Biopolym. Cell. 2003; 19(1):43-63.
http://dx.doi.org/10.7124/bc.00063B
Структура та функції біополімерів
Ультрафіолетові спектри піримідинових основ і нуклеозидів у контексті метилзаміщення та взаємодії з карбоксильною групою амінокислот
1Степанюгін А. В., 1Коломієць І. М., 1Потягайло А. Л., 1Самійленко С. П., 1Говорун Д. М.
  1. Інститут молекулярної біології і генетики НАН України
    Вул. Академіка Заболотного, 150, Київ, Україна, 03680

Abstract

У зневодненому ДМСО досліджено УФ спектри піримідинових нуклеотидних основу нуклеозидів, низки їхніх похідних та аналогів. Простежено вплив на УФ спектри взаємодії з нейтральною та депротонованою формами карбоксильної групи амінокислот Встановлено, що метилювання 1-го та 5-го положень піримідинових основ спричиняє батохромний зсув максимуму смуги поглинання від 5 до 12 нм. Показано, шр Cyt та більшість його похідних, за винятком m3Cyt та isoCyt, специфічно взаємодіють з нейтральною карбоксильною групою. Для Ura, Thy та їхніх twxidnux, крім chx1Ura, s2Ura і dU, характерною є взаємодія лише з депротонованою карбоксильною групою. Зроблено висновок про те, що заміщення 1-го положення піримідинових основ супроводжується падінням комплексотвірної здатності з обома формами карбоксильної групи, а заміщення 5-го положення підсилює взаємодію з нейтральною карбоксильною групою та послаблює взаємодію з карбоксилат-іоном. Обговорюється біологічна значущість отриманих результатів.
Повний текст: (PDF, українською)

References

[1] Handbook of biochemistry and molecular biology. Nucleic acids. Ed. G. D. Fasman. Boca Raton: CRC press, 1986. 637 p.
[2] Dodonova NYa, Tsyganenko NM, Kuzicheva EA, Simakov MB. Abiotic synthesis of uridine nucleosides under vacuum ultraviolet radiation. Biofizika. 1994; 39(1): 26-31.
[3] Miyakawa S, Murasawa K, Kobayashi K, Sawaoka AB. Cytosine and uracil synthesis by quenching with high-temperature plasma. J Am Chem Soc. 1999;121(36):8144–5.
[4] Sowerby SJ, Cohn CA, Heckl WM, Holm NG. Differential adsorption of nucleic acid bases: Relevance to the origin of life. Proc Natl Acad Sci U S A. 2001;98(3):820-2.
[5] Sheina GG, Radchenko ED, Plokhotnichenko AM, Blago? IuP. [Electron-oscillatory spectra of pyrimidine bases of nucleic acids in argon matrices]. Biofizika. 1982;27(6):983-6.
[6] Radchenko ED, Plokhotnichenko AM, Sheina GG, Blago? IuP. [Infrared spectra of uracil and thymine in an argon matrix]. Biofizika. 1983;28(6):923-7.
[7] Radchenko ED, Plokhotnichenko AM, Ivanov AYu, Sheina GG, Blagoy YuP. Ketoenole tautomeria of guanine and isocytosine molecules. Biofizika. 1986; 31(3):373-81.
[8] Sheina GG, Radchenko ED, Plokhotnichenko AM, Blagoi YuP. IR spectra of associated and hydrated pyrimidine bases of nucleic acidas in AR matrix. Biofizika. 1988; 33(5):741-6.
[9] Stepanian SG, Sheina GG, Radchenko ED, Blagoi YuP. Infrared spectra and tautomerism isocytosine in an argon matrix. Zh Fiz Khim. 1989; 63(11):3008-14.
[10] Stepanian SG, Sheina GG, Radchenko ED, Blagoi YP. Proton transfer in autoassociates and hydrates of pyrimidine bases: an MNDO/M study. J Mol Struct. 1992;270:459–79.
[11] Vranken H, Smets J, Maes G, Lapinski L, Nowak MJ, Adamowicz L. Infrared spectra and tautomerism of isocytosine; an ab initio and matrix isolation study. Spectrochim Acta. 1994;50(5):875–89.
[12] Smets J, Adamowicz L, Maes G. Matrix-Isolation FT-IR Studies and ab Initio Calculations of Hydrogen-Bonded Complexes of Molecules Modeling Cytosine or Isocytosine Tautomers. 5. 1-CH 3 -Cytosine Complexes with H 2 O in Ar Matrices . J Phys Chem. 1996;100(16):6434–44.
[13] Szczepaniak K, Person WB, Leszczynski J, Kwiatkowski IS. Matrix isolation and DFT quantum mechanical studies of vibrational spectra of uracil and its methylated derivatives. Polish J Chem. 1998; 72:402-20.
