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Structure, Thermodynamics and Energetics of Drug-DNA Interactions: Computer Modeling and Experiment

  • Maxim P. EvstigneevEmail author
  • Anna V. Shestopalova
Chapter
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 17)

Abstract

In this chapter we demonstrate the large usefulness of using complex approach for understanding the mechanism of binding of biologically active compounds (antitumour antibiotics, mutagens etc.) with nucleic acids (NA). The applications of various biophysical methods and computer modeling to determination of structural (Infra-red and Raman vibrational spectroscopies, computer modeling by means of Monte-Carlo, molecular docking and molecular dynamics methods) and thermodynamic (UV-VIS spectrophotometry, microcalorimetry, molecular dynamics simulation) parameters of NA-ligand complexation with estimation of the role of water environment in this process, are discussed. The strategy of energy analysis of the NA-ligand binding reactions in solution is described, which is based on decomposition of experimentally measured net Gibbs free energy of binding in terms of separate energetic contributions from particular physical factors. The main outcome of such analysis is to answer the questions “What physical factors and to what extent stabilize/destabilize NA-ligand complexes?” and “What physical factors most strongly affect the bioreceptor binding affinity?”

Keywords

DNA RNA Drug Complexation Thermodynamics Structure Anticancer antibiotics Energy analysis Energy decomposition Computer modeling Intercalation Minor groove binding 

Notes

Acknowledgments

The authors express their special thanks to the following people which, in part, created the background, contributed and stimulated further the results reviewed in this chapter: Professor Vladimir Ya. Maleev (IRE NASU), Professor Mikhail A. Semenov (IRE NASU), Dr. Elena B. Kruglova (IRE NASU), Dr. Ekaterina G. Bereznyak (IRE NASU), Dr. Viktor V. Kostjukov (SevNTU). Support from the Ministry of Education and National Academy of Sciences of Ukraine via the grants 0103U002268 (2002–2006), 0107U001331 (2007–2009), 0107U001079 (2007–2011), 0110U001683 (2010–2012), F27/60-2010 is greatly acknowledged.

References

  1. 1.
    Ramos MJ, Fernandes PA (2006) Atomic-level rational drug design Curr Comp-Aided Drug Des 2:57–81Google Scholar
  2. 2.
    Nelson SM, Ferguson LR, Denny WA (2004) DNA and the chromosome—varied targets for chemotherapy. Cell Chromosome 3(1):1–26Google Scholar
  3. 3.
    Hurley LH (2002) DNA and its associated processes as targets for cancer therapy. Nat Rev Cancer 2(3):188–199Google Scholar
  4. 4.
    Au JL, Panchal N, Li D, Gan Y (1997) Apoptosis: a new pharmacodynamic endpoint. Pharm Res 14(12):1659–1671Google Scholar
  5. 5.
    Selwood DL (2013) Beyond the hundred dollar genome—drug discovery futures. Chem Biol Drug Des. 81(1):1–4Google Scholar
  6. 6.
    Ren J, Chaires JB (1999) Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry 38(49):16067–16075Google Scholar
  7. 7.
    Dervan PB (2001) Molecular recognition of DNA by small molecules. Bioorg Med Chem 9(9):2215–2235Google Scholar
  8. 8.
    Veselkov AN, Maleev VYa, Glibin EN, Karawajew L, Davies DB (2003) Structure–activity relation for synthetic phenoxazone drugs. Evidence for a direct correlation between DNA binding and pro-apoptotic activity. Eur J Biochem 270(20):4200–4207Google Scholar
  9. 9.
    Murthy VR, Raghuram DV, Murthy PN (2007) Drug, dosage, activity, studies of antimalarials by physical methods—II. Bioinformation 2(1):12–16.Google Scholar
  10. 10.
    Sobell HM, Jain SC (1972) Stereochemistry of actinomycin binding to DNA. II. Detailed molecular model of actinomycin-DNA complex and its implications. J Mol Biol 68(1):21–34.Google Scholar
  11. 11.
