Change of hydration on complexation of the ligands with dna (mini-review)
Keywords:
complexation, ligand, DNA, hydration, water release/uptake
Abstract
In the present work analytical review of published data on changes of water shell of the ligand and the
DNA on complexation with account of recently published new results obtained by the method of
microwave dielectrometry, was performed. The results of both experimental (microwave dielectrometry,
volumetry, osmometry) and theoretical (molecular modeling) studies are presented. It is shown that there
is a fundamental difference between the osmometry, demonstrating the uptake of additional water
molecules on ligand binding with DNA, and all other methods, which give, in contrast, partial release of
water. At the same time differences in hydration gained from microwave dielectrometry and molecular
modeling are in good agreement between each other, however, underestimate hydration in relation to
volumetry. The analysis highlights the need for revision of the method of osmometry in application to
ligand-DNA systems.
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References
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24. Hydration Changes Accompanying the Binding of Minor Groove Ligands with DNA / N.N. Degtyareva, B.D. Wallace, A.R. Bryant, [et al.] // Biophys. J. – 2007. – V.92. – P. 959–965.
25. Sidorova N.Y. The osmotic sensitivity of netropsin analog binding to DNA / N.Y. Sidorova, D.C. Rau // Biopolymers.–1995.–V.35.–P. 377–384.
26. Neto J.R. Water Regulation of Actinomycin-D Binding to DNA: The Interplay Among Drug Affinity, DNA Long-Range Conformation, and Hydration / J.R. Neto, M.F. Colombo // Biopolymers.–2000.–V.53.–P. 46–59.
27. Hydration Changes in the Association of Hoechst 33258 with DNA / J.R. Kiser, R.W. Monk, R.L. Smalls, J.T. Petty // Biochemistry. – 2005. – V.44. – P. 16988-16997.
28. Kostjukov V.V. Jenergija interkaljacii aromaticheskih geterociklicheskih ligandov v DNK i ee razdelenie na additivnye sostavljajuwie / V.V. Kostjukov // Biopolimery i kletka. - 2011. - T. 27. - S. 258–267.
29. Shimizu S. Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments / S. Shimizu // Proc. Natl. Acad.Sci. USA. – 2004. - V.101. – P. 1195–1199.
30. Parsegian V.A. Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives / V.A. Parsegian, R.P. Rand, D.C. Rau // Proc. Natl. Acad. Sci. USA. – 2000. - V.97. – P. 3987-3992.
31. Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro / E.S. Courtenay, M.W. Capp, C.F. Anderson, M.T. Record // Biochemistry. 2000. – V.39. – P. 4455-71.
32. Timasheff S.N. Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components / S.N. Timasheff // Proc. Natl. Acad. Sci. USA. – 2002. - V.99. – P. 9721-9726.
33. Interpreting the effects of small uncharged solutes on protein-folding equilibria / P.R. Davis-Searles, A.J. Saunders, D.A. Erie, [et al.] // Annu. Rev. Biophys. Biomol. Struct. -2001. – V.30. – P. 271-306.
2. Schwabe J.W. The role of water in protein-DNA interactions / J.W. Schwabe // Curr. Opin. Struct. Biol. – 1997. – V.7. – P. 126-134.
3. Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition / C. Bailly, G. Chessari, C. Carrasco, [et al.] // Nucleic Acids Res. - 2003. – V.31. – P. 1514-1524.
4. Pal S.K. Water at DNA surfaces: Ultrafast dynamics in minor groove recognition / S.K. Pal, L. Zhao, A.H. Zewail // Proc. Natl. Acad. Sci. U.S.A. – 2003. – V.100. – P. 8113-8118.
5. Nguyen B. A Role for Water Molecules in DNA−Ligand Minor Groove Recognition / B. Nguyen, S. Neidle, W.D. Wilson // Acc. Chem. Res. – 2009. – V.42. - P. 11–21.
6. Spectroscopic and calorimetric study of DNA interaction with a new series of actinocin derivatives / V. Maleev, M. Semenov, E. Kruglova, [et al.] // J. Mol. Struct. – 2003. – V.645. – P. 145-158.
7. Williams H.E.L. Structure, dynamics and hydration of the nogalamycin-d(ATGCAT)2 complex determined by NMR and molecular dynamics simulations in solution / H.E.L. Williams, M.S. Searle // J. Mol. Biol. - 1999. – V.290. – P. 699-716.
8. Liepinsh E. NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution / E. Liepinsh, G. Otting, K. Wüthrich // Nucleic Acids Res. – 1992. – V.20. – P. 6549–6553.
9. Subramanian P.S. Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation / P.S. Subramanian, G. Ravishanker, D.L. Beveridge // Proc. Natl. Acad. Sci. U.S.A. – 1988. – V.85. – P. 1836-1840.
10. Kostjukov V.V. Izmenenie gidratacii pri kompleksoobrazovanii aromaticheskih ligandov s DNK: modelirovanie metodom molekuljarnoj dinamiki / V.V. Kostjukov, N.M. Homutova, M.P. Evstigneev // Biopolimery i kletka.–2010.–T.26.–C. 1–9.
11. Kashpur V.A. Izmenenija gidratacii pri obrazovanii kompleksov DNK-ligand po dannym dijelektrometrii / V.A. Kashpur, O.V. Horunzhaja, V.Ja. Maleev // Dokl. NANU. – 2010. - №7. – S. 170 – 175.
