Biopolym. Cell. 1991; 7(5):15-22.
Structure and Function of Biopolymers
1D- and 2D-1H NMR investigation of self-association of deoxytetraribonucleoside triphosphates of different base sequence in aqueous solution
1Veselkov A. N., 2Djimant L. N., 1Davies D., 2Parkes H., 2Shipp D.
  1. Sevastopol Instrument Engineering Institute
    33, Universitetskaya Str., Sevastopol, Ukraine, 99053
  2. Birkbeck, University of London
    Malet Str., Bloomsbury, London WC1E 7HX, UK

Abstract

Equilibrium behaviour of self-complementary deoxytetranucleoside triphosphates 5'-d(GpCpGpC), 5'-d(CpGpCpG), 5'-d(ApGpCpT) and 5'-d(ApCpGpT) in aqueous solution have been studied by the method of PMR spectroscopy (500 MHz). Assignments of the tetranucleotides protons have been obtained from both two-dimensional homo-nuclear COSY and NOESY experiments. Concentration and temperature dependences of proton chemical shifts have been investigated. Equilibrium association constants and thermodynamical parameters of molecules self-association have been calculated using theoretical models and regression equations based on experimental results.

References

[1] Krugh TR, Reinhardt CG. Evidence for sequence preferences in the intercalative binding of ethidium bromide to dinucleoside monophosphates. J Mol Biol. 1975;97(2):133-62.
[2] Patel DJ, Canuel LL. Sequence specificity of mutagen-nucleic acid complexes in solution: intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes. Proc Natl Acad Sci U S A. 1977;74(7):2624-8.
[3] Scott EV, Jones RL, Banville DL, Zon G, Marzilli LG, Wilson WD. 1H and 31P NMR investigations of actinomycin D binding selectivity with oligodeoxyribonucleotides containing multiple adjacent d(GC) sites. Biochemistry. 1988;27(3):915-23.
[4] Reid DG, Salisbury SA, Williams DH. Proton nuclear overhauser effect study of the structure of an actinomycin D complex with a self-complementary tetranucleoside triphosphate. Biochemistry. 1983;22(6):1377-85.
[5] Clore GM, Gronenborn AM. Internal mobility in a double-stranded B DNA hexamer and undecamer. A time-dependent proton-proton nuclear Overhauser enhancement study. FEBS Lett. 1984;172(2):219-25.
[6] Mellema JR, Pieters JM, van der Marel GA, van Boom JH, Haasnoot CA, Altona C. Sequence-dependent structural variation in single-helical DNA. Proton NMR studies of d(T-A-T-A) and d(A-T-A-T) in aqueous solution. Eur J Biochem. 1984;143(2):285-301.
[7] Delepierre M, Langlois D'Estaintot B, Igolen J, Roques BP. Conformational studies of d(m5CpGpm5CpG) and d(CpGpCpG) by 1H and 31P NMR. Eur J Biochem. 1986;161(3):571-7.
[8] 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.
[9] Gronenborn AM, Clore GM, Kimber BJ. An investigation into the solution structures of two self-complementary DNA oligomers, 5'-d(C-G-T-A-C-G) and 5'-d(A-C-G-C-G-C-G-T), by means of nuclear-Overhauser-enhancement measurements. Biochem J. 1984;221(3):723-36.
[10] Nilges M, Clore GM, Gronenborn AM, Brunger AT, Karplus M, Nilsson L. Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry. 1987;26(12):3718-33.
[11] Delepierre M, Van Heijenoort C, Igolen J, Pothier J, Le Bret M, Roques BP. Reassessment of structural characteristics of the d(CGCG)2:actinomycin D complex from complete 1H and 31P NMR. J Biomol Struct Dyn. 1989;7(3):557-89.
[12] Freier SM, Albergo DD, Turner DH. Solvent effects on the dynamics of (dG-dC)3. Biopolymers. 1983;22(4):1107-31.
[13] Veselkov AN, Dymant LN, Kulikov E. Application of variational methods of experimental data in the study of molecular aggregation acridine dyes by high-resolution NMR. Khimicheskaya Fizika. 1984;3(8):1101-8.
[14] Veselkov AN, Djimant LN, Karawajew L, Kulikov EL. Investigation of the aggregation of acridine dyes in aqueous solution by proton NMR. Stud. Biophys. 1985;106(3):171—80.
[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] Veselkov AN, Dymant LN, BaranovskiÄ­ SF. Determination of thermodynamic parameters of proflavine interaction with ribodinucleoside monophosphates CpG and PpC in an aqueous solution from data of proton magnetic resonance. Mol Biol (Mosk). 1987;21(4):1110-6.
[17] 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.
[18] Gusnin SYu, Omel'yanov GA, Reznikov GV, Sirotkin VS. Minimization in engineering calculations on a computer. Biblioteka programm. M., 1981. 120 p.
[19] Marky LA, Breslauer KJ. Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules. Biopolymers. 1982;21(11):2185-94.
[20] 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.