    Porumb H (1978) The solution spectroscopy of drugs and the drug-nucleic acid interactions. Prog Biophys Mol Biol 34(3):175–195Google Scholar
  12. 12.
    Yielding LW, Yielding KL (1984) Ethidium binding to deoxyribonucleic acid: spectrophotometric analysis of analogs with amino, azido, and hydrogen substituents. Biopolymers 23(1):83–110Google Scholar
  13. 13.
    Barcelo F, Ortiz-Lombardia M, Portugal J (2001) Heterogenous DNA binding modes of berenil. Biochim Biophys Acta 1519(3):175–184Google Scholar
  14. 14.
    Barcelo F, Capo D, Portugal J (2002) Thermodynamic characterization of the multiplay binding of chartreusin to DNA. Nucleic Acids Res 30(20):4567–4573Google Scholar
  15. 15.
    Sovenyhazy K, Bolderon J, Petty J (2003) Spectroscopic studies of the multiple binding modes of trimetine-bridget cyanine dye with DNA. Nucleic Acids Res 31(10):2561–2569Google Scholar
  16. 16.
    Ghosh R, Bhowmik S, Bagchi A, Das D, Ghosh S (2010) Chemotherapeutic potential of 9-phenyl acridine: biophysical studies on its binding to DNA. Eur Biophys J 39(8):1243–1249Google Scholar
  17. 17.
    Kumar S, Pandya P, Pandav K, Gupta SP, Chopra AN (2012) Structural studies on ligand–DNA systems: a robust approach in drug design. J Biosci 37(3): 553–561Google Scholar
  18. 18.
    Kruglova EB, Gladkovskaya NA, Maleev VY (2005) The use of the spectrophotometry analysis for the calculation of the thermodynamic parameters in actinocin derivative-DNA systems. Biophysics 50(2):253–264Google Scholar
  19. 19.
    McGhee JD, von Hippel PH (1974) Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a onedimensional homogeneous lattice. J Mol Biol 86(2):469–489Google Scholar
  20. 20.
    Nechipurenko YuD (1984) Cooperative effects on binding of large ligands to DNA. II. Contact cooperative interactions between bound ligand molecules. Mol Biol 18(6):1066–1079Google Scholar
  21. 21.
    Kruglova EB, Gladkovskaya NA (2002) Comparison of the binding of the therapeutically active nucleotides to DNA molecules with different level of lesions. Proceedings of SPIE 4938:241–245 and Iermak Ie (2011). Light-absorption spectroscopy of mutagen—DNA complex: binding model selection and binding parameters calculation J Appl Electromagn 13(1):15–22Google Scholar
  22. 22.
    Hajan R, Guan HT (2013) Spectrophotometric studies on the thermodynamics of the ds-DNA interaction with irinotecan for a better understanding of anticancer drug-DNA interactions. J Spectrosc. ID 380352. http://dx.doi.org/10.1155/2013/380352
  23. 23.
    Neault JF, Tajmir-Rihi HA. (1996) Diethylstilbestrol-DNA interaction studied by Fourier transform infrared and Raman spectroscopy. J Biol Chem 271(14):8140–8143Google Scholar
  24. 24.
    Neault, J.-F. & Tajmir-Riahi, H. A. (1998). DNA-chlorophyllin interaction. J Phys Chem B 102(4):1610–1614Google Scholar
  25. 25.
    Deng H, Bloomfield VA, Benevides JM, Thomas GJ (1999) Dependence of the Raman signature of genomic B-DNA on nucleotide base sequence. Biopolymers 50(6):656–666Google Scholar
  26. 26.
    Quameur AA, Tajmir-Riahi H-A (2004) Structural analysis of DNA interactions with biogenic polyamines and cobalt(III)hexamine studied by Fourier transform infrared and capillary electrophoresis. J Biol Chem 279(40):42041–42054Google Scholar
  27. 27.
