Biopolym. Cell. 1998; 14(3):184-190.
Structure and Function of Biopolymers
Self-association of deoxyoligonucleotide d(GpApCpApTpGpTpC) in aqueous solution: 1H-NMR thermodynamical analysis of the octamer duplex formation
1Veselkov A. N., 1Osetrov S. G., 1Pahomov V. I., 1Veselkova N. V., 2Davies D. B.
  1. Sevastopol National Technical University
    33, Universytetska Str., Sevastopol, Ukraine, 99053
  2. Birkbeck, University of London
    Malet Str., Bloomsbury, London WC1E 7HX, UK


Self-association of deoxyoctanucleotide 5'-d(GpApCpApTpGpTpC) in aqueous solution has been studied by one-dimensional and two-dimensional 1H-NMR spectroscopy (500 and 600 MHz). Two-dimensional homonudear PMR spectroscopy (2D-TOCSY and 2D-NOESY) was used for complete assignments of deoxyoligonucleotide proton signals. Concentration (at temperatures T1 = – 298 K and T2 – 308 K) and temperature dependences of proton chemical shifts of the octamer have been measured. Experimental results have been analysed using the proposed method based on a dimer model of association of the molecules. Equilibrium association constant, malting temperature of the duplex, thermodynamical parameters ΔH and ΔS of the reaction of duplex formation of the octamer in aqueous solution liave been determined. A comparative analysis has been made of the characteristics of the self-association of the deoxyoligonucleotide d(GpApCpApTpGpTpC) with previous data for deoxytetranucleotides of different base sequence.


[1] Albergo DD, Marky LA, Breslauer KJ, Turner DH. Thermodynamics of (dG--dC)3 double-helix formation in water and deuterium oxide. Biochemistry. 1981;20(6):1409-13.
[2] Petersheim M, Turner DH. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 1983;22(2):256-63.
[3] Bailey SA, Graves DE, Rill R, Marsch G. Influence of DNA base sequence on the binding energetics of actinomycin D. Biochemistry. 1993;32(22):5881-7.
[4] Veselkov AN, Djimant LN, Davies D, Parkes H, Shipp D. 1D- and 2D-1H NMR investigation of self-association of deoxytetraribonucleoside triphosphates of different base sequence in aqueous solution. Biopolym Cell. 1991; 7(5):15-22.
[5] Veselkov AN, Djimant LN, Kodinzec VV, Lisutin VA, Parkes H, Davies D. 1H-NMR investigation of deoxytetranucleoside triphosphates D(TpGpCpA) self-association in aqueous solution. Biofizika. 1995; 40(2):283-92.
[6] Cheng YK, Pettitt BM. Stabilities of double- and triple-strand helical nucleic acids. Prog Biophys Mol Biol. 1992;58(3):225-57.
[7] Davies DB, Veselkov AN. Structural and thermodynamical analysis of molecular complexation by 1H NMR spectroscopy. Intercalation of ethidium bromide with the isomeric deoxytetranucleoside triphosphates 5'-d(GpCpGpC) and 5?-d(CpGpCpG) in aqueous solution. Faraday Trans. 1996;92(19):3545-57.
[8] Davies DB, Karawajew L, Veselkov AN. 1H-NMR structural analysis of ethidium bromide complexation with self-complementary deoxytetranucleotides 5'-d(ApCpGpT), 5'-d(ApGpCpT), and 5'-d(TpGpCpA) in aqueous solution. Biopolymers. 1996;38(6):745-57.
[9] Veselkov AN, Baranovsky SF, Petrenko NV, Osetrov SG, Veselkov DA, Djimant LN., Tucker A, Parkes H, Davies D. 1H-NMR investigation of the self-association of non-complementary deoxytetranucleotides of different base sequences in aqueous solution. Biopolym Cell. 1996; 12(4):38-48.
[10] Wjimenga SS, Mooten MW, Hilbers CW. NMR of nucleic acids: from spectrum to structure. NMR of macromolecules. A practical approach. London: Oxf. Univ. press, 1993: 217.
[11] Chen H, Patel DJ. Solution Structure of the Menogaril-DNA Complex. J Am Chem Soc. 1995;117(22):5901–13.
[12] Veselkov AN, Djimant LN, Karawajew NS, Kulikov EL. Investigation of the aggregation of acridine dyes in aqueous solution by !H NMR. Stud biophys. 1985; 120(3): 171-80.
[13] Freier SM, Albergo DD, Turner DH. Solvent effects on the dynamics of (dG-dC)3. Biopolymers. 1983;22(4):1107-31.
[14] Marky LA, Breslauer KJ. Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules. Biopolymers. 1982;21(11):2185-94.
[15] Dymant LN, Veselkov AN. Proton magnetic resonance study of autoassociation of diribonucleosidmonophasphates GpG and GpC in water solution. Biofizika. 1988; 33(4):728.
[16] Chaires JB. Thermodynamics of the daunomycin-DNA interaction: ionic strength dependence of the enthalpy and entropy. Biopolymers. 1985;24(2):403-19.
[17] Rentzeperis D, Marky LA, Dwyer TJ, Geierstanger BH, Pelton JG, Wemmer DE. Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure. Biochemistry. 1995;34(9):2937-45.
[18] Kollman PA, Weiner PK, Dearing A. Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers. Biopolymers. 1981;20(12):2583–621.
[19] Wada A, Yabuki S, Husimi Y. Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies. CRC Crit Rev Biochem. 1980;9(2):87-144.
[20] Sponer J, Leszczynski J, Hobza P. Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies. J Biomol Struct Dyn. 1996;14(1):117-35.