Biopolym. Cell. 2000; 16(6):495-504.
Structure and Function of Biopolymers
Conformational transitions of poly(C) and poly(dC): study by the proton buffer capacity method
1Zarudnaya M. I., 1Potyahaylo A. L., 1Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

On the basis of the literature data the pH-dependencies of proton buffer capacity ofpoly(C) (at 0,1 M Na+ ) and poly(dC) (at 0,05 M Na+ ) are computed. These dependencies are expanded into basic functions corresponding to ionized groups of equal pK. It is found that the buffer capacity curve of poly(C) has four peaks: two narrow and two wide ones. The first narrow peak (pK-5,6) reflects the process of cooperative formation of double helices, which is induced by the profanation of the N3 atom of the nucleotide bases partly exposed in the solution. The second narrow peak (pK-2,9) is assigned to the cooperative dissociation of these helices. The first wide peak (pK–5,3) corresponds to the noncooperative process of the poly(C) double helices profanation at the N3 nitrogen atom. The second wide peak (pK – 3,1) is assigned to the noncooperative profanation of electroneutral cytidine bases at the oxygen atom with cis-orientation of added proton about glycoside bond. This reaction leads to the decrease of thermodynamic stability of the poty(C) double helices and finally results in their dissociation. The confor-mational transitions of the poly(dC) induced by its protonation are discussed as well.