    Deng H, Bloomfield VA, Benevides JM (2000) Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. Nucleic Acids Res 28(17):3379–3385Google Scholar
  28. 28.
    Benevides JM, Thomas GJ (2005) Local conformational changes induced in B-DNA by ethidium intercalation. Biochemistry 44(8):2993–2999Google Scholar
  29. 29.
    Kyogoku Y, Lord RC, Rich A (1967) The effect of substituents on the hydrogen bonding of adenine and uracil derivatives. J Am Chem Soc 89(3):496–504Google Scholar
  30. 30.
    Starikov EB, Semenov MA, Maleev VYa, Gasan AI (1991) Evidental study of correlated events in biochemistry: physico-chemical mechanisms of nucleic acids hydration as revealed by factor analysis. Biopolymers 31(2):255–273Google Scholar
  31. 31.
    Hartman KA, Lord RC, Thomas GJ (1973) Structural studies of nucleic acids and polynucleotides by infrared and Raman Spectroscopy In: J. Duchesne (ed) Physio–chemical properties of nucleic acids. Academic, New York, pp. 1–89Google Scholar
  32. 32.
    Semenov MA, Blyzniuk IuN, Bolbukh TV, Shestopalova AV, Evstigneev MP, Maleev VY (2012) Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy. Spectrochimica Acta Part A: Mol Biomol Spectrosc 95(2):224–229Google Scholar
  33. 33.
    Martin JC, Wartell RM, O’Shea I (1978) Conformational features of distamycin-DNA and netropsin-DNA complexes by Raman spectroscopy. Proc Natl Acad Sci USA 75(12):5483–5487Google Scholar
  34. 34.
    Smulevich G, Angeloni L, Marzocchi MP (1980) Raman exitation profiles of actinomycin D. Biochim Biophys Acta 610(2):384–391Google Scholar
  35. 35.
    Ruiz-Chica J, Medina MA, Sanchez F (2001) Fourier transform Raman study of the structural specificities on the interaction between DNA and biogenic polyamines. Biophys J 80(2):449–454Google Scholar
  36. 36.
    Kruglova EB, Bolbukh TV, Gladkovskaya NA, Bliznyuk JuN (2005) The binding of actinocin antibiotics to polyphosphate matrix. Biopolym Cell 21(2):358–364Google Scholar
  37. 37.
    Bliznyuk YuN, Kruglova EB, Bolbukh TV, Ovchinnikov DV (2009) Influence of solution acidity on structure of actinocin derivatives and their affinity to DNA studies as a function of pH by Raman spectroscopy. Spectrosc Lett 42(3):498–505Google Scholar
  38. 38.
    Tsuboi M, Benevides JM, Thomas GJ (2009) Raman tensors and their application in structural studies of biological systems. Proc Jpn Acad Ser B Phys Biol Sci 85(1):83–97Google Scholar
  39. 39.
    Blyzniuk IuN, Bolbukh TV, Kruglova OB, Semenov MA, Maleev VYa (2009) Investigation of complexation of ethidium bromide with DNA by the method of Raman spectroscopy. Biopolym Cell 25(1):126–132Google Scholar
  40. 40.
    Lane AN, Jenkins TC (2000) Thermodynamics of nucleic acids and their interactions with ligands. Q Rev Biophysics 33(3):255–306Google Scholar
  41. 41.
    Qu X, Chaires JB (2001) Hydration changes for DNA intercalation reactions. J Am Chem Soc 123(1):1–7Google Scholar
  42. 42.
    Pal SK, Zhao L, Zewail AH (2003) Water at DNA surfaces: ultrafast dynamics in minor groove recognition. Proc Natl Acad Sci USA 100(14):8113–8118Google Scholar
  43. 43.
    Parsegian VA, Rand RP, Rau DC (2000) Osmotic stress, crowding, preferential hydration, and binding: a comparison of perspectives. Proc Natl Acad Sci USA 97(8):3987–3992Google Scholar
  44. 44.
