53
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):3987–3992
44. Schneider B, Ginell SL, Berman HM (1992) Low temperature structures of dCpG-proflavine conformational and hydration effects. Biophys J 63(6):1572–1578
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):1195–1199
46. Marky LA, Kupke DW, Kankia BI (2001) Volume changes accompanying interaction of
ligands with nucleic acids. Methods Enzymol 340:149–165
47. Han F, Chalikian TV (2003) Hydration changes accompanying nucleic acid intercalation
reactions: volumetric characterizations. J Am Chem Soc 125(24):7219–7229
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 165–198
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):2860–2875
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):5971–5981
51. Maleev VYa, Semenov MA, Gasan AI, Kashpur VA (1993) Physical properties of the system DNA-water. Biophysics 38(3):768–790
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):213–217
53. Semenov MA, Bereznyak EG (2000) Hydration and stability of nucleic acids in the condensed state. Comments Mol Cell Biophys 10(1):1–23
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):51–61
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):1019–1026
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):2857–2870
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):5701–5715
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):3–18
59. Cooper A (1999) Thermodynamic analysis of biomolecular interactions. Curr Opin Chem
Biol 3(5):557–563
60. O’Brien R, Haq I (2004) Applications of biocalorimetry: binding, stability and enzyme kinetics. In: Ladbury JE, Michael Doyle M (eds) Biocalorimetry 2. Wiley. Budapest, Hungary
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):2011–2020
62. Celej S, Fidelio G, Dassie S (2005) Protein unfolding coupled to ligand binding: differential
scanning calorimetry simulation approach. J Chem Educ 82(1):85–92
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):277–284
2 Structure, Thermodynamics and Energetics of Drug-DNA Interactions
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):3987–3992
44. Schneider B, Ginell SL, Berman HM (1992) Low temperature structures of dCpG-proflavine conformational and hydration effects. Biophys J 63(6):1572–1578
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):1195–1199
46. Marky LA, Kupke DW, Kankia BI (2001) Volume changes accompanying interaction of
ligands with nucleic acids. Methods Enzymol 340:149–165
47. Han F, Chalikian TV (2003) Hydration changes accompanying nucleic acid intercalation
reactions: volumetric characterizations. J Am Chem Soc 125(24):7219–7229
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 165–198
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):2860–2875
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):5971–5981
51. Maleev VYa, Semenov MA, Gasan AI, Kashpur VA (1993) Physical properties of the system DNA-water. Biophysics 38(3):768–790
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):213–217
53. Semenov MA, Bereznyak EG (2000) Hydration and stability of nucleic acids in the condensed state. Comments Mol Cell Biophys 10(1):1–23
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):51–61
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):1019–1026
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):2857–2870
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):5701–5715
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):3–18
59. Cooper A (1999) Thermodynamic analysis of biomolecular interactions. Curr Opin Chem
Biol 3(5):557–563
60. O’Brien R, Haq I (2004) Applications of biocalorimetry: binding, stability and enzyme kinetics. In: Ladbury JE, Michael Doyle M (eds) Biocalorimetry 2. Wiley. Budapest, Hungary
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):2011–2020
62. Celej S, Fidelio G, Dassie S (2005) Protein unfolding coupled to ligand binding: differential
scanning calorimetry simulation approach. J Chem Educ 82(1):85–92
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):277–284
2 Structure, Thermodynamics and Energetics of Drug-DNA Interactions