[14] Tsuboi M. Infrared and Raman spectroscopy. Basic principle in nucleic acid chemistry. Ed. P. O. P. Ts'o. New York; London: Acad, press, 1974. 636 p.
[15] Clowney L, Jain SC, Srinivasan AR, Westbrook J, Olson WK, Berman HM. Geometric Parameters in Nucleic Acids: Nitrogenous Bases. J Am Chem Soc. 1996;118(3):509–18.
[16] 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.
[17] Callis PR. Electronic States and Luminescence of Nucleic Acid Systems. Annu Rev Phys Chem. 1983;34(1):329–57.
[18] Morozov YuV, Bazhulina NP. Electronic structure, spectroscopy and reactivity of the molecules. Moscow: Mir, 1989. 288 p.
[19] Biological applications of magnetic resonance. Ed R. G. Shulman. New York; San Francisco; London: Acad, press, 1979. 595 p.
[20] Danilov VI, Kventsel GF. Electronic submission to the theory of point mutations. Kiev: Naukova Dumka, 1971; 82 p.
[21] Sharma BD, McConnell JF. The crystal and molecular structure of isocytosine. Acta Crystallogr. 1965;19(5):797-806.
[22] Pivovarov VB, Sheina GG. Isocytosine tautomerism in solution. Biopolym Cell. 1992; 8(1):51-6.
[23] Rubin YV, Morozov Y, Venkateswarlu D, Leszczynski J. Prototropic Equilibria in 4-Thiouracil: A Combined Spectroscopic and ab Initio SCF-MO Investigation. J Phys Chem A. 1998;102(12):2194–200.
[24] Lamsabhi M, Alcam? M, M? O, Bouab W, Esseffar M, Abboud JL-M, et al. Are the Thiouracils Sulfur Bases in the Gas-phase? J Phys Chem. 2000;104(21):5122–30.
[25] Samijlenko SP, Alexeeva IV, Palchykivs'ka LH, Kondratyuk IV, Stepanyugin AV, Shalamay AS, Hovorun DM. 1H NMR investigation on 6-azacytidine and its derivatives. Spectrochim Acta - Part A: Mol Biomol Spectrosc. 1999; 55(5):1133-41.
[26] Samijlenko SP, Alexeeva IV, Palchykivs'ka LH, Kondratyuk IV, Stepanyugin AV, Shalamay AS, Hovorun DM. Structural peculiarities of 6-azacytosine and its derivatives imply intramolecular H-bonds. J Mol Struct. 1999; 484(1-3):31-8.
[27] Orozco M, Hernandez B, Luque FJ. Tautomerism of N-methyl derivatives of uracil, thymine and 5-bromouracil. Is tautomerism the basis for mutagenicity of 5-bromouridine?. J Phys Chem. 1998; 102(26): 5228-33.
[28] Tian SX, Zhang CF, Zhang ZJ, Chen XJ, Xu KZ. How many uracil tautomers there are? Density functional studies of stability ordering of tautomers. Chem Phys. 1999;242(2):217–25.
[29] Kryachko ES, Nguyen MT, Zeegers-Huyskens T. Theoretical Study of Tautomeric Forms of Uracil. 1. Relative Order of Stabilities and Their Relation to Proton Affinities and Deprotonation Enthalpies. J Phys Chem. 2001;105(8):1288–95.
[30] Kryachko ES, Nguyen MT, Zeegers-Huyskens T. Theoretical Study of Uracil Tautomers. 2. Interaction with Water. J Phys Chem. 2001;105(10):1934–43.
[31] Kobayashi R. A CCSD(T) Study of the Relative Stabilities of Cytosine Tautomers. J Phys Chem. 1998;102(52):10813–7.
[32] Gorb L, Podolyan Y, Leszczynski J. A theoretical investigation of tautomeric equilibria and proton transfer in isolated and monohydrated cytosine and isocytosine molecules. J Mol Struct : THEOCHEM. 1999;487(1-2):47–55.
[33] 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.
[34] Shukla MK, Leszczynski J. Investigations of the excited-state properties of isocytosine: An ab initio approach. Int J Quant Chem. 2000; 77(1): 240-54.
[35] Tsuboi M, Takahashi S. Infrared and Raman spectra of nucleic acids. Vibrations in the base-residues. Physico-chemical properties of nucleic acids. Ed J Duchesre. New York: Acad, press. 1973; Pt. 2:91-145.
[36] Zhizhina GP, Oleinik EF. Infrared spectroscopy of nucleic acids. Russ Chem Rev. 1972; 41 (3):258–80. http://dx.doi.org/ 10.1070/RC1972v041n03ABEH002043
[37] Podolyan Y, Gorb L, Leszczynski J. Protonation of Nucleic Acid Bases. A Comprehensive Post-Hartree?Fock Study of the Energetics and Proton Affinities. J Phys Chem. 2000;104(31):7346–52.