    Schneider B, Ginell SL, Berman HM (1992) Low temperature structures of dCpG-proflavine conformational and hydration effects. Biophys J 63(6):1572–1578Google Scholar
  45. 45.
    Shimizu S (2004) Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments. Proc Nat Acad Sci USA 101(5):1195–1199Google Scholar
  46. 46.
    Marky LA, Kupke DW, Kankia BI (2001) Volume changes accompanying interaction of ligands with nucleic acids. Methods Enzymol 340:149–165Google Scholar
  47. 47.
    Han F, Chalikian TV (2003) Hydration changes accompanying nucleic acid intercalation reactions: volumetric characterizations. J Am Chem Soc 125(24):7219–7229Google Scholar
  48. 48.
    Auffinger P, Westhof R (1999) Role of hydration on the structure and dynamics of nucleic acids In: Ross YH (ed) Water management in the design and distribution of quality foods. Technomic Publishing Co, Basel, pp 165–198Google Scholar
  49. 49.
    Korolev N, Lyubartsev AP, Laaksonen A (2002) On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study. Biophys J 82(6):2860–2875Google Scholar
  50. 50.
    Korolev N., Lyubartsev AP, Laaksonen A (2003) A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations. Nucleic Acids Res 3(20):5971–5981Google Scholar
  51. 51.
    Maleev VYa, Semenov MA, Gasan AI, Kashpur VA (1993) Physical properties of the system DNA-water. Biophysics 38(3):768–790Google Scholar
  52. 52.
    Semenov MA, Bolbukh TV, Maleev VYa (1997) Infrared study of the influence of water on DNA stability in the dependence on AT/GC composition. J Mol Struct 408/409(2):213–217Google Scholar
  53. 53.
    Semenov MA, Bereznyak EG (2000) Hydration and stability of nucleic acids in the condensed state. Comments Mol Cell Biophys 10(1):1–23Google Scholar
  54. 54.
    Maleev V, Semenov M, Kashpur V, Bolbukh T, Shestopalova A, Anishchenko D (2002) Structure and hydration of polycytidylic acid from the data of infrared spectroscopy, EHF dielectrometry and computer modeling. J Mol Struct 605(1):51–61Google Scholar
  55. 55.
    Bereznyak EG, Semenov MA, Bol’bukh TV, Dukhopel’nikov EV, Shestopalova AV, Maleev VYa (2002) A study of the effect of water on the interaction of DNA with actinoxcin derivatives having different lengths of aminoalkyl chains by the methods of IR spectroscopy and computer simulation. Biophysics 47(6):1019–1026Google Scholar
  56. 56.
    Marky LA, Blumenfeld KS, Breslauer KJ (1983) Calorimetric and spectroscopic investigation of drug-DNA interactions. I. The binding of netropsin to poly d(AT). Nucleic Acids Res 11(9):2857–2870Google Scholar
  57. 57.
    Marky LA, Snyder JG, Breslauer KJ (1983) Calorimetric and spectroscopic investigation of drug-DNA interactions: II. Dipyrandium binding to poly d(AT). Nucleic Acids Res 11(16):5701–5715Google Scholar
  58. 58.
    Jelesarov I, Bosshard HR (1999) Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition. J Mol Recognit 12(1):3–18Google Scholar
  59. 59.
    Cooper A (1999) Thermodynamic analysis of biomolecular interactions. Curr Opin Chem Biol 3(5):557–563Google Scholar
  60. 60.
    O’Brien R, Haq I (2004) Applications of biocalorimetry: binding, stability and enzyme kinetics. In: Ladbury JE, Doyle M (eds) Biocalorimetry 2. Wiley.Google Scholar
  61. 61.
    Bruylants G, Wouters J, Michaux C (2005) Diï¬erential scanning calorimetry in life science: thermodynamics, stability, molecular recognition and application in drug design. Curr Med Chem 12(17):2011–2020Google Scholar
  62. 62.
