduced Inactivation of Viruses: Adsorption of Methylene Blue, Thionine, and Thiopyronine on Beta Bacteriophage,” Proceeding of National Academy of Sciences USA, Vol. 93, No. 15, 1996, pp. 7446-7451. |doi:10.1073/pnas.93.15.7446
[11]	C. Dohno, E. D. A. Stemp and J. K. Barton, “Fast Back Electron Transfer Prevents Guanine Damage by Photoexcited Thionine Bound to DNA” Journal of American Chemical Society, Vol. 125, No. 32, 2003, pp. 9586-9587. doi:10.1021/ja036397z
[12]	Y. Xu, L. Yang, X. Ye, P. He and Y. Fang, “ImpedanceBased DNA Biosensor Employing Molecular Beacon DNA as Probe and Thionine as Charge Neutralizer,” Electroanalysis, Vol. 18, No. 9, 2006, pp. 873-881. doi:10.1002/elan.200503465
[13]	E. M. Tuite and J. M. Kelly, “The Interaction of Methylene Blue, Azure B, and Thionine with DNA: Formation of Complexes with Polynucleotides and Mononucleotides as Model Systems,” Biopolymers, Vol. 35, No. 5, 1995, pp. 419-433. doi:10.1002/bip.360350502
[14]	Y. J. Ihaya and T. Nakamura, “Optical Activity of Nucleic Acid-Thionine Complexes,” Bulletin of the Chemical Society of Japan, Vol. 44, 1971, pp. 951-957.
[15]	C. V. Kumar and E. H. Asuncion, “DNA Binding Studies and Site Selective Fluorescence Sensitization of an Anthryl Probe,” Journal of American Chemical Society, Vol. 115, No. 19, 1993, pp. 8547-8553. doi:10.1021/ja00072a004
[16]	E. M. Tuite and J. M. Kelly, “New Trends in Photobiology: Photochemical Interactions of Methylene Blue and Analogues with DNA and Other Biological Substrates,” Journal of Photo chemistry and Photobiology, B: Biology, Vol. 21, No. 2-3, 1993, pp. 103-124. doi:10.1016/1011-1344(93)80173-7
[17]	T. C. Chang, Y. P. Yang, K. H. Huang, C. C. Chang and C. Hecht, “Investigation of Thionine-DNA Interaction by Satellite Hole Spectroscopy,” Optics and Spectroscopy, Vol. 98, No. 5, 2005, pp. 716-721. doi:10.1134/1.1929049
[18]	C. Hecht, J. Friedrich and T. C. Chang, “Interactions of Thionin with DNA Strands: Intercalation versus External Stacking,” Journal of Physical Chemistry B, Vol. 108, No. 29, 2004, pp. 10241-10244. doi:10.1021/jp0372993
[19]	C. Hecht, P. Hermann, J. Friedrich and T. C. Chang, “Thionin in a Cyclodextrin Nanocavity: Measuring Local Compressibilities by Pressure Tuning Hole Burning Spectroscopy,” Chemical Physics Letters, Vol. 413, No. 4-6, 2005, pp. 335-341. doi:10.1016/j.cplett.2005.08.002
[20]	B. H. Zimm and J. K. Bragg, “Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains,” Journal of Chemical Physics, Vol. 31, No. 2, 1959, pp. 526-535. doi:10.1063/1.1730390
[21]	S. Srivastava, V. D. Gupta, P. Tandon, S. Singh and S. B. Katti, “Drug Binding and Order-Order and Order-Disorder Transitions in DNA Triple Helices,” Journal of Macromolecular Science Physics, Vol. 38, No. 4, 1999, pp. 349-366. doi:10.1080/00222349908212437
[22]	S. Srivastava, S. Srivastava, S. Singh and V. D. Gupta, “Stability and Transition in a DNA Tetraplex: A Model for Telomeres,” Journal of Macromolecular Science Physics, Vol. 40, No. 1, 2001, pp. 1-14. doi:10.1081/MB-100000050
[23]	G. Yunus, S. Srivastava and V. D. Gupta, “Stability of DNA Binding with Dipyrandium: A Theoretical Study,” International Journal of Physical Sciences, Vol. 6, No. 36, 2011, pp. 8151-8156. doi: 10.5897/IJPS11.1335
[24]	S. Srivastava, I. A. Khan, S. Srivastava and V. D. Gupta, “A Theoretical Study of the Stability of DNA Binding with Cis/Trans Platin,” Indian Journal of Biochemistry and Biophysics, Vol. 41, No. 6, 2004, pp. 305-310.
[25]	N. Poklar, D. S. Pilch, S. J. Lippard, E. A. Redding, S. U. Dunham and K. J. Breslauer, “Influence of Cisplatin Intrastrand Crosslinking on the Conformation, Thermal Stability, and Energetics of a 20-mer DNA Duplex,” Proceeding of National Academy of Sciences USA, Vol. 93, No. 15, 1996, pp. 7606-7611. doi:10.1073/pnas.93.15.7606
[26]	K. A. Roles and B. Wunderlich, “Heat Capacities of Solid Poly(Amino Acids). I. Polyglycine, Poly(L-Alanine), and Poly(L-Valine),” Biopolymers, Vol. 31, No. 5, 1991, pp. 477-487. doi:10.1002/bip.360310503
[27]	D. L. Ma, D. S. Chan, P. Lee, M. H. Kwan and C. H. Leung, “Molecular Modeling of Drug-DNA Interactions: Virtual Screening to Structure-Based Design,” Biochimie, Vol. 93, No. 8, 2011, pp. 1252-1266. doi:10.1016/j.biochi.2011.04.002
[28]	J. Yuan, W. Guo and E. Wang, “Oligonucleotide Stabilized Silver Nanoclusters as Fluorescence Probe for DrugDNA Interaction Investigation,” Analitica Chimica Acta, Vol. 706, No. 2, 2011, pp. 338-342. doi:10.1016/j.aca.2011.08.043
[29]	F. Araya, G. Huchet, I. McGroarty, G. G. Skellern and R. D. Waigh, “Capillary Electrophoresis for Studying DrugDNA Interactions,” Methods, Vol. 42, No. 2, 2007, pp. 141-149. doi:10.1016/j.ymeth.2006.09.006
[30]	M. M. Islam, S. R. Chowdhury and G. S. Kumar, “Spectroscopic and Calorimetric Studies on the Binding of Alkaloids Berberine, Palmatine and Coralyne to Double Stranded RNA Polynucleotides,” Journal of Physical Chemistry B, Vol. 113, No. 4, 2009, pp. 1210-1224. doi:10.1021/jp806597w
[31]	V. Gonzalez-Ruiz, A. I. Olives, M. A. Martin, P. Ribelles, M. T. Ramos and J. C. Menendez, “An Overview of Analytical Techniques Employed to Evidence Drug-DNA Interactions. Applications to the Design of Genosensors,” In: M. A. Komorowska and S. Olsztynska-Janus, Eds., Biomedical Engineering, Trends, Research and Technologies, 2011, InTech, Castle Rock, pp. 65-90. doi:10.5772/13586
[32]	A. Kunwar, S. Emmanuel, U. Singh, R. K. Chittela, D. Sharma, S. K. Sandur and I. K. Priyadarsini, “Interaction of a Curcumin Analogue Dimethoxycurcumin with DNA,” Chemical Biology and Drug Design, Vol. 77, No. 4, 2011, pp. 281-287. doi:10.1111/j.1747-0285.2011.01083.x