Biopolym. Cell. 2000; 16(5):384-402.
Structure and Function of Biopolymers
Influence of methylation and interactions with amino acid carboxylic group on UV spectra of purine nucleotide bases and nucleosides in dimethylsulfoxide. 2. Guanine
1Stepanyugin A. V., 1Kotomiets I. M., 1Potyahaylo A. L., 1Samijlenko S. P.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Uy absorption spectra of guanine derivatives m9Gua, m2 2,9Gua, m1Gua, m21,7Gua, G, dG, m1G, m2G, m7G as well as of its analogue isoGua have been studied in anhydrous DMSO. The changes in UV absorption of the Gua derivatives in the presence of the amino acid derivatives with neutral carboxylic group – ac-Asp, ac-Glu, ac-Gly, ac-Asp-OMe and f-GlyONa and NaAc with deprotonated carboxylic groups have been investigated and interpreted. It has been shown that m7Gua and m Gua exist as the N9H tautomers in anhydrous DMSO. It has been established that most part of the Gua derivatives interact only with deprotonated carboxylic group, excluding m7G, isoGua and m3Gua which are capable to form the complexes with neutral carboxylic group as well. Energetic charac­teristics of the Gua prototropic tautomers and their complexes with carboxylate ion were calculated by the semiempirical MNDO/H method at vacuum approximation.

References

[1] Stepanyugin AV, Kolomiets IM, Samijlenko SP. Influence of methylalion and interactions with amino acid carboxylic group on UV spectra of purine nucleotide bases and nucleosides in dimethylsulfoxide. 1. Adenine. Biopolym Cell. 1999; 15(5):422-31.
[2] Nechaev AP, Eremenko TV. Organic chemistry. M.: Vysshaya shkola., 1985. 463 p.
[3] Heterocyclic compounds. Ed. Elderfield RC. Vol 8 Tetrazoles, Tetrazines and Purines and related ring systems. Wiley and Sons 1976.
[4] Mishra PC. Vibrational structures and intensity distributions in the electronic absorption spectra of nucleic acid bases: evidence for non-planarity of guanine. J Mol Struct. 1986;144(3-4):309–17.
[5] Delabar J-M, Majoube M. Infrared and Raman spectroscopic study of 15N and D-substituted guanines. Spectrochim Acta A. 1978;34(2):129–40.
[6] Szczepaniak K, Szczesniak M. Matrix isolation infrared studies of nucleic acid constituents: Part 4. Guanine and 9-methylguanine monomers and their keto—enol tautomerism. J Mol Struct. 1987;156(1-2):29-42.
[7] Scott JF, Sinsheimer RL, Loofbourow JR. Factors Involved in the Sharpening of the Ultraviolet Absorption Spectrum of Guanine at Reduced Temperatures 1 . J Am Chem Soc. 1952;74(1):275–7.
[8] Gumeniuk VA. [Effect of water on guanine crystallization: absorption spectra in the infrared and ultraviolet range]. Biofizika. 1980;25(5):793-5. Russian.
[9] Gorbachevski IO. About crystallized xanthine and guanine. Zbirka matematychno pryrodopysnoyi likars?koyi sektsiyi NTSH. 1897; 1(1):1-19.
[10] Lesnik EA, Kochkina IM, Tikhonenko AS, Varshavski? IaM. [Structure of polyriboguanylic acid in solution]. Mol Biol (Mosk). 1980;14(4):820-9.
[11] Sorokin VA. Study of the interaction of cupric ions with polyriboguanyl and polyribouridylic acids. Mol Biol (Mosk) 1988; 22(6): 1590-8.
[12] Blagoi YuP, Galkin VL, Gladchenko GO, Kornilova SV, Sorokin VA, Shkorbatov A.G. Metal complexes of nucleic acids in solutions Kiev: Naukova dumka, 1991 272 p
[13] Abraham RJ, Smith PE. Charge calculations in molecular mechanics 6: the calculation of partial atomic charges in nucleic acid bases and the electrostatic contribution to DNA base pairing. Nucleic Acids Res. 1988;16(6):2639-57.
[14] 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.
[15] Greco F, Liguori A, Sindona G, Uccella N. Gas-phase proton affinity of deoxyribonucleosides and related nucleobases by fast atom bombardment tandem mass spectrometry. J Am Chem Soc. 1990;112(25):9092–6.