    Celej S, Fidelio G, Dassie S (2005) Protein unfolding coupled to ligand binding: differential scanning calorimetry simulation approach. J Chem Educ 82(1):85–92Google Scholar
  63. 63.
    Celej S, Dassie S, Gonzalez M, Bianconi M, Fidelio G (2006) Differential scanning calorimetry as a tool to estimate binding parameters in multiligand binding proteins. Anal Biochem 350(2):277–284Google Scholar
  64. 64.
    Dukhopelnikov EV, Bereznyak EG, Khrebtova AS, Lantushenko AO, Zinchenko AV (2012) Determination of ligand to DNA binding parameters from two-dimensional DSC curves. J Therm Anal Calorim. doi:10.1007/s10973–012-2561–6Google Scholar
  65. 65.
    Orozco M, Luque FJ (2000) Theoretical methods for the description of the solvent effect in biomolecular systems. Chem Rev 100(11):4187–4225Google Scholar
  66. 66.
    Lazaridis T (2002) Binding affinity and specificity from computational studies. Cur Organ Chem 6(14):1319–1332Google Scholar
  67. 67.
    Schlick T (2010) Molecular modelling and simulation: an interdisciplinary guide, 2nd edn. Springer, New YorkGoogle Scholar
  68. 68.
    Cheatham TE III (2004) Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr Opin Struct Biol 14(3):360–367Google Scholar
  69. 69.
    Dolenc J, Oostenbrink Ch, Koller J, van Gunsteren WF (2005) Molecular dynamics simulation and free energy calculations of netropsin and distamycin binding to AAAAA DNA binding site. Nucleic Acids Res 33(2):725–733Google Scholar
  70. 70.
    Ruiz R, García B, Ruisi G, Silvestri A, Barone G (2009) Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2. J Mol Struct: THEOCHEM 915(1):86–92Google Scholar
  71. 71.
    Sasikala WD, Mukherjee A (2012) Molecular mechanism of direct proflavine–DNA Intercalation: evidence for drug-induced minimum base-stacking penalty pathway. J Phys Chem B 116(40):12208–12212Google Scholar
  72. 72.
    Schneider G, Bohm H-J (2002) Virtual screening and fast automated docking methods. Drug Discov Today 7(1):64–70Google Scholar
  73. 73.
    Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 47 (4):409–415Google Scholar
  74. 74.
    Smith GR, Sternberg MJE (2002) Prediction of protein–protein interactions by docking methods. Curr Opin Struct Biol 12(1):28–35Google Scholar
  75. 75.
    Lauria A, Diana P, Barraja P, Montalbano A, Dattolo G, Cirrincione G (2004) Docking of indolo- and pyrrolo-pyrimidines to DNA. New DNA-interactive polycycles from amino-indoles/pyrroles and BMMA. ARKIVOC 5(2):263–271Google Scholar
  76. 76.
    Miroshnychenko KV, Shestopalova AV (2010) The effect of drug-DNA interactions on the intercalation site formation. Int J Quant Chem 110(1):161–176Google Scholar
  77. 77.
    Danilov VI, Tolokh IS (1990) Hydration of uracil and thymine methylderivatives: a Monte Carlo simulation. J Biomol Struct Dyn 7(5):1167–1183Google Scholar
  78. 78.
    Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL (1997) The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by the Monte Carlo method. J Biomol Struct Dyn 15(1):69–80Google Scholar
  79. 79.
    Teplukhin AV, Malenkov GG, Poltev VI (1998) Monte Carlo simulation of DNA fragment hydration in the presence of alkaline cations using novel atom-atom potential functions. J Biomol Struct Dyn 16(2):289–300Google Scholar
  80. 80.
    Alderfer JL, Danilov VI, Poltev VI, Slyusarchuk ON (1999) A study of the hydration of deoxydinucleoside monophosphates containing thymine, uracil and its 5-halogen derivatives: Monte Carlo simulation. J Biomol Struct Dyn 16(5):1107–1117Google Scholar
  81. 81.
