Biopolym. Cell. 1991; 7(6):5-15.
http://dx.doi.org/10.7124/bc.0002FB
Structure and Function of Biopolymers
Investigation of interaction of proflavine with deoxytetraribonucleoside triphosphate 5'-d(ApCpGpT) by the method of 1H-NMR spectroscopy
1Veselkov A. N., 2Davies D. B., 1Djimant L. N., 2Parkes H. G.
  1. Sevastopol Instrument Engineering Institute
    33, Universitetskaya Str., Sevastopol, Ukraine, 99053
  2. Birkbeck, University of London
    Malet Str., Bloomsbury, London WC1E 7HX, UK

Abstract

Complex formation between acridine dye proflavine and self-complementary deoxytetra-ribonucleoside triphosphate 5'-d(ApCpGpT) in water-salt solution has been studied by the method of one-dimensional and two-dimensional 1H-NMR spectroscopy (500 MHz). Two-dimensional homonuclear 1H-NMR spectroscopy (2D-COSY and 2D-NOESY) was used for complete assignments of proton signals of molecules in solution and for qualitative analysis of the nature of interactions of proflavine with tetranucleotide. Concentration dependences of proton chemical shifts of the molecules have been measured at 293 K. Analysis of relative content of different types of complexes has been made and special features of dynamic equilibrium have been revealed as a function of correlation of dye and tetranucleotide concentrations. Based on the obtained results a conclusion has been made about preferential intercalation of proflavine to CG-site of tetranucleotide in duplex form. The most favourable structure of 1 : 2 complex of dye with tetranucleotide has been constructed using calculated values of induced chemical shifts of proflavine protons and 2D-NOESY spectra.
Full text: (PDF, in Russian)

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] 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.
[6] Veselkov AN, Dymant LN, BaranovskiД­ 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.
[7] Veselkov AN, Dymant LN, Baranovskiy SF. Proton magnetic resonance study of complex formation between proflavine and isomeric diribodinucleotide monophosphates CpG and GpC. Mol Biol (Mosk). 1986; 20(5):1244-50.
[8] Veselkov AN, Karawajew L, Djimant LN. Proton magnetic resonance study of complex formation between proflavine and ribodinucleotide monophosphates in aqueous solution. Stud biophys. 1987; 120(1):37-107.
[9] Neidle S, Achari A, Taylor GL, Berman HM, Carrell HL, Glusker JP, Stallings WC. Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction. Nature. 1977;269(5626):304-7.
[10] Neidle S. Structural aspects of drug-DNA complexes: molecular modelling of intercalative interactions. Drugs Exp Clin Res. 1986;12(6-7):455-62.
[11] Albert A. The acridines L. New York: Edward Arnold LTD, 1966; 604 p.
[12] 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.
[13] Reid BR. Sequence-specific assignments and their use in NMR studies of DNA structure. Q Rev Biophys. 1987;20(1-2):1-34.
[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 AN, Dymant LN, Baranovskiy SF. Thermodynamic parameters of self-association of the molecules in an aqueous solution of proflavine. Khimicheskaya Fizika. 1989;8(9):1282-5.
[16] 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.
[17] Mathematical Software UCS. Unconstrained minimization. Minsk. Izd-vo Inst Mathematics Akad Nauk BelSSSR 1981; Iss 17. 134 p.
[18] Gusnin SYu, Omel'yanov GA, Reznikov GV, Sirotkin VS. Minimization in engineering calculations on a computer. Biblioteka programm. M., 1981. 120 p.
[19] Delepierre M, Delbarre A, Langlois d'Estaintot B, Igolen J, Roques BP. 1H-NMR studies of a monointercalating drug into a d[CpGpCpG]2 minihelix. Biopolymers. 1987;26(7):981-1000.
[20] Delepierre M, Dinh TH, Roques BP. 1H-NMR studies of a monointercalating drug into a d(CpGpApTpCpG)2 minihelix. Biopolymers. 1989;28(12):2097-113.
[21] Delepierre M, Dinh TH, Roques BP. Bisintercalation of ditercalinium into a d(CpGpApTpCpG)2 minihelix: a 1H- and 31P-NMR study. Biopolymers. 1989;28(12):2115-42.
[22] Giessner-Prettre C, Pullman B. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q Rev Biophys. 1987;20(3-4):113-72.
[23] Berman HM, Neidle S, Stodola RK. Drug-nucleic acid interactions: conformational flexibility at the intercalation site. Proc Natl Acad Sci U S A. 1978;75(2):828-32.
[24] Reid BR, Banks K, Flynn P, Nerdal W. NMR distance measurements in DNA duplexes: sugars and bases have the same correlation times. Biochemistry. 1989;28(26):10001-7.