References

[1] Zarudna MI, Hovorun DM. Self-associated homopolymer tracts of cellular RNAs: physical mechanisms of formation and function. Physics of the Alive. 1999; 7(2): 38-52.
[2] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[3] Samijlenko SP, Kolomiets IM, Kondratyuk IV, Stepanyugin AV. Model considerations on physico-chemical nature of protein-nucleic acid contacts through amino acid carboxylic groups: spectroscopic data. Biopolym Cell. 1998;14(1):47-53.
[4] Takenaka A, Sasada Y. Elementary patterns in protein-nucleic acid interactions. III. Crystal structure of adenine:phthalic acid (3:1) complex hexahydrate. Bull Chem Soc Jpn. 1982;55(3):680–6.
[5] Fujita S, Takenaka A, Sasada Y. Crystal structure of adenine-1-(2-carboxyethyl)uracil (1:1) complex. A model for interactions of amino acid side chains with nucleic acid base pair. Bull Chem Soc Jpn. 1983;56(8):2234–7.
[6] Hartman KA, McDonald-Ordzie PE, Kaper JM, Prescott B, Thomas GJ Jr. Studies of virus structure by laser-Raman spectroscopy. Turnip yellow mosaic virus and capsids. Biochemistry. 1978;17(11):2118-23.
[7] Prescott B, Sitaraman K, Argos P, Thomas GJ Jr. Protein-RNA interactions in belladonna mottle virus investigated by laser Raman spectroscopy. Biochemistry. 1985;24(5):1226-31.
[8] Hellendoorn K, Michiels PJ, Buitenhuis R, Pleij CW. Protonatable hairpins are conserved in the 5'-untranslated region of tymovirus RNAs. Nucleic Acids Res. 1996;24(24):4910-7.
[9] Fundamental Virology. Eds Fields BN, Knipe DM. Raven press. New York 1986.
[10] Martin LR, Duke GM, Osorio JE, Hall DJ, Palmenberg AC. Mutational analysis of the mengovirus poly(C) tract and surrounding heteropolymeric sequences. J Virol. 1996;70(3):2027-31.
[11] Antao VP, Gray DM. CD spectral comparisons of the acid-induced structures of poly[d(A)], poly[r(A)], poly[d(C)], and poly[r(C)]. J Biomol Struct Dyn. 1993;10(5):819-39.
[12] Zarudnaia MI. [Study of conformational transitions in poly(A) using the buffer capacity method]. Mol Biol (Mosk). 1998;32(3):508-14.
[13] Zarudnaya M. I. Double helical forms of poly (A): possible involvement in biological processes. Biopolym Cell. 1999; 15(3):195-9.
[14] Holcomb DN, Timasheff SN. Temperature dependence of the hydrogen ion equilibria in poly(riboadenylic acid). Biopolymers. 1968;6(4):513-29.
[15] Akinrimisi EO, Sander C, Ts'o PO. Properties of helical polycytidylic acid. Biochemistry. 1963;2:340-4.
[16] Hartman KA Jr, Rich A. The tautomeric form of helical polyribocytidylic acid. J Am Chem Soc. 1965;87:2033-9.
[17] Guschlbauer W. Protonated polynucleotide structures. I. The thermal denaturation of polycytidylic acid in acid solution. Proc Natl Acad Sci U S A. 1967;57(5):1441-8.
[18] Klymp H. A calorimetric study of the helix-coil transition of poly(cytidylic acid) in acid solution. Biochim Biophys Acta. 1975;383(1):1-8.
[19] Chou CH, Thomas GJ Jr. Raman spectral studies of nucleic acids. XVI. Structures of polyribocytidylic acid in aqueous solution. Biopolymers. 1977;16(4):765-89.
[20] Langridge R, Rich A. Molecular structure of helical polycytidylic acid. Nature. 1963;198:725-8.
[21] Suleimanova RS, Apolonnik NV, Kuznetsov IA. Acid-basic properties of isoionic solutions of polyribocytidylic acids. Biofizika. 1987; 32(3):413-6.
[22] Apolonnik NV, Suleimanova RS, Kuznetsov IA. Conductometric corrobaration of the existence of completely protonated double helix of polyribocytidylic acid. Mol Biol (Mosk). 1987. 21(2):428-33.
[23] Opanasenko VK, Gerts SM, Makarov AD. [Buffer capacity of polyproton substances]. Biokhimiia. 1978;43(8):1357-68.
[24] Sukhorukov BI, Montrel' MM, Opanasenko VK, Zolotareva EK. [Study of DNA-interaction with protons of the medium by means of buffer capacity method]. Mol Biol (Mosk). 1983;17(5):1009-18.
[25] Zarudna MI, Hovorun DM. Structural transitions in poliadeniloviy acid: possible molecular mechanisms of the functioning of mRNA poly (A) tails. Dopovidi Nats Akad Nauk Ukrainy. 1998;(12):155-60.
[26] Opanasenko VK. A technique for assaying chloroplast buffer capacity and analysis of its dependence on the medium pH. Fiziologiia rasteniy. 1980; 27(1):195-202.
[27] Guschlbauer W, Blandin M, Drocourt JL, Thang MN. Poly-2'-deoxy-2'-fluoro-cytidylic acid: enzymatic synthesis, spectroscopic characterization and interaction with poly-inosinic acid. Nucleic Acids Res. 1977;4(6):1933-43.
[28] Thiele D, Guschlbauer W. [Protonated polynucleotides. VII. Thermal transitions between different complexes of polyinosinic acid and polycytidylic acid in an acid medium]. Biopolymers. 1969;8(3):361-78.
[29] Aronssohn G, Travers F. Electrostatic potential modulations on polynucleotides as a function of ionic content: potentiometric determinations. Nucleic Acids Res. 1976;3(5):1373-85.
[30] 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.
[31] Mishchuk YaR. Study of physical and chemical nature of the elementary acts of protein-nucleic acid and nucleic-nucleic acid recognition in low-model systems: Author. Thesis. ... Kand biol nauk. Kyiv: IMBG NAS Ukraine, 1993 21 p.
[32] Hovorun DM, Kondratyuk IV. Gas-phase acid-alkaline properties of canonical nucleotide bases. Dopovidi Nats Akad Nauk Ukrainy. 1998; (1):207-12.
[33] Flori?n J, Baumruk V, Leszczy?ski J. IR and Raman spectra, tautomeric stabilities, and scaled quantum mechanical force fields of protonated cytosine . J Phys Chem. 1996;100(13):5578–89.
[34] Vo?tiuk AA, Blizniuk AA. [Effect of protonation of nucleic acid bases on the energy of formation of the Watson-Crick pairs]. Mol Biol (Mosk). 1988;22(4):1080-6.
[35] Zundel G. Proton polarizability of hydrogen bonds and proton transfer processes, their role in electrochemistry and biology. Munchen.: Inst Phys. Chem. der Univ., 1997-250 p.
[36] Sowers LC, Shaw BR, Veigl ML, Sedwick WD. DNA base modification: ionized base pairs and mutagenesis. Mutat Res. 1987;177(2):201-18.
[37] Wr?bel A, Rabczenko A, Shugar D. Conformation of acid forms of poly C: temperature and ionic strength dependence of protonation of cytidine and cytidine-5'-phosphate. Acta Biochim Pol. 1970;17(4):339-49.
[38] Green G, Mahler HR. Comparative study of polyribonucleotides in aqueous and glycol solutions. Biochemistry. 1970;9(2):368-87.
[39] O’Connor T, Scovell WM. pH-Dependent Raman spectra and thermal melting profiles for polycytidylic acid. Biopolymers. 1981;20(11):2351–67.
[40] Inman RB. Transitions of DNA homopolymers. J Mol Biol. 1964;9:624-37.
[41] Gehring K, Leroy JL, Gu?ron M. A tetrameric DNA structure with protonated cytosine.cytosine base pairs. Nature. 1993;363(6429):561-5.
[42] Gu?ron M, Leroy JL. The i-motif in nucleic acids. Curr Opin Struct Biol. 2000;10(3):326-31.
[43] Lacroix L, Mergny JL, Leroy JL, H?l?ne C. Inability of RNA to form the i-motif: implications for triplex formation. Biochemistry. 1996;35(26):8715-22.
[44] Collin D, Gehring K. Stability of Chimeric DNA/RNA cytosine tetrads: implications for i -motif formation by RNA. J Am Chem Soc. 1998;120(17):4069–72.
[45] Janik B, Sommer RG, Bobst AM. Polarography of polynucleotides. II. Conformations of poly(adenylic acid) at acidic pH. Biochim Biophys Acta. 1972;281(2):152-68.
[46] Zarudnaya MI, Zheltovsky NV. Affinity electrophoresis study on the interaction between homopolyribonucleotides and divalent lysine complex. Mol Biol (Mosk). 1992; 26(1):110-7.