[16] Hovorun DM, Kondratyuk IV. Gas-phase acid-alkaline properties of canonical nucleotide bases. Dopovidi Nats Akad Nauk Ukrainy. 1998; (1):207-12.
[17] Hovorun DM, Mishchuk YaR, Kondratyuk IV. On a quantum-chemical nature of a stereochemical nonrigidity of canonical nucleotide bases. Biopolym Cell. 1996; 12(5):5-12.
[18] Williams LD, Williams NG, Shaw BR. In a model cytosine:guanine base pair, one amino group rotates and the other does not. J Am Chem Soc. 1990;112(2):829–33.
[19] Hovorun DM, Mishchuk YaR. Energy intermolecular hydrogen bonds in crystals and cocrystalised DNA bases: a study using spectral calorimetery. Ukr Fiz Zh. 1997; 42(8):933-8.
[20] Borodavkin AV, Budovskiy EI, Morozov YuV, Savin FA, Simukova NA. Electronic structure of the UV absorption spectra and reactivity of the components of nucleic acids. The results of science and technology. Ed. Vol'kenshten. M .: VINITI, (Molecular. Biology, vol. 14). 1977. 227 p.
[21] Morozov YuV, Bazhulin YaYa Electronic structure, spectroscopy and reactivity of molecules. Nucleobases B vitamins and their analogs. Ed. Vol'kenshten. M .: Nauka, 1989. 288 p.
[22] Elcock AH, Richards WG. Relative hydration free energies of nucleic acid bases. J Am Chem Soc. 1993;115(17):7930–1.
[23] Tselepi-Kalouli E, Katsaros N. Ruthenium(III) ion complexes with nucleic acid bases and nucleosides. J Inorg Biochem. 1988;34(1):63-74.
[24] Raznoshinskiy AYa, Shcherbo SYa, Yuzhakov VI. Electronic structure and spectral-luminescent properties of some methylated purines. Zh Fiz Khim. 1990; 64(5):1266-72.
[25] Serebriany? AM, Andrievski? GV, Bekker AR, Sibel'dina LA, Sharova OL. [The structure of products of modification of nucleotides and DNA by ethyleneimine and thio-TEPA]. Bioorg Khim. 1987;13(6):786-92.
[26] Tsiganenko YaM. Phototransformations components of nucleic acids under the action of radiation in the vacuum ultraviolet region of the spectrum: Auth. Thes. ... kand fiz-mat nauk. Leningrad: LGU, 1987. 16 p.
[27] Sheina GG, Radchenko ED, Stepanian SG, Blagoi YuP. Prototropic tautomerizm of nucleic acid purine bases. Stud biophys. 1986; 114(1-3):123-31
[28] Sheina GG, Stepanian SG, Radchenko ED, Blagoi YP. IR spectra of guanine and hypoxanthine isolated molecules. J Mol Struct. 1987;158:275–92.
[29] Szczepaniak K, Szczesniak M, Person WB. Infrared studies and the effect of ultraviolet irradiation on the tautomers of 9-methylguanine isolated in an argon matrix. Chem Phys Lett. 1988;153(1):39–44.
[30] Leszczynski J. The potential energy surface of guanine is not flat: an ab initio study with large basis sets and higher order electron correlation contributions. J Phys Chem A. 1998;102(13):2357–62.
[31] Leszczy?ski J. Guanine, 6-thioguanine and 6-selenoguanine: ab initio HF/DZP and MP2/DZP comparative studies. J Mol Struct Theochem. 1994;311:37–44.
[32] Latajka Z, Person WB, Morokuma K. An ab initio calculation of the infrared spectrum and tautomerism of guanine. J Mol Struct THEOCHEM. 1986;135:253–66.
[33] Leszczynski J. Tautomers of 6-thioguanine: structures and properties. J Phys Chem. 1993;97(14):3520–4.
[34] Flori?n J, Leszczy?ski J, Scheiner S. Ab initio study of the structure of guanine-cytosine base pair conformers in gas phase and polar solvents . Mol Phys 1995;84(3):469–80.
[35] Kwiatkowski JS, Person WB. Tautomerism of nucleic acid bases revisited: from non-interacting to interacting bases. Theor. Biochem. Mol. Biophys. Eds D. L. Beveridge, L. Lavery. New York.: Adenine, 1990: 153-171.