[38] Barsky D, Colvin ME. Guanine?Cytosine Base Pairs in Parallel-Stranded DNA: An ab Initio Study of the Keto?Amino Wobble Pair versus the Enol?Imino Minor Tautomer Pair. J Phys Chem A. 2000;104(37):8570–6.
[39] 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.
[40] Chen L, Cai L, Zhang X, Rich A. Crystal structure of a four-stranded intercalated DNA: d(C4). Biochemistry. 1994;33(46):13540-6.
[41] Snoussi K, Nonin-Lecomte S, Leroy JL. The RNA i-motif. J Mol Biol. 2001;309(1):139-53.
[42] 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.
[43] Leitner D, Schr?der W, Weisz K. Direct Monitoring of Cytosine Protonation in an Intramolecular DNA Triple Helix. J Am Chem Soc. 1998;120(28):7123–4.
[44] Semenov SG, Tulub AA, Stesenko AI, Skaletskiy EK. Quantum chemical and UV spectroscopic study isocytosine. Zh Obshch Khim. 1988; 58(4):901-5.
[45] Tulub AA, Semenov SG, Stetsenko AI, Yudovich EE. Spectroscopic and quantum chemical studies of isocytosine. Theor Exp Chem. 1988;24(1):26–32.
[46] Zhanpeisov N., Leszczynski J. Specific solvation effects on the structures and properties of Watson–Crick and reverse Watson–Crick isocytosine–cytosine and guanine–cytosine base pairs: a theoretical ab initio study. J Mol Struct: THEOCHEM. 1999;487(1-2):107–15.
[47] Zhanpeisov NU, Leszczynski J. Ab initio study of the structure of isocytosine-cytosine standard Watson-Crick base pairs in the gas phase and in water. Int J Quant Chem. 1998. 69(1):37-47.
[48] Shukla MK, Leszczynski J. Investigations of the excited-state properties of isocytosine: an ab initio approach. Int J Quant Chem. 2000; 77(1): 240-254.
[49] Sugiyama H, Ikeda S, Saito I. Remarkably Stable Parallel-Stranded Oligonucleotides Containing 5-Methylisocytosine and Isoguanine. J Am Chem Soc. 1996;118(41):9994–5.
[50] Toyama A, Takeuchi H, Harada I. Ultraviolet resonance Raman spectra of adenine, uracil and thymine derivatives in several solvents. Correlation between band frequencies and hydrogen-bonding states of the nucleic acid bases. J Mol Struct. 1991;242:87–98.
[51] Morsy MA, Al-Somali AM, Suwaiyan A. Fluorescence of Thymine Tautomers at Room Temperature in Aqueous Solutions. J Phys Chem B. 1999;103(50):11205–10.
[52] Suwaiyan A, Morsy MA, Odah KA. Room temperature fluorescence of 5-chlorouracil tautomers. Chem Phys Lett. 1995;237(3-4):349–55.
[53] Tsuchiya Y, Tamura T, Fujii M, Ito M. Keto-enol tautomer of uracil and thymine. J Phys Chem. 1988;92(7):1760–5.
[54] Chandra AK, Nguyen MT, Zeegers-Huyskens T. Theoretical Study of the Interaction between Thymine and Water. Protonation and Deprotonation Enthalpies and Comparison with Uracil. J Phys Chem A. 1998;102(29):6010–6.
[55] Nguyen MT, Uchimaru T, Zeegers-Huyskens T. Protonation and Deprotonation Enthalpies of Guanine and Adenine and Implications for the Structure and Energy of Their Complexes with Water: Comparison with Uracil, Thymine, and Cytosine. J Phys Chem. 1999; 103(44): 8853-8860.
[56] Kurinovich MA, Lee JK. The Acidity of Uracil from the Gas Phase to Solution: The Coalescence of the N1 and N3 Sites and Implications for Biological Glycosylation. J Am Chem Soc. 2000;122(26):6258–62.
[57] Johnson RC, Power TD, Holt JS, Immaraporn B, Monat JE, Sissoko AA, et al. Electron-Correlated Calculations of Electric Properties of Nucleic Acid Bases. J Phys Chem. 1996;100(48):18875–81.
[58] ?poner J, Leszczynski J, Hobza P. Thioguanine and Thiouracil: Hydrogen-Bonding and Stacking Properties. J Phys Chem A. 1997;101(49):9489–95.
[59] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[60] Kryachko E, Nguyen MT, Zeegers-Huyskens T. Thiouracils: Acidity, Basicity, and Interaction with Water. J Phys Chem A. 2001;105(13):3379–87.
[61] Fuelscher MP, Roos BO. Theoretical Study of the Electronic Spectrum of Cytosine. J Am Chem Soc. 1995;117(7):2089–95.
