51
References
1. Ramos MJ, Fernandes PA (2006) Atomic-level rational drug design Curr Comp-Aided Drug
Des 2:57–81
2. Nelson SM, Ferguson LR, Denny WA (2004) DNA and the chromosome—varied targets for
chemotherapy. Cell Chromosome 3(1):1–26
3. Hurley LH (2002) DNA and its associated processes as targets for cancer therapy. Nat Rev
Cancer 2(3):188–199
4. Au JL, Panchal N, Li D, Gan Y (1997) Apoptosis: a new pharmacodynamic endpoint. Pharm
Res 14(12):1659–1671
5. Selwood DL (2013) Beyond the hundred dollar genome—drug discovery futures. Chem
Biol Drug Des. 81(1):1–4
6. Ren J, Chaires JB (1999) Sequence and structural selectivity of nucleic acid binding ligands.
Biochemistry 38(49):16067–16075
7. Dervan PB (2001) Molecular recognition of DNA by small molecules. Bioorg Med Chem
9(9):2215–2235
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):4200–4207
9. Murthy VR, Raghuram DV, Murthy PN (2007) Drug, dosage, activity, studies of antimalarials by physical methods—II. Bioinformation 2(1):12–16.
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.
11. Porumb H (1978) The solution spectroscopy of drugs and the drug-nucleic acid interactions.
Prog Biophys Mol Biol 34(3):175–195
12. Yielding LW, Yielding KL (1984) Ethidium binding to deoxyribonucleic acid: spectrophotometric analysis of analogs with amino, azido, and hydrogen substituents. Biopolymers
23(1):83–110
13. Barcelo F, Ortiz-Lombardia M, Portugal J (2001) Heterogenous DNA binding modes of
berenil. Biochim Biophys Acta 1519(3):175–184
14. Barcelo F, Capo D, Portugal J (2002) Thermodynamic characterization of the multiplay
binding of chartreusin to DNA. Nucleic Acids Res 30(20):4567–4573
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):2561–2569
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–
1249
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): 553–561
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):253–264
19. McGhee JD, von Hippel PH (1974) Theoretical aspects of DNA-protein interactions: cooperative and non-co-operative binding of large ligands to a onedimensional homogeneous
lattice. J Mol Biol 86(2):469–489
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):1066–1079
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):15–22
2 Structure, Thermodynamics and Energetics of Drug-DNA Interactions
References
1. Ramos MJ, Fernandes PA (2006) Atomic-level rational drug design Curr Comp-Aided Drug
Des 2:57–81
2. Nelson SM, Ferguson LR, Denny WA (2004) DNA and the chromosome—varied targets for
chemotherapy. Cell Chromosome 3(1):1–26
3. Hurley LH (2002) DNA and its associated processes as targets for cancer therapy. Nat Rev
Cancer 2(3):188–199
4. Au JL, Panchal N, Li D, Gan Y (1997) Apoptosis: a new pharmacodynamic endpoint. Pharm
Res 14(12):1659–1671
5. Selwood DL (2013) Beyond the hundred dollar genome—drug discovery futures. Chem
Biol Drug Des. 81(1):1–4
6. Ren J, Chaires JB (1999) Sequence and structural selectivity of nucleic acid binding ligands.
Biochemistry 38(49):16067–16075
7. Dervan PB (2001) Molecular recognition of DNA by small molecules. Bioorg Med Chem
9(9):2215–2235
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):4200–4207
9. Murthy VR, Raghuram DV, Murthy PN (2007) Drug, dosage, activity, studies of antimalarials by physical methods—II. Bioinformation 2(1):12–16.
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.
11. Porumb H (1978) The solution spectroscopy of drugs and the drug-nucleic acid interactions.
Prog Biophys Mol Biol 34(3):175–195
12. Yielding LW, Yielding KL (1984) Ethidium binding to deoxyribonucleic acid: spectrophotometric analysis of analogs with amino, azido, and hydrogen substituents. Biopolymers
23(1):83–110
13. Barcelo F, Ortiz-Lombardia M, Portugal J (2001) Heterogenous DNA binding modes of
berenil. Biochim Biophys Acta 1519(3):175–184
14. Barcelo F, Capo D, Portugal J (2002) Thermodynamic characterization of the multiplay
binding of chartreusin to DNA. Nucleic Acids Res 30(20):4567–4573
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):2561–2569
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–
1249
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): 553–561
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):253–264
19. McGhee JD, von Hippel PH (1974) Theoretical aspects of DNA-protein interactions: cooperative and non-co-operative binding of large ligands to a onedimensional homogeneous
lattice. J Mol Biol 86(2):469–489
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):1066–1079
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):15–22
2 Structure, Thermodynamics and Energetics of Drug-DNA Interactions