[36] Colominas C, Luque FJ, Orozco M. Tautomerism and Protonation of Guanine and Cytosine. Implications in the Formation of Hydrogen-Bonded Complexes. J Am Chem Soc. 1996;118(29):6811–21.
[37] Maslova RN, Lesnik EA, Varshavski? IaM. [Kinetics and mechanism of the 3H to 1H in C(8)H groups of purine derivatives]. Mol Biol (Mosk). 1975;9(2):310-20.
[38] Boerth DW, Harding FX. Theoretical investigation of acidity and isotope exchange in purine nucleotide cations. J Am Chem Soc. 1985;107(10):2952–69.
[39] Fujita S, Takenaka A, Sasada Y. A model for interactions of amino acid side chains with Watson-Crick base pair of guanine and cytosine. Crystal structures of 9-(2-carboxyethyl)guanine and its crystalline complex with 1-methylcytosine. Bull Chem Soc Jpn. 1984;57(7):1707–12.
[40] Lancelot G. Hydrogen bonding of amino acid side chains to nucleic acid bases. Biochimie. 1977;59(7):587-96.
[41] Lancelot G. Hydrogen bonding between nucleic acid bases and carboxylic acids. J Am Chem Soc. 1977;99(21):7037-42.
[42] Lancelot G, H?l?ne C. Selective recognition of nucleic acids by proteins: the specificity of guanine interaction with carboxylate ions. Proc Natl Acad Sci U S A. 1977;74(11):4872-5.
[43] Lancelot G, Mayer R, H?l?ne C. Models of interaction between nucleic acids and proteins. Hydrogen bonding of arginine with nucleic acid bases, phosphate groups and carboxylic acids. Biochim Biophys Acta. 1979;564(2):181-90.
[44] Bruskov VI, Bushuev VN. [Study by the proton magnetic resonance method of complex formation between nucleosides and compounds modeling amino acid residues of proteins in dimethyl sulfoxide]. Biofizika. 1977;22(1):26-31.
[45] Lancelot G, Mayer R. The specific interaction of guanine with carboxylate ions in water. FEBS Lett. 1981;130(1):7–11.
[46] Zheltovsky NV, Samoilenko SA, Kolomiets IN, Kondratyuk IV, Gubaidullin MI. Some structural aspects of protein-nucleic acid recognition point mechanisms involving amino acid carboxylic groups. J Mol Struct. 1989;214:15–26.
[47] Kolomiets IN, Kondratyuk IV, Stepanyugin AV, Samoilenko SA, Zheltovsky NV. Influence of methylation of nucleic acid purine bases on their interactions with amino acids through the carboxylic group. J Mol Struct 1991;250(1):1–11.
[48] Zheltovsky NV, Samoilenko SA, Kondratyuk IV, Kolomiets IN, Stepanyugin AV. Recognition of purine bases and nucleosides by the amino acid carboxylic group. J Mol Struc. 1995;344(1-2):53–62.
[49] Zheltovskiy NV, Samoylenko SA, Kolomiets IN, Kondratiuk IV. Interaction of nucleobases with the amino acids carboxyl grouP in DMSO: a model of Point Protein-nucleic contacts. Doklady Akad Nauk Ukr SSR. Ser B. 1988; (8):68-71.
[50] 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.
[51] 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.
[52] Zimmerman SB, Cohen GH, Davies DR. X-ray fiber diffraction and model-building study of polyguanylic acid and polyinosinic acid. J Mol Biol. 1975;92(2):181-92.
[53] Williamson JR, Raghuraman MK, Cech TR. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell. 1989;59(5):871-80.
[54] Souleil C, Panijel J. Immunochemistry of polyribonucleotides. Study of polyriboinosinic and polyriboguanylic acids. Biochemistry. 1968;7(1):7-13.
[55] Walmsley JA, Burnett JF. A new model for the K+-induced macromolecular structure of guanosine 5'-monophosphate in solution. Biochemistry. 1999;38(42):14063-8.
[56] Lawley PD, Brookes P. Further studies on the alkylation of nucleic acids and their constituent nucleotides. Biochem J. 1963;89:127-38.
