55
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):457–479
87. Takusagawa F, Carlson RG, Weaver RF (2001) Anti-Leukemia selectivity in Actinomycin
Analogues. Bioorg Med Chem 9(3):719–725
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):297–306
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):145–158
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–
117
91. Shestopalova AV (2006) Computer simulation of the association of caffeine and actinocin
derivatives in aqueous solution. Biophysics 51(3):389–401
92. Miroshnychenko KV, Shestopalova AV (2005) Flexible docking of DNA fragments and
actinocin derivatives. Mol Simulation 31(8):567–574
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 483
94. Ihmels H, Otto D (2005) Intercalation of organic dye molecules into double-stranded
DNA—general principles and recent developments. Top Curr Chem 258:161–204
95. Armitage OJ (2002) The role of mitoxantrone in non-Hodgkin’s lymphoma. Oncology
16(4):490–512
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):8209–8219
97. Haq I (2002) Thermodynamics of drug–DNA interactions Arch. Biochem Biophys
403(1):1–15
98. Gilli P, Ferretti V, Gilli G, Borea PA (1994) Enthalpy-entropy compensation in drug-receptor binding. J Phys Chem 98(5):1515–1518
99. Dill KA (1997) Additivity principles in biochemistry. J Biol Chem 272(2):701–704
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):1244–1245
101. Luo R, Gilson HSR., Potter MJ, Gilson MK (2001) The physical basis of nucleic acid base
stacking in water. Biophys J 80(1):140–148
102. Ren J, Jenkins TC, Chaires JB (2000) Energetics of DNA intercalation reactions. Biochemistry 39(29):8439–8447
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):9747–9755
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):10682–10693
105. Chow CS, Bogdan FM (1997) A structural basis for RNA-ligand interactions. Chem Rev
97(5):1489–1513
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):1047–1069
107. Kostjukov VV, Khomytova NM, Evstigneev MP (2009) Partition of thermodynamic energies of drug–DNA complexation. Biopolymers 91(9):773–790
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):5588–5600
2 Structure, Thermodynamics and Energetics of Drug-DNA Interactions
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):457–479
87. Takusagawa F, Carlson RG, Weaver RF (2001) Anti-Leukemia selectivity in Actinomycin
Analogues. Bioorg Med Chem 9(3):719–725
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):297–306
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):145–158
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–
117
91. Shestopalova AV (2006) Computer simulation of the association of caffeine and actinocin
derivatives in aqueous solution. Biophysics 51(3):389–401
92. Miroshnychenko KV, Shestopalova AV (2005) Flexible docking of DNA fragments and
actinocin derivatives. Mol Simulation 31(8):567–574
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 483
94. Ihmels H, Otto D (2005) Intercalation of organic dye molecules into double-stranded
DNA—general principles and recent developments. Top Curr Chem 258:161–204
95. Armitage OJ (2002) The role of mitoxantrone in non-Hodgkin’s lymphoma. Oncology
16(4):490–512
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):8209–8219
97. Haq I (2002) Thermodynamics of drug–DNA interactions Arch. Biochem Biophys
403(1):1–15
98. Gilli P, Ferretti V, Gilli G, Borea PA (1994) Enthalpy-entropy compensation in drug-receptor binding. J Phys Chem 98(5):1515–1518
99. Dill KA (1997) Additivity principles in biochemistry. J Biol Chem 272(2):701–704
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):1244–1245
101. Luo R, Gilson HSR., Potter MJ, Gilson MK (2001) The physical basis of nucleic acid base
stacking in water. Biophys J 80(1):140–148
102. Ren J, Jenkins TC, Chaires JB (2000) Energetics of DNA intercalation reactions. Biochemistry 39(29):8439–8447
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):9747–9755
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):10682–10693
105. Chow CS, Bogdan FM (1997) A structural basis for RNA-ligand interactions. Chem Rev
97(5):1489–1513
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):1047–1069
107. Kostjukov VV, Khomytova NM, Evstigneev MP (2009) Partition of thermodynamic energies of drug–DNA complexation. Biopolymers 91(9):773–790
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):5588–5600
2 Structure, Thermodynamics and Energetics of Drug-DNA Interactions