12. Izmenenija gidratacii pri obrazovanii kompleksov DNK s nekotorymi interkaljatorami / O.V. Horunzhaja, V.A. Kashpur, D.A. Pesina, V.Ja. Maleev // Biofiz. visnik. – 2010. - Vip. 24 (1). – S. 5 – 13.
13. Maleev V.Ya. A spectroscopic and calorimetric study of dna complexation with a new series of actinocin derivatives (ActII-ActV) / V.Ya. Maleev, M.A. Semenov, E.B. Kruglova // in “Anti-Cancer Drug Design: Biological and Biophysical Aspects of Synthetic Phenoxazone Derivatives”, Ed. by A.N. Veselkov and D.B. Davies, SevNTU press, 2002, P. 47-126.
14. Han F. Association of the minor groove binding drug Hoechst 33258 with d(CGCGAATTCGCG)2: volumetric, calorimetric, and spectroscopic characterizations / F. Han, N. Taulier, T.V. Chalikian // Biochemistry. – 2005. – V.44. – P. 9785-9794.
15. Parsegian V.A. Macromolecules and water: probing with osmotic stress / V.A. Parsegian, R.P. Rand, D.C. Rau // Methods Enzymol. – 1995. - V.259. – P. 43-94.
16. Kostjukov V.V. Izmenenie gidratacii pri svjazyvanii ligandov s malym zhelobkom DNK / V.V. Kostjukov, M.P. Evstigneev // Fizika zhivogo. - 2010. - T.18. - S. 34-40.
17. Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site / J. Dolenc, C. Oostenbrink, J. Koller, W.F. van Gunsteren // Nucleic Acids Res. – 2005. - V.33. – P. 725–733.
18. On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes / A. Mukherjee, R. Lavery, B. Bagchi, J.T. Hynes // J. Am. Chem. Soc. – 2008. – V.130. – P. 9747–9755.
19. Influence of Drug Binding on DNA Hydration: Acoustic and Densimetric Characterizations of Netropsin Binding to the Poly(dAdT)•Poly(dAdT) and Poly(dA)•Poly(dT) Duplexes and the Poly(dT)•Poly(dA)•Poly(dT) Triplex at 25 °C / T.V. Chalikian, G.E. Plum, A.P. Sarvazyan, K.J. Breslauer // Biochemistry. – 1994. – V.33. – P. 8629-8640.
20. Han F. Hydration Changes Accompanying Nucleic Acid Intercalation Reactions:Volumetric Characterizations / F. Han, T.V. Chalikian // J. Am. Chem. Soc. – 2003. – V.125. – P. 7219-7229.
21. Qu X. Contrasting Hydration Changes for Ethidium and Daunomycin Binding to DNA / X. Qu, J.B. Chaires // J. Am. Chem. Soc. - 1999. - Vol.121. – P. 2649 – 2650.
22. Qu X. Hydration Changes for DNA Intercalation Reactions / X. Qu, J.B. Chaires // J. Am. Chem. Soc.–2001.–V.123.–P. 1–3.
23. Hydration of Drug−DNA Complexes: Greater Water Uptake for Adriamycin Compared to Daunomycin / H. Yu, J. Ren, J.B. Chaires, X. Qu // J. Med. Chem. – 2008. – V.51. – P. 5909–5911.
24. Hydration Changes Accompanying the Binding of Minor Groove Ligands with DNA / N.N. Degtyareva, B.D. Wallace, A.R. Bryant, [et al.] // Biophys. J. – 2007. – V.92. – P. 959–965.
25. Sidorova N.Y. The osmotic sensitivity of netropsin analog binding to DNA / N.Y. Sidorova, D.C. Rau // Biopolymers.–1995.–V.35.–P. 377–384.
26. Neto J.R. Water Regulation of Actinomycin-D Binding to DNA: The Interplay Among Drug Affinity, DNA Long-Range Conformation, and Hydration / J.R. Neto, M.F. Colombo // Biopolymers.–2000.–V.53.–P. 46–59.
27. Hydration Changes in the Association of Hoechst 33258 with DNA / J.R. Kiser, R.W. Monk, R.L. Smalls, J.T. Petty // Biochemistry. – 2005. – V.44. – P. 16988-16997.
28. Kostjukov V.V. Jenergija interkaljacii aromaticheskih geterociklicheskih ligandov v DNK i ee razdelenie na additivnye sostavljajuwie / V.V. Kostjukov // Biopolimery i kletka. - 2011. - T. 27. - S. 258–267.
29. Shimizu S. Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments / S. Shimizu // Proc. Natl. Acad.Sci. USA. – 2004. - V.101. – P. 1195–1199.
30. Parsegian V.A. Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives / V.A. Parsegian, R.P. Rand, D.C. Rau // Proc. Natl. Acad. Sci. USA. – 2000. - V.97. – P. 3987-3992.
31. Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro / E.S. Courtenay, M.W. Capp, C.F. Anderson, M.T. Record // Biochemistry. 2000. – V.39. – P. 4455-71.
32. Timasheff S.N. Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components / S.N. Timasheff // Proc. Natl. Acad. Sci. USA. – 2002. - V.99. – P. 9721-9726.
33. Interpreting the effects of small uncharged solutes on protein-folding equilibria / P.R. Davis-Searles, A.J. Saunders, D.A. Erie, [et al.] // Annu. Rev. Biophys. Biomol. Struct. -2001. – V.30. – P. 271-306.
Cited
How to Cite
Kostjukov, V. V., & Evstigneev, M. P. (1). Change of hydration on complexation of the ligands with dna (mini-review). Biophysical Bulletin, 2(27). Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/2525
Section
Molecular biophysics
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