[57] Handbook of Biochemistry and Molecular Biology: Nucleic Acids. Ed. G. D. Fasman. New York: CRC press, 1986. Vol. I. 637 p.
[58] Handbook of Biochemistry and Molecular Biology: Nucleic Acids. Ed. G. D. Fasman. New York: CRC press, 1986. Vol. II. 923 p.
[59] Lejbkowicz F, Goyer C, Darveau A, Neron S, Lemieux R, Sonenberg N. A fraction of the mRNA 5' cap-binding protein, eukaryotic initiation factor 4E, localizes to the nucleus. Proc Natl Acad Sci U S A. 1992;89(20):9612-6.
[60] Michelson AM, Pochon F. Polynucleotide analogues. VII. Methylation of polynucleotides. Biochim Biophys Acta. 1966;114(3):469-80.
[61] Pochon F, Michelson AM. Polynucleotide analogues. XI. Poly N-1-methylguanylic acid and other methylated polynucleotides. Biochim Biophys Acta. 1967;145(2):321-7.
[62] Nowak MJ, Lapinski L, Kwiatkowski JS. An infrared matrix isolation study of tautomerism in purine and adenine. Chem Phys Lett. 1989;157(1-2):14-8.
[63] Takenaka A, Sasada Y. Studies on protein-nucleic acid interactions by model crystals. Nihon Kessho Gakkaishi. 1985;27(5):324–36.
[64] Kamiichi K, Doi M, Nabae M, Ishida T, Inoue M. Structural studies of the interaction between indole derivatives and biologically important aromatic compounds. Part 19. Effect of base methylation on the ring-stacking interaction between tryptophan and guanine derivatives: a nuclear magnetic resonance investigation. Journal of the Chemical Society, Perkin Transactions 2.1987;(12):1739-45.
[65] Samijlenko SP, Kondratyuk IV. NMR investigation on the role of glycosylic OH groups in complexes modelling point protein-nucleic acid contacts. Spectroscopy of Biological Molecules: Modern Trends. Annex. Eds P. Carmona, R. Navarro, A. Hernanz. Madrid: UNED, 1997: 67-8.
[66] Arni R, Heinemann U, Tokuoka R, Saenger W. Three-dimensional structure of the ribonuclease T1 2'-GMP complex at 1.9-A resolution. J Biol Chem. 1988;263(30):15358-68.
[67] Kan LS, Schweighardt FK, Kao S, Li ND. Penicillin interaction with guanosine. Biochem Biophys Res Commun. 1972;46(1):22-7.
[68] Perona JJ, Swanson RN, Rould MA, Steitz TA, S?ll D. Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes. Science. 1989;246(4934):1152-4.
[69] Namba K, Pattanayek R, Stubbs G. Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction. J Mol Biol. 1989;208(2):307-25.
[70] Chantot JF, Sarocchi MT, Guschlbauer W. Physico-chemical properties of nucleosides. 4. Gel formation by quanosine and its analogues. Biochimie. 1971;53(3):347-54.
[71] Ishida T, Doi M, Ueda H, Inoue M, Scheldrick GM. Specific ring stacking interaction on the tryptophan-7-methylguanine system: comparative crystallographic studies of indole derivatives-7-methylguanine base, nucleoside, and nucleotide complexes. J Am Chem Soc. 1988;110(7):2286–94.
[72] Boiteux S, Belleney J, Roques BP, Laval J. Two rotameric forms of open ring 7-methylguanine are present in alkylated polynucleotides. Nucleic Acids Res. 1984;12(13):5429-39.
[73] Barbarella G, Bertoluzza A, Tugnoli V. Nitrogen-15 NMR characterization of the neutral form of 7-methylguanosine. Nucleic Acids Res. 1988;16(14B):7202.
[74] Abola JE, Abraham DJ, Townsend LB. The crystal and molecular structure of 3-methylguanine, a potentially miscoding base. Tetrahedron Lett. 1976;17(39):3483–6.
[75] Norinder U. A theoretical reinvestigation of the nucleic bases adenine, guanine, cytosine, thymine and uracil using AM1. J Mol Struct. 1987;151:259–69.
[76] Chaput JC, Switzer C. A DNA pentaplex incorporating nucleobase quintets. Proc Natl Acad Sci U S A. 1999;96(19):10614-9.