Biopolym. Cell. 1994; 10(2):61-68.
Ethonium interaction with single-chain homopolynucleotides
1Sorokin V. A., 1Valeev V. A., 1Gladchenko G. O., 1Blagoi Yu. P., 1Ryazanova O. A., 2Sukhodub L. F.
  1. B. I. Verkin Institute for Low Temperature Physics and Engineering, NAS of Ukraine
    47, Prospekt Lenina, Kharkiv, Ukraine, 61103
  2. Institute of Applied Physics, NAS of Ukraine
    58, Petropavlivska Str., Sumy, Ukraine, 40030

Abstract

The interaction of single-chain homopolynucleotides and individual ribo- and desoxyribo-nucleotides with the effective antimicrobic preparation ethonium belonging to the group of nonintercalating substances is studied by the method of differential UV spectroscopy. Under conditions close to the physiological ones (pH 6, 0,1 M Na + ), ethonium does not bind to heteroatoms of individual nucleotides. However, in polymers ethonium is found to interact strongly with N(7) and N(l) of poly(A), N(3) of poly(C) and O(4) of poly (U). The affinity of ethonium for three atoms is much higher than for the oxygens of the phosphate groups of polymers. Its nucleotide selectivity of binding corresponds to the row: poly (A)>poly (U) >poly(C). Ethonium cannot substitute protons at N(3) of poly(U) and O(2) of poly(C) ribose, neither it interacts with O(2) of this polynucleotide.

References

[1] Zakrzewska K, Lavery R, Pullman B. A theoretical study of the sequence specificity in binding of lexitropsins to B-DNA. J Biomol Struct Dyn. 1987;4(5):833-43.
[2] Sorokin VA, Valeev VA, Gladchenko GO, Blagoi YuP, Sukhodub LF. Interaction between antimicrobic ethonium drug and natural DNA. Biopolym Cell. 1994; 10(1):82-9.
[3] Lowry OH, Rosebrough NJ, Farr AL, Randall RJ. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951;193(1):265-75.
[4] Shatkin A. colorimetric methods for the determination of DNA, RNA and protein. Virology and molecular methods. biology. M Mir. 1972: 184-9.
[5] Rifkind JM, Shin YA, Heim JM, Eichhorn GL. Cooperative disordering of single-stranded polynucleotides through copper crosslinking. Biopolymers. 1976;15(10):1879-1902.
[6] Shin YA. Interaction of metal ions with polynucleotides and related compounds. XXII. Effect of divalent metal ions on the conformational changes of polyribonucleotides. Biopolymers. 1973;12(11):2459-75.
[7] Sorokin VA, Levchenko IV, Valeyev VA, Blagoy YUP. Detection of weak electron interactions in the study of helix-coil transition in homopolynucleotides. Mol Biol (Mosk). 1988; 22(1): 151-8.
[8] Sorokin VA, BlagoÄ­ IuP, Valeev VA, Gladchenko GO, Sukhodub LF, VolianskiÄ­ IuL. The study of complex-formation of DNA with the antimicrobial drug decamethoxine. Mol Biol (Mosk). 1990;24(1):214-9.
[9] Sorokin VA, Blagoi IuP, Silina LK, Dalian EB, Babaian IuS. Spectroscopic study of the effect of binding of bivalent manganese ions on the conformation of polyriboadenylic acid Mol Biol (Mosk). 1982;16(6):1223-33.
[10] Borodavkin AV, Budovskiy EI, Morozov YuV, et al. Electronic structure, UV absorPtion and reactivity of comPonents of nucleic acids. Itogi nauki i tekhniki. Moscow, VINITI, 1977; (Ser. Molekularnaya biologiya; Vol. 14). 227 p.
[11] Sorokin VA. Metal complexes of nucleic acids: Dis .... Doc. fiz- mat. nauk. M., 1992. 387 p.
[12] Yamada A, Akasaka K, Hatano H. Proton and phosphorus-31 magnetic relaxation studies on the interaction of polyriboadenylic acid with Mn2+. Biopolymers. 1976;15(7):1315-31.
[13] Pullman B, Perahia D, Cauchy D. The molecular electrostatic potential of the B-DNA helix. VI. The regions of the base pairs in poly (dG.dC) and poly (dA.dT). Nucleic Acids Res. 1979;6(12):3821-9.
[14] Lavery R, Pullman A, Pullman B. Steric accessibility of reactive centers in B-DNA. Int J Quantum Chem. 1981;20(1):49–62.
[15] Sorokin VA, Blagoi YP, Valeev VA, Antonova OA. Studies of bivalent copper ion binding to poly C. J Inorg Biochem. 1985;24(2):97-111.
[16] Sorokin VA, Blagoi YuP, Valeev VA. et al. Spectroscopic studies of bivalent metal ion binding to single-stranded poly C. Stud. biophys. 1986; 114(1-3):269-76.
[17] AntonovskiÄ­ VL, Gukovskaia AS, Prokop'eva TM, Sukhoroukov BI. Protonation of thymine, uracil and its 5-haloid-derivatives. Dokl Akad Nauk SSSR. 1972;205(2):461-4.
[18] Sorokin VA, Levchenko IV, Valeev VA. et al. Studies of formation of bivalent metal ion complexes with poly U. Makromol Chem. 1989; 190:1595-602.
[19] Pullman A, Ebbesen T, Rholam M. Cation binding to biomolecules. VI. SCF ab initio (pseudopotential) computations on the interaction of Zn 2+ with purine and pyrimidine bases of the nucleic acids. Theoret Chim Acta. 1979;51(3):247–54.
[20] Krakauer H. A thermodynamic analysis of the influence of simple mono-and divalent cations on the conformational transitions of polynucleotide complexes. Biochemistry. 1974;13(12):2579-89.
[21] Lavery R, Pullman B. The dependence of the surface electrostatic potential of B-DNA on environmental factors. J Biomol Struct Dyn. 1985;2(5):1021-32.
[22] Luck G, Reinert KE, Baguley B, Zimmer C. Interaction of the nonintercalative antitumour drugs SN-6999 and SN-18071 with DNA: influence of ligand structure on the binding specificity. J Biomol Struct Dyn. 1987;4(6):1079-94.
[23] Burckhardt G, Zimmer C, Baguley B. Binding of nonintercalative antitumor drugs to DNA-polymers: structural effects of bisquaternary ammonium heterocycles. J Biomol Struct Dyn. 1987;4(5):813-31.
[24] BlagoÄ­ IuP, Sorokin VA, Valeev VA. Spectral studies of binding between DNA bases and magnesium or calcium ions. Mol Biol (Mosk). 1980;14(3):595-605.
[25] Sorokin VA, Blagoi YP, Valeev VA, Lisnyak YV. Studies of calcium ion binding to poly A. J Inorg Biochem. 1983;19(2):143-52.