Molecular mechanisms of caffeine interaction with different structural forms of polyriboadenylic acid: experiment and computer simulation

  • A. V. Shestopalova Usikov Institute of Radiophysics and Electronics, Nat. Acad. Sci.
  • T. V. Bolbukh Usikov Institute of Radiophysics and Electronics, Nat. Acad. Sci. Ukraine
  • M. A. Semenov Usikov Institute of Radiophysics and Electronics, Nat. Acad. Sci. Ukraine
Keywords: IR-spectroscopy, piezogravimetry, Monte Carlo method, polyriboadenylic acid, protonation, caffeine, hydration

Abstract

The investigation of interaction of caffeine (Cf) with neutral single-stranded (polyrA) and protonated double-helical forms of polyriboadenylic acid (рolyr(AH-AH) has been carried out by IR-spectroscopy, piezogravimetry and Monte Carlo methods. The hydration isotherms and IR-spectra for wet films of complexes at various relative humidity have been obtained. It was shown that Cf does not influence on formation of the ordered forms of polyrA. In complex with single-helical polyrA Cf decreases the hydration of polynucleotide matrix, but in the complex double-helical polyrA-Cf the hydration of polynucleotide matrix is increased in the comparison with their hydration in isolated state. The data obtained by computer modeling (energetic and structural characteristics and instantaneous configurations) allows us to suggest the molecular models of investigated complexes. In Cf-single-helical polyrA complex two types of Cf binding are possible. The first type is the external binding of Cf molecules and the second type is the partial intercalation of Cf molecule between planes of adjacent adenines. In the complex of Cf with double-stranded helical polyrA only one type of Cf binding near sugar-phosphate backbone of polynucleotide matrix is realized. The results of Monte Carlo simulations are in agree with experimental data for all investigated systems.

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Author Biographies

A. V. Shestopalova, Usikov Institute of Radiophysics and Electronics, Nat. Acad. Sci.

 12 Akad.Proskury str., Kharkiv, 61085, Ukraine

T. V. Bolbukh, Usikov Institute of Radiophysics and Electronics, Nat. Acad. Sci. Ukraine

12 Akad.Proskury str., Kharkiv, 61085, Ukraine

M. A. Semenov, Usikov Institute of Radiophysics and Electronics, Nat. Acad. Sci. Ukraine

12 Akad.Proskury str., Kharkiv, 61085, Ukraine

References

Nurminen ML, Niittynen L, Korpela R, Vapaatalo H. Eur.J.ClimNutr. 1999;53:831-9.

Brauer LH, Buican B, De Wit H. Behav. Pharmaco. 2002;5:111-8.

Sivak A, Rudenko L, Teaque LG. Environ.Mutag. 1982;4:143-62.

Vexler ZB, Eidus LKh, Vexler AM. Studia biophys. 1984;45:157-9.

Selby CP, Sancar A. Proceed.Nat Acad.Sci. USA. 1990;87:3522-5.

Tempel K, von Zallinger C. Z.Naturforsch. 1997;52:466-74.

Kan L-S, Borer PN, Cheng DM, Ts'o POP. Biopolymers. 1980;19:1641-54.

Fritzsche H, Lang H, Sprinz H, Pohle W. Biophys.Chem. 1980;11:121-31.

Lang H. Studia Biophys. 1976;55:137-56.

Shestopalova AV, Starikov EB, Semenov MA, Bolbukh TV. Issledovanie gidratatcii kofeina i kompleksa DNK-kofein vo vlazhnykh plenkakh metodami IK-spektroskopii i pezogravimetrii. 1987. 22p. (in Russian)

Frizsche H, Petri I, Schutz H, Weller K, Sedmera R, Lang H. Biophys. Chem.1980;11:109-19.

Jafari M, Rabbani A. Metabolism. 2004;53:687-92.

Brauer LH, Buican B, De Wit H. Oncogene. 2003;22:8283-92.

Marheineke K, Hyrien O. J.Biol.Chem. 2004;279:28071-81.

Vavrova J, Marekova-Rezacova M, Vokurkova D. Radiat.Environ Biophys. 2003;42:193-9.

Bedher E, Du L, Traganos F, Darzynkiewicz Z. Cytometry. 2001;43:38-45.

Lyles MB, Cameron IL. Cell Biology International. 2002;26:145-54.

Johnson IM, Bhuvan Kumar SG, Malathi R. J.Biomol.Stuc.Dyn. 2003;20:687-92.

Semenov MA, Bolbukh TV, Starikov EB. Studia biophysica. 1985;106:181-92.

Bolbukh TV, Starikov EB, Semenov MA. Studia biophysica. 1985;108:199-207.

Semenov MA. Molekuliarnaia biologiia i biofizika. KGU. 1984;9:25-33. (in Russian)

Bolbukh TV, Semenov MA, Maleev VIa, Sechkin VV. Ispolzovanie metoda kvartcevogo rezonatora dlia izucheniia izoterm gidratatcii polinukleotidov. 1983. 19p. (in Russian)

Danilov VI, Tolokh IS. J.Biomol.Struct. Dyn. 1990;7:1167-83.

Danilov VI. J.Biomol.Struct.Dyn. 1997;15:69-80.

Danilov VI. J.Biomol.Struct.Dyn. 1999;16:1107-17.

Saenger W, Riecke J, Suck D. J.Mol.Biol. 1975;93:529-34.

Finch JT, Klug A. J.Mol.Biol.1969;46:597-8.

Lerner DB, Kearns DR. Biopolymers. 1981;20:803-16.

Rich A, Davies DR, Crick FHC, Watson JD. J.Mol.Biol. 1961;3:71-86.

Zenger V. Printcipy strukturnoi organizatcii nukleinovykh kislot. M.:Mir; 1987. 584p.(in Russian)

Cornell WD, Cieplak P, Bayly CI. J. Amer. Chem. Soc. 1995;117:5179-97.

Shestopalova AV. Croatica Chem.Acta. 1989;62:825-34.
Published
2006-06-06
Cited
How to Cite
Shestopalova, A. V., Bolbukh, T. V., & Semenov, M. A. (2006). Molecular mechanisms of caffeine interaction with different structural forms of polyriboadenylic acid: experiment and computer simulation. Biophysical Bulletin, 1(17), 24-35. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/12845