56
M. P. Evstigneev and A. V. Shestopalova
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–
935
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):031919
111. Rocchia W, Alexov E, Honig B (2001) Extending the applicability of the nonlinear PoissonBoltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B
105(28):6507–6514
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):711–721
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):133–141
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):606–615
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–
44
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):1424–1434
117. Kostyukov VV (2011) Energy of intercalation of aromatic heterocyclic ligands into DNA
and its partition into additive components. Biopolym Cell 27(4):264–272
118. Kostyukov VV (2011) Energetics of complex formation of the DNA hairpin structure
d(GCGAAGC) with aromatic ligands. Biophysics 56(1):28–39
119. Neidle S, Pearl LH, Herzyk P, Berman HM (1988) A molecular model for proflavine-DNA
intercalation. Nucleic Acids Res 16(18):8999–9016
120. Brana MF, Cacho M, Gradillas A, de Pascual-Teresa B, Ramos A (2001) Intercalators as
anticancer drugs. Curr Pharm Des 7(17):1745–1780
121. Pullman B (1989) Molecular mechanism of specificity in DNA-antitumor drug interactions.
Adv Drug Res 18(1):2–112
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):680–690
123. Kostjukov VV, Evstigneev MP (2014) Energy analysis of non-covalent ligand binding to
nucleic acids: present and future. Biophysics 59(4):673–677
124. Chaires JB (1997) Energetics of Drug-DNA interactions. Biopolymers 44(3):201–215
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):280–290
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):12122–12128
127. Nelson SM, Ferguson LR, Denny WA (2007) Non-covalent ligand/DNA interactions: minor
groove binding agents. Mutation Res 623(1):24–40
128. Cai X, Gray PJ, Von Hoff DD (2009) DNA minor groove binders: back in the groove. Cancer Treatment Rev 35(5):437–450
129. Kostjukov VV, Rogova OV, Evstigneev MP (2014) General features of the energetics of
complex formation between ligand and nucleic acids. Biophysics 59(4):666–672
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):81–99
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):77–85
M. P. Evstigneev and A. V. Shestopalova
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–
935
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):031919
111. Rocchia W, Alexov E, Honig B (2001) Extending the applicability of the nonlinear PoissonBoltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B
105(28):6507–6514
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):711–721
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):133–141
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):606–615
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–
44
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):1424–1434
117. Kostyukov VV (2011) Energy of intercalation of aromatic heterocyclic ligands into DNA
and its partition into additive components. Biopolym Cell 27(4):264–272
118. Kostyukov VV (2011) Energetics of complex formation of the DNA hairpin structure
d(GCGAAGC) with aromatic ligands. Biophysics 56(1):28–39
119. Neidle S, Pearl LH, Herzyk P, Berman HM (1988) A molecular model for proflavine-DNA
intercalation. Nucleic Acids Res 16(18):8999–9016
120. Brana MF, Cacho M, Gradillas A, de Pascual-Teresa B, Ramos A (2001) Intercalators as
anticancer drugs. Curr Pharm Des 7(17):1745–1780
121. Pullman B (1989) Molecular mechanism of specificity in DNA-antitumor drug interactions.
Adv Drug Res 18(1):2–112
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):680–690
123. Kostjukov VV, Evstigneev MP (2014) Energy analysis of non-covalent ligand binding to
nucleic acids: present and future. Biophysics 59(4):673–677
124. Chaires JB (1997) Energetics of Drug-DNA interactions. Biopolymers 44(3):201–215
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):280–290
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):12122–12128
127. Nelson SM, Ferguson LR, Denny WA (2007) Non-covalent ligand/DNA interactions: minor
groove binding agents. Mutation Res 623(1):24–40
128. Cai X, Gray PJ, Von Hoff DD (2009) DNA minor groove binders: back in the groove. Cancer Treatment Rev 35(5):437–450
129. Kostjukov VV, Rogova OV, Evstigneev MP (2014) General features of the energetics of
complex formation between ligand and nucleic acids. Biophysics 59(4):666–672
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):81–99
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):77–85