The effect of two binding types on parameters of helix – coil transition in polynuleotides
Keywords:
DNA, actinocin derivatives, intercalation, external binding, melting parameters, calorimetry, spectrophotometry
Abstract
An interaction of actinocin derivatives Act II and Act III with DNA is studied by differential scanning calorimetry and spectrophotometry. The equilibrium concentrations of intercalational and external types of complexes in Act – DNA systems at different relative DNA concentration are calculated from spectrophotometric titration data. The binding parameters for each type of actinocin derivatives – DNA complexes are obtained. The heat capacity curves of Act – DNA complexes were obtained at different relative ligand concentrations. Calorimetric study achieved that intercalation binding type leads to increase of enthalpy, entropy and melting temperature of DNA, while the external type induces the rise of the helix thermal stability only. The comparison of helix – coil transition parameters of DNA in the complexes with actinocin derivatives and proflavine is performed. The effect of ligands on DNA melting parameters correlates to binding constants obtained by spectrophotometry.
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References
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29. Thermodynamics of interactions of water-soluble porphyrins with RNA duplexes / A.A. Ghazaryan, Y.B. Dalyan, S.G. Haroutiunian, et al // J. Am. Chem. Soc. – 2006. – V. 128. – P. 1914-1921.
2. A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterisation by calorimetric and volumetric techniques / T.V. Chalikian, T. Volker, G.E. Plum, K.J. Breslauer // Proc. Nath. Acad. Sci. USA. – 1999. – V. 96. – P. 7853–7858.
3. Esposito D. A thermodynamic study of herring protamine–DNA complex by differential scanning calorimetry / D. Esposito, P. Del Vecchio, G. Barone // Phys Chem Chem Phys. – 2001. – V. 3. – P. 5320–5325.
4. Lane A.N. Thermodynamics of nucleic acids and their interactions with ligands / A.N. Lane, T.S. Jenkins // Quart. Rev. Biophys. – 2000. – V. 33 (3). – P. 255–306.
5. Chaires J.B. A thermodynamic signature for drug – DNA binding mode / J.B. Chaires // Archives of Biochemistry and Biophysics. – 2006. – V. 453. – P. 24–29.
6. Breslauer K.J. Calorimetry: a tool for DNA and ligand – DNA studies / K.J. Breslauer, E. Freire, M. Straume // Methods Enzymol. – 1992. – V. 211. – P. 533–567.
7. Patel D.J. Mutagen – nucleic acid complexes at the polynucleotide duplex level in solution: Intercalation of proflavine into poly(dA-dT) and the melting transition of the complex / D.J. Patel // Biopolymers. – 1977. – V. 16 (12). – P. 2739–2754.
8. Bjordnal M.T. DNA melting in the presence of fluorescent intercalating oxazole yellow dyes measured with a gel-based assay / M.T. Bjordnal, D.K. Fygenson // Biopolymers. – 2002. – V. 65. – P. 40–44.
9. Theory of helix-coil transition on DNA-ligand complexes: the effect to two types of interaction of ligand on the parameters of transition / A.T. Karapetian, P.O. Vardevanian, G.A.Tarzikian, M.D. Frank-Kamenetskii // J. Biomol. Struct. Dyn. – 1990. – V. 8 (1). – P. 123–30.
10. Haq I. Thermodynamics of drug–DNA interactions / I. Haq // Arch. Biochem. Biophys. – 2002. – V. 403. – P. 1–15.
11. Barcelo F. Thermodynamic characterization of the multivalent binding of chartreusin to DNA / F. Barcelo, D. Capo, J. Portugal // Nucleic Acids Res. – 2002. – V. 30 (20). – P. 4567–4573.
12. Kumar C.V. Groove binding of a styrylcyanine dye to the DNA double helix: the salt effect/ C.V. Kumar, R.S. Turner, E.H. Asuncion // Journal of Photochemistry and Photobiology A: Chemistry. – 1993. – V. 74 (2–3). – P. 231–238.
13. Barcelo F. Heterogenous DNA binding modes of berenil / F. Barcelo, M. Ortiz-Lombardia, J. Portugal // Bioch. Biophys. Acta. – 2001. – V. 1519. – P. 175–184.
14. Sovenyhazy K. Spectroscopic studies of the multiple binding modes of trimetine-bridget cyanine dye with DNA /K. Sovenyhazy, J. Bolderon, J. Petty // Nucleic Acids Res. – 2003. – V. 31 (10). – P. 2561–2569.
15. Stokke T. Multiple binding modes for Hoechst 33248 to DNA / T. Stokke, H.B. Steen // J. Histochem. Cytochem. – 1985. – V. 33 (4). – P. 333–338.
16. Калориметрическое и спектрофотометричеcкое исследование связывания ДНК из молок лосося с профлавином // Е.Г. Березняк, Е.В. Духопельников, Н.А. Гладковская, А.С. Хребтова, А.В. Зинченко / Біофізичний вісник. – 2010. – Т. 25 (2). – С. 23–29. / Kalorimetricheskoye i spektrofotometricheskoye issledovaniye svyazyvaniya DNK iz molok lososya s proflavinom // Ye.G. Bereznyak, Ye.V. Dukhopel'nikov, N.A. Gladkovskaya, A.S. Khrebtova, A.V. Zinchenko / Bíofízichniy vísnik. – 2010. – T. 25 (2). – S. 23–29.
