Consideration of the effect of heat capacity in the analysis of thermodynamics of formation of self-complementary deoxyoligonucleotide duplexes in aqueous solution

  • S.F. Baranovsky Department of Physics, Sevastopol National Technical University
  • P.A. Bolotin Department of Physics, Sevastopol National Technical University
  • A. Hernandez Santiago Department of Physics and Mathematics, Autonomous Universitv of Puebla
  • S.G. Osetrov Department of Physics, P.S. Nakhimov Sevastopol Navy Institute
  • Yu. V. Mukhina Department of Physics, Sevastopol National Technical University
  • A.N. Veselkov Department of Physics, Sevastopol National Technical University
Keywords: oligonucleotide, nucleic acid, DNA, self-association, chemical shift, heat capacity, enthalpy, NMR spectroscopy

Abstract

Thermodynamics of formation of self-complementary deoxyoligonucleotide duplexes 5'-d(TpGpCpA), 5'-d(ApGpCpT), 5'-d(CpGpCpG), 5'-d(GpCpGpC), 5'-d(CpGpCpGpCpG), 5'-d(CpGpTpApCpG) and 5'-d(GpCpApTpGpC), in aqueous solution has been studied by the method of 1H NMR spectroscopy (500 MHz). Thermodynamical parameters have been determined using temperature dependences of proton chemical shifts of the oligomers and the theoretical model, taking into consideration the finite value of the heat capacity change and the temperature dependence of the enthalpy of duplex formation. The mean value of heat capacity change of duplex formation of the investigated deoxyoligonucleotide sequences, <delta Cp>=-(86±32) cal/(mol base pairs K), is in good agreement with experimental data, obtained by calorimetric methods for longer deoxyoligonucleotides and polynucleotide sequences.

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Author Biographies

S.F. Baranovsky, Department of Physics, Sevastopol National Technical University

Streletskaya Bay, 4, Sevastopol, 99053, Crimea, Ukraine

P.A. Bolotin, Department of Physics, Sevastopol National Technical University

Streletskaya Bay, 4, Sevastopol, 99053, Crimea, Ukraine

A. Hernandez Santiago, Department of Physics and Mathematics, Autonomous Universitv of Puebla

Puebla, 72570, Mexico

S.G. Osetrov, Department of Physics, P.S. Nakhimov Sevastopol Navy Institute

Dybenko Str., I-a, Sevastopol, 99053, Crimea, Ukraine

Yu. V. Mukhina, Department of Physics, Sevastopol National Technical University

Streletskaya Bay, 4, Sevastopol, 99053, Crimea, Ukraine

A.N. Veselkov, Department of Physics, Sevastopol National Technical University

Streletskaya Bay, 4, Sevastopol, 99053, Crimea, Ukraine

References

Lane AN, Jenkins TS. Quart. Rev. Biophys. 2000;33:255-306.

Veselkov AN, Davies DB. Anti-Cancer Drug Design: Biological and Biophysical Aspects of Synthetic Phenoxazone Derivatives: SevNTU Press; 2002. 259p.

Plum GE, Breslauer KJ. J. Molec. Biol. 1995;248:679-95.

SantaLucia J. Proc. Nath. Acad. Sci. USA.1998;95:1460-5.

Chalikian TV, Volker T, Plum GE, Breslauer KJ, Proc. Nath. Acad. Sci. USA. 1999;96:7853-8.

Jelesarov I. Grane-Robinson C, Privalov PL. J. Molec. Biol. 1999;294:981-95.

Veselkov AN,Devis D, Dymant LN, Parkes Kh, Shipp D. Biopolimery i kletka. 1991;7(5):15-22. (in Russian)

Veselkov AN, Dymant LN, Kodintcev VV, Lisiutin VA, Parkes Kh, Devis D. Biofizika. 1995;40:283-92. (in Russian)

Veselkov AN, Pakhomov VI, Iton RDzh, Devis DB. Biofizika. 2000;45(1):20-6. (in Russian)

Veselkov AN, Pakhomov VI, Rogova OV, Volynkin VS, Dymant LN, Iton RDzh, Devis DB. Biofizika. (in Russian)

Veselkov AN, Pakhomov VI, Iton RDzh, Devis DB. Doklady NAN Ukrainy. 2001;5:95-101. (in Russian)

Hopkins HP, Fumero JrJ, Wilson WD. Biopolym. 1990;29:449-59.

Veselkov AN, Devis D, Dymant LN, Parkes Kh. Biofizika. 1993;38:627-35. (in Russian)

Albergo D, Turner DH, Marky LA, Breslauer KJ. Biochemistry. 1981;20(6):1409-13.

Veselkov AN, Djimant LN, Karawajew LS, Kulikov EL. Studia Biophysica. 1985;120:171-80.

Gusnin SIu, Omelianov GA, Reznikov GV, Sirotkin VS. Minializatciia v inzhenernykh raschetakh na EVM. Biblioteka programm. M.: Mashinostroenie; 1981. 120p. (in Russian)

Holbrock JA, Capp MW, Saecker RM, Record MTJr. Biochemistry. 1999;38:8409-22.

Virnik KM, Gasan AI, Shestopalova AV, Maleev VIa. Biofizicheskii vestnik. 1998;1:41-9. (in Russian)

Chalikian TV, Sarvazian AP, Plum E, Breslauer K. 1994;33:2394-2401.
Published
2003-06-05
Cited
How to Cite
Baranovsky, S., Bolotin, P., Hernandez Santiago, A., Osetrov, S., Mukhina, Y. V., & Veselkov, A. (2003). Consideration of the effect of heat capacity in the analysis of thermodynamics of formation of self-complementary deoxyoligonucleotide duplexes in aqueous solution. Biophysical Bulletin, 2(13), 23-29. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/12368