[62] Lorentzon J, Fuelscher MP, Roos BO. Theoretical Study of the Electronic Spectra of Uracil and Thymine. J Am Chem Soc. 1995;117(36):9265–73.
[63] Broo A, Pearl G, Zerner MC. Development of a Hybrid Quantum Chemical and Molecular Mechanics Method with Application to Solvent Effects on the Electronic Spectra of Uracil and Uracil Derivatives. J Phys Chem A. 1997;101(13):2478–88.
[64] Broo A, Holm?n A. Calculations and Characterization of the Electronic Spectra of DNA Bases Based on ab Initio MP2 Geometries of Different Tautomeric Forms . J Phys Chem A. 1997;101(19):3589–600.
[65] Sowers LC, Sedwick WD, Shaw BR. Hydrolysis of N3-methyl-2'-deoxycytidine: model compound for reactivity of protonated cytosine residues in DNA. Mutat Res. 1989;215(1):131-8.
[66] Sowers LC, Shaw BR, Sedwick WD. Base stacking and molecular polarizability: effect of a methyl group in the 5-position of pyrimidines. Biochem Biophys Res Commun. 1987;148(2):790-4.
[67] Zheltovsky NV, Samoilenko SA, Gubaidullin MI, Kondratyuk IV. Vibrational spectrum and structure of the cytosine complex with N-formyl glycine in the solid phase. Doklady Akad Nauk Ukr SSR. Ser B. 1988; (5):75-8.
[68] 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.
[69] Tamura C, Hata T, Sato S, Sakurai N. Studies on Intermolecular Complex Formation. II. Crystal Structure of Cytosine-N-Benzoylglycine Complx Monohydrate. Bull Chem Soc Jpn. 1972;45(11):3254–61.
[70] Ohki M, Takenaka A, Shimanouchi H, Sasada Y. Complexes between Nucleotide Base and Amino Acid. I. Crystal Structure of Cytosine: N-Formylglycine. Bull Chem Soc Jpn. 1975;48(3):848–52.
[71] Zheltovsky NV, Samoilenko SA, Kolomiets IN, Kondratyuk IV, Stepanyugin AV. Interactions of methyl and glycosyl derivatives of pyrimidine nucleotide bases with amino acid carboxylic group. Biopolym Cell. 1994; 10(6):45-51.
[72] Kondratyuk IV, Kolomiets IN, Samoilenko SA, Zheltovsky NV. A study of complexes between cytosine bases and amino acid carboxylic group by NMR spectroscopy. Biopolym Cell. 1989; 5(6):21-25.
[73] Lancelot G. Hydrogen bonding of amino acid side chains to nucleic acid bases. Biochimie. 1977;59(7):587-96.
[74] Lancelot G. Hydrogen bonding between nucleic acid bases and carboxylic acids. J Am Chem Soc. 1977;99(21):7037-42.
[75] Adams RL. DNA methylation. The effect of minor bases on DNA-protein interactions. Biochem J. 1990;265(2):309-20.
[76] Klimasauskas S, Kumar S, Roberts RJ, Cheng X. Hhal methyltransferase flips its target base out of the DNA helix. Cell. 1994;76(2):357–69.
[77] 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.
[78] 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.
[79] Takenaka A, Sasada Y. Studies on protein-nucleic acid interactions by model crystals. Nihon Kessho Gakkaishi. 1985;27(5):324–36.
[80] Destro R, Marsh RE. The crystal structure of 6-methyluracil-5-acetic acid. Acta Crystallogr B Struct Crystallogr Cryst Chem. 1972;28(10):2971–7.
[81] 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.
[82] Kvick A. Hydrogen bond studies. 89. A neutron diffraction study of hydrogen bonding in 1-methylthymine. J Chem Phys. 1974;61(7):2711-9.
[83] Suck D, Saenger W, Rohde W. X-ray structure of thymidine 5'-carboxylic acid, an inhibitor of thymidine and thymidylate kinase: preferred nucleobase-carboxylic acid hydrogen bonding scheme. Biochim Biophys Acta. 1974;361(1):1-10.
[84] Schwabe JW. The role of water in protein-DNA interactions. Curr Opin Struct Biol. 1997;7(1):126-34.
[85] Bogdanov AA, Ledneva RK. Nucleic-protein recognition. M.: VINITI (Itogi NAuki i Tekhniki, Ser Mol Biol vol 5), 1975; 151 p.
[86] Dewar MJ, Storch DM. Alternative view of enzyme reactions. Proc Natl Acad Sci U S A. 1985;82(8):2225-9.
[87] Petruska J, Sowers LC, Goodman MF. Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity. Proc Natl Acad Sci U S A. 1986;83(6):1559-62.
[88] Petruska J, Goodman MF, Boosalis MS, Sowers LC, Cheong C, Tinoco I Jr. Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc Natl Acad Sci U S A. 1988;85(17):6