17. Veselkov A.N. Anti-cancer drug desgn: biological and biophysical aspects of synthetic phenoxazone derivatives / A.N. Veselkov, D.B. Davies. – Sevastopol: SevNTU Press, 2002. – 259 p.
18. Structure–activity relation for synthetic phenoxazone drugs. Evidence for a direct correlation between DNA binding and pro-apoptotic activity / A.N. Veselkov, V.Ya Maleev, E.N. Glibin et al. // Eur. J. Biochem. – 2003. – V. 270. – P. 4200–4207.
19. Круглова Е.Б. Использование метода спекрофотометрического анализа для вычисления термодинамических параметров связывания в системах актиноциновые производные – ДНК / Е.Б. Круглова, Н.А. Гладковская, В.Я. Малеев // Биофизика. – 2005. – Т. 50 (2). – С. 253–264. / Kruglova Ye.B. Ispol'zovaniye metoda spektrofotometricheskogo analiza dlya vychisleniya termodinamicheskikh parametrov svyazyvaniya v sistemakh aktinotsinovyye proizvodnyye – DNK / Ye.B. Kruglova, N.A. Gladkovskaya, V.Ya. Maleyev // Biofizika. – 2005. – T. 50 (2). – S. 253–264.
20. Спектрофотометрический анализ димеризации производных актиноцина с разной длиной боковых цепей / Е.Б. Круглова, В.Я. Малеев, Е.Н. Глибин, А.Н. Веселков // Біофізичний вісник. – 2002. – В. 1 (10). – С. 12–20. / Spektrofotometricheskiy analiz dimerizatsii proizvodnykh aktinomitsina s raznoy dlinoy bokovykh tsepey / Ye.B. Kruglova, V.Ya. Maleyev, Ye.N. Glibin, A.N. Veselkov // Bíofízichniy vísnik. – 2002. – V. 1 (10). – S. 12–20.
21. Круглова Е.Б. Моделирование процессов связывания актиноциновых антибиотиков с ДНК при разных ионных силах и температурах / Круглова Е.Б. Гладковская Н.А. Малеев В.Я. // Біофізичний вісник. – 2003. – В. 1 (12). – С. 53–63. / Kruglova Ye.B. Modelirovaniye protsessov svyazyvaniya aktinotsinovykh antibiotikov s DNK pri raznykh ionnykh silakh i temperaturakh / Kruglova Ye.B. Gladkovskaya N.A. Maleyev V.YA. // Bíofízichniy vísnik. – 2003. – V. 1 (12). – S. 53–63.
22. Marky L.A. Calorimetric and spectroscopic investigation of drug – DNA interactions. I. The binding of netropsin to poly d(AT) / L. A. Marky, K. S. Blumenfeld, K. J. Breslauer // Nucleic Acids Res. – 1983. – V. 11 (9). – P. 2857–2870.
23. McGhee J.D. Theoretical calculations of the helix-coil transition of DNA in the presence of large cooperatively binding ligands / J.D. McGhee // Biopolymers. – 1976. – V. 15 (7). – P. 1345–1375.
24. Westhof E. X-ray-structure of a cytidylyl-3',5'-adenosine-proflavine complex: a self-paired parallel-chain double helical dimer with an intercalated acridine dye / E. Westhof, M. Sundaralingam // Proc. Natl. Acad. Sci. USA. – 1980. – V. 77 (4). – P. 1852-1856.
25. Chaires J. B. Calorimetry and thermodynamics in drug design / J. B. Chaires // Annu. Rev. Biophys. – 2008. – V. 37. – P. 135–151.
26. Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2 / R. Ruiz, B. Garcнa, G. Ruisi, et al. // J. Mol. Struct.: Theochem. – 2009. – V. 915 (1–3). – P. 86–92.
27. Miroshnychenko K.V. Flexible docking of DNA fragments and actinocin derivatives / K.V. Miroshnychenko, A.V. Shestopalova // Molecular Simulation. – 2005. – V. 31 (8). – P. 567–574.
28. Исследование влияния воды на взаимодействие ДНК и производных актиноцина с различной длиной аминоалкильных цепочек методами ИК-спектроскопии и компьютерного моделирования / Е.Г. Березняк, М.А. Семенов, Т.В. Больбух и др. // Биофизика. – 2002. – Т. 47 (6). – С. 1005–1015. / Issledovaniye vliyaniya vody na vzaimodeystviye DNK i proizvodnykh aktinotsina s razlichnoy dlinoy aminoalkil'nykh tsepochek metodami IK-spektroskopii i komp'yuternogo modelirovaniya / Ye.G. Bereznyak, M.A. Semenov, T.V. Bol'bukh i dr. // Biofizika. – 2002. – T. 47 (6). – S. 1005–1015.
29. Thermodynamics of interactions of water-soluble porphyrins with RNA duplexes / A.A. Ghazaryan, Y.B. Dalyan, S.G. Haroutiunian, et al // J. Am. Chem. Soc. – 2006. – V. 128. – P. 1914-1921.
Published
2016-07-25
Cited
How to Cite
Хребтова, А. С., Гладковская, Н. А., Березняк, Е. Г., Духопельников, Е. В., Фомин, А. В., & Зинченко, А. В. (2016). The effect of two binding types on parameters of helix – coil transition in polynuleotides. Biophysical Bulletin, 2(34), 24-33. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/5605
Section
Molecular biophysics
Copyright (c) 2015 Г. С. Хребтова, Н. О. Гладковська, К. Г. Березняк, Є. В. Духопельников, О. В. Фомін, О. В. Зінченко
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