    Resat H, Mezei M (1996) Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate. Biophysical J 71(3):1179–1190Google Scholar
  82. 82.
    Alcaro S, Coleman RS (2000) A molecular model for DNA cross-linking by the antitumor agent azinomycin B. J Med Chem 43(15):2783–2788Google Scholar
  83. 83.
    Shestopalova AV (2002) Hydration of nucleic acids components in dependence of nucleotide composition and relative humidity: a Monte Carlo simulation. Europ Phys J D 20(1):331–337Google Scholar
  84. 84.
    Shestopalova AV (2007) The binding of actinocin derivative with DNA fragments (Monte Carlo simulation). Biopolym Cell 23(1):35–44Google Scholar
  85. 85.
    Auffinger P, Westhof E (1997) Molecular dynamics: simulations of nucleic acids. Rev Comp Chem 11(2):317–328Google Scholar
  86. 86.
    Chen H, Liu X, Patel DJ (1996) DNA binding and unwinding associated with Actinomycin D antibiotics bound to partially overlapping sites in DNA. J Mol Biol 258(3):457–479Google Scholar
  87. 87.
    Takusagawa F, Carlson RG, Weaver RF (2001) Anti-Leukemia selectivity in Actinomycin Analogues. Bioorg Med Chem 9(3):719–725Google Scholar
  88. 88.
    Karawajew L, Ruppert V, Wutcher C, Kosser A, Schappe M, Dorken B, Ludwing WD (2000) Inhibition in vitro spontaneous apoptosis by IL-7 correlates with upregulation of Bcl-2, cortical/mature immunophenotype, and bettercytoreduction in childhood T-ALL. Blood 98(1):297–306Google Scholar
  89. 89.
    Maleev VYa, Semenov MA, Kruglova EB, Bolbukh TV, Gasan AI, Bereznyak EG, Shestopalova AV (2003) Spectroscopic and calorimetric study of DNA interaction with a new series of actinocin derivatives. J Mol Struct 645(1):145–158Google Scholar
  90. 90.
    Shestopalova AV (2006) The investigation of the association of caffeine and actinocin derivatives in aqueous solution: a molecular dynamics simulation. J Mol Liquids 127 (1):113–117Google Scholar
  91. 91.
    Shestopalova AV (2006) Computer simulation of the association of caffeine and actinocin derivatives in aqueous solution. Biophysics 51(3):389–401Google Scholar
  92. 92.
    Miroshnychenko KV, Shestopalova AV (2005) Flexible docking of DNA fragments and actinocin derivatives. Mol Simulation 31(8):567–574Google Scholar
  93. 93.
    Demeunynck M, Bailly C, Wilson WD (eds) (2003) Small molecule DNA and RNA binders: from synthesis to nucleic acid complexes, vol 2. Wiley-VCH, Weinheim, p 483Google Scholar
  94. 94.
    Ihmels H, Otto D (2005) Intercalation of organic dye molecules into double-stranded DNA—general principles and recent developments. Top Curr Chem 258:161–204Google Scholar
  95. 95.
    Armitage OJ (2002) The role of mitoxantrone in non-Hodgkin’s lymphoma. Oncology 16(4):490–512Google Scholar
  96. 96.
    Portugal J, Cashman DJ, Trent JO, Ferrer-Miralles N, Przewloka T, Fokt I, Priebe W, Chaires JB (2005) A new bisintercalating anthracycline with picomolar DNA binding affinity. J Med Chem 48(26):8209–8219Google Scholar
  97. 97.
    Haq I (2002) Thermodynamics of drug–DNA interactions Arch. Biochem Biophys 403(1):1–15Google Scholar
  98. 98.
    Gilli P, Ferretti V, Gilli G, Borea PA (1994) Enthalpy-entropy compensation in drug-receptor binding. J Phys Chem 98(5):1515–1518Google Scholar
  99. 99.
