Biopolym. Cell. 1996; 12(6):36-49.
1H-NMR investigation of complex fonnation of ethidium bromide with single-stranded non-complementary deoxytetranucleotide 5'-d(CpGpApA) in aqueous solution
1Veselkov A. N., 1Baranovsky S. F., 1Djimant L. N., 1Petrenko N. V., 1Osetrov S. G., 2Tucker A., 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

Abstract

Complex formation between the aromatic dye ethidium bromide (3,8-diamino-6-phenyl-5-ethyl-phenan-thridine) and single-stranded non-complementary deoxytetranucleotide 5'-d(CpGpApA) in aqueous solution has been studied by one- and two-dimensional H-NMR spectroscopy (500 and 600 MHz). Concentration dependences of proton chemical shifts of the interacting molecules were measured at different temperatures T1 – 298 K and T2 – 305 K. Investigations of the self-association of the tetranucleotide molecules have shown that there is a very tow probability of duplex formation at the experimental conditions studied. Itfollows that the complexations of the dye molecules with the monomer of the tetranucleotide play the main rote in the complex equilibrium in solution giving an opportunity to analyze the specificity of interactions of aromatic ligand with the single-stranded DNA. Different schemes of complex formation have been examined, equilibrium reaction constants and limiting chemical shifts of dye protons in different complexes have been determined. Analysis of the relative content of different types of complexes was made and special features of the dynamic equilibrium were revealed as a function of both the dye and tetranucleotide concentrations. The analysis has shown that there is a sequence-specific binding of ethidium bromide with the single-stranded oligonucleotide. The most favorable structures of1:1 complexes of the dye with the single strand of the tetranucleotide corresponding to the drug binding from the opposite aromatic rings of the phenanthridine chromophore were constructed using the calculated values of induced chemical shifts of ethidium bromide protons.

References

[1] Lewin B. Genes. (2nd Edition). New York, John Wiley & Sons, 1985; 734 p.
[2] Rill RL, Hecker KH. Sequence-specific actinomycin D binding to single-stranded DNA inhibits HIV reverse transcriptase and other polymerases. Biochemistry. 1996;35(11):3525-33.
[3] Graves DE. Sequence selective binding of actinomycin D to duplex and single-strand DNA. Book of abstracts. Workshop on DNA-drug interactions (Madrid, 15-17 Nov., 1993): 39.
[4] Davies DB, Djimant LN, Veselkov AN. 1 H NMR structural analysis of the interactions of proflavine with self-complementary deoxytetranucleosides of different base sequence. Nucleosides Nucleotides. 1994;13(1-3):637–55.
[5] Veselkov AN., Djumant LN, Bolotin PA, Baranovsky SF, Parkes HG, Davies DB. Investigation of interaction of ethidium bromide with tetradeoxyribonucleotide 5'-d(GpCpGpC) by 1H NMR spectroscopy. Mol Biol (Mosk). 1995; 29(2):326-38.
[6] Veselkov AN, Djimant LN, Bolotin PA, Baranovsky SF, Veselkov DA, Shipp D, Davies DB. Investigation of the interaction of ethidium bromide with self complementary deoxytetranucleotide 5'-d (ApCpGpT) in aqueous solution by the method of 1H NMR spectroscopy. Biopolym Cell. 1995; 11(3-4):42-54.
[7] Veselkov AN, Dymant LN, Bolotin PA, Baranovskii SF, Shipp D, Davies D. 1H NMR study of the interaction between ethidium bromide and self-complementary and self-complementary deoxytetranucleotide 5?-d(CpGpCpG) in an aqueous solution. J Struct Chem. 1996;37(1):65–75.
[8] Takenaka S, Mamabe M, Yokoyama M, Nishi M, Tanaka J, Kondo H. Specific binding to poly A of a naphthalene diimide carrying thymine groups. Chem Comm. 1996;(3):379.
[9] 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.
[10] Bailey SA, Graves DE, Rill R. Binding of actinomycin D to the T(G)nT motif of double-stranded DNA: determination of the guanine requirement in nonclassical, non-GpC binding sites. Biochemistry. 1994;33(38):11493-500.
[11] Bresloff JL, Crothers DM. Equilibrium studies of ethidium--polynucleotide interactions. Biochemistry. 1981;20(12):3547-53.
[12] 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.
[13] Davies DB, Djimant LN, Veselkov AN. 1H NMR investigation of self-association of aromatic drug molecules in aqueous solution. Structural and thermodynamical analysis. Faraday Trans. 1996;92(3):383-90.
[14] 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.
[15] Veselkov AV, Djimant LN, Karawajew LS, Kulikov EL. Investigation of the aggregation of acridine dyes in aqueous solution by 1H NMR. Stud Biophys. 1985. 106(3):171-80.
[16] Veselkov AN, Dymant LN, Bolotin PA, BaranovskiÄ­ SF, Zav'ialova OS, Veselkov DA, Parkes Kh, Davis D. [Study of complex formation of ethidium bromide with the self-complementary deoxytetranucleotide 5'-d(ApGpCpT) by unidimensional and two- dimensional 1H NMR spectroscopy]. Biofizika. 1995;40(6):1189-201.
[17] Giessner-Prettre C, Pullman B. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q Rev Biophys. 1987;20(3-4):113-72.
[18] Abraham RJ. The application of aromatic ring currents in the elucidation of drug-ligand and metallo-porphyrin complexations. Nuclear magnetic resonance spectroscopy in molecular biology. Dordrecht: D. Reidel publ. comp., 1978: 461-79.
[19] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[20] Poltev VI, Teplukhin AV. [Base interaction and conformation manifestations of repetitive nucleotide sequences]. Mol Biol (Mosk). 1987;21(1):102-15.
[21] Dickerson RE. Definitions and nomenclature of nucleic acid structure parameters. J Biomol Struct Dyn. 1989;6(4):627-34.
[22] Searle MS. NMR studies of drug-DNA interactions. Prog Nucl Magn Reson Spectrosc. 1993; 25(5): 403-80.
[23] Jain SC, Tsai CC, Sobell HM. Visualization of drug-nucleic acid interactions at atomic resolution. II. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodocytidylyl (3'-5') guanosine. J Mol Biol. 1977;114(3):317-31.
[24] Veselkov AN, Zavyalova OS, Djimant LN,, Davies D. Study the complex formation of ethidium bromide with self-complementary deoxy tetranucleotide 5'-d (TGCA) by 1 H-NMR spectroscopy. Zh Fiz Khim. 1996; 70(9):1623-30.