    Dill KA (1997) Additivity principles in biochemistry. J Biol Chem 272(2):701–704Google Scholar
  100. 100.
    McKay SL, Haptonstall B, Gellman SH (2001) Beyond the hydrophobic effect: attractions involving heteroaromatic rings in aqueous solution. J Am Chem Soc 123(6):1244–1245Google Scholar
  101. 101.
    Luo R, Gilson HSR., Potter MJ, Gilson MK (2001) The physical basis of nucleic acid base stacking in water. Biophys J 80(1):140–148Google Scholar
  102. 102.
    Ren J, Jenkins TC, Chaires JB (2000) Energetics of DNA intercalation reactions. Biochemistry 39(29):8439–8447Google Scholar
  103. 103.
    Mukherjee A, Lavery R, Bagchi B, Hynes JT (2008) On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes. J Am Chem Soc 130(30):9747–9755Google Scholar
  104. 104.
    Treesuwan W, Wittayanaraku K, Anthony NG, Huchet G, Alniss G, Hannongbua S, Khalaf AI, Suckling CJ, Parkinson JA, Mackay SP (2009) A detailed binding free energy study of 2:1 ligand–DNA complex formation by experiment and simulation. Phys Chem Chem Phys 11(45):10682–10693Google Scholar
  105. 105.
    Chow CS, Bogdan FM (1997) A structural basis for RNA-ligand interactions. Chem Rev 97(5):1489–1513Google Scholar
  106. 106.
    Gilson MK, Given JA, Bush BL, McCammon JA (1997) The statistical-thermodynamical basis for computation of binding affinities: a critical review. Biophys J 72(3):1047–1069Google Scholar
  107. 107.
    Kostjukov VV, Khomytova NM, Evstigneev MP (2009) Partition of thermodynamic energies of drug–DNA complexation. Biopolymers 91(9):773–790Google Scholar
  108. 108.
    Kostjukov VV, Hernandez Santiago AA, Rodriguez FR, Castilla SR, Parkinson JA, Evstigneev MP (2012) Energetics of ligand binding to the DNA minor groove. Phys Chem Chem Phys 14(16):5588–5600Google Scholar
  109. 109.
    Beshnova DA, Lantushenko AO, Evstigneev MP (2010) Does the ligand-biopolymer equilibrium binding constant depend on the number of bound ligands? Biopolymers 93(11):932–935Google Scholar
  110. 110.
    Kostjukov VV, Evstigneev MP (2012) Relation between the change in DNA elasticity on ligand binding and the binding energetics. Phys Rev E 86(3 Pt 1):031919Google Scholar
  111. 111.
    Rocchia W, Alexov E, Honig B (2001) Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B 105(28):6507–6514Google Scholar
  112. 112.
    Kostjukov VV, Khomytova NM, Hernandez Santiago AA, Licona Ibarra R, Davies DB, Evstigneev MP (2011) Calculation of the electrostatic charges and energies for intercalation of aromatic drug molecules with DNA. Int J Quantum Chem 111(3):711–721Google Scholar
  113. 113.
    Kostjukov VV, Khomutova NM, Lantushenko AO, Evstigneev MP (2009) Hydrophobic contribution to the free energy of complexation of aromatic ligands with DNA. Biopolym Cell 25(2):133–141Google Scholar
  114. 114.
    Kostyukov VV, Khomutova NM, Evstigneev MP (2009) Contribution of changes in translational, rotational, and vibrational degrees of freedom to the energy of complex formation of aromatic ligands with DNA. Biophysics 54(4):606–615Google Scholar
  115. 115.
    Kostjukov VV, Khomytova NM, Evstigneev MP (2010) Hydration change on complexation of aromatic ligands with DNA: molecular dynamics simulations. Biopolym Cell 26(1):36–44Google Scholar
  116. 116.
    Kostjukov VV, Khomytova NM, Hernandez Santiago AA, Tavera A-M C, Alvarado JS, Evstigneev MP (2011) Parsing of the free energy of aromatic–aromatic stacking interactions in solution. J Chem Thermodyn 43(10):1424–1434Google Scholar
  117. 117.
    Kostyukov VV (2011) Energy of intercalation of aromatic heterocyclic ligands into DNA and its partition into additive components. Biopolym Cell 27(4):264–272Google Scholar
  118. 118.
    Kostyukov VV (2011) Energetics of complex formation of the DNA hairpin structure d(GCGAAGC) with aromatic ligands. Biophysics 56(1):28–39Google Scholar
  119. 119.
    Neidle S, Pearl LH, Herzyk P, Berman HM (1988) A molecular model for proflavine-DNA intercalation. Nucleic Acids Res 16(18):8999–9016Google Scholar
  120. 120.
    Brana MF, Cacho M, Gradillas A, de Pascual-Teresa B, Ramos A (2001) Intercalators as anticancer drugs. Curr Pharm Des 7(17):1745–1780Google Scholar
  121. 121.
    Pullman B (1989) Molecular mechanism of specificity in DNA-antitumor drug interactions. Adv Drug Res 18(1):2–112Google Scholar
  122. 122.
    Kostjukov VV, Khomytova NM, Davies DB, Evstigneev MP (2008) Electrostatic contribution to the energy of binding of aromatic ligands with DNA. Biopolymers 89(8):680–690Google Scholar
  123. 123.
    Kostjukov VV, Evstigneev MP (2014) Energy analysis of the reactions of noncovalent ligand binding with nucleic acids: present and future. Biophysics 59(4):673–677Google Scholar
  124. 124.
    Chaires JB (1997) Energetics of Drug-DNA interactions. Biopolymers 44(3):201–215Google Scholar
  125. 125.
    Kubar T, Hanus M, Ryjacek F, Hobza P (2005) Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: quantum chemical calculations and molecular mechanics simulations. Chem Eur J 12(1):280–290Google Scholar
  126. 126.
    Buisine E, de Villiers K, Egan TG, Biot C (2006) Solvent-induced effects: self-association of positively charged π systems. J Am Chem Soc 128(37):12122–12128Google Scholar
  127. 127.
    Nelson SM, Ferguson LR, Denny WA (2007) Non-covalent ligand/DNA interactions: minor groove binding agents. Mutation Res 623(1):24–40Google Scholar
  128. 128.
    Cai X, Gray PJ, Von Hoff DD (2009) DNA minor groove binders: back in the groove. Cancer Treatment Rev 35(5):437–450Google Scholar
  129. 129.
    Kostjukov VV, Rogova OV, Evstigneev MP (2014) of complex formation between ligand and nucleic acids. Biophysics 59(4):666–672Google Scholar
  130. 130.
    Shaikh SA, Ahmed SR, Jayaram B (2004) A molecular thermodynamic view of DNA–drug interactions: a case study of 25 minor-groove binders. Arch Biochem Biophys 429(1):81–99Google Scholar
  131. 131.
    Dolenc J, Borstnik U, Hodoscek M, Koller J, Janezic D (2005) An ab initio QM/MM study of the conformational stability of complexes formed by netropsin and DNA. The importance of van der Waals interactions and hydrogen bonding. J Mol Struct 718(1):77–85Google Scholar
  132. 132.
    Kostjukov VV, Evstigneev MP (2012) Energy of ligand-RNA complex formation. Biophysics 57(4):450–463Google Scholar
  133. 133.
    Latham MP, Zimmermann GR, Pardi A (2009) NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer. J Am Chem Soc 131(14):5052–5053Google Scholar
  134. 134.
    Lee SW, Zhao L, Pardi A, Xia T (2010) Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands. Biochemistry 49(13):2943–2951Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Sevastopol National Technical University (SevNTU)SevastopolUkraine
  2. 2.A.Usikov Institute for Radiophysics and Electronics National Academy of Sciences of Ukraine (IRE NASU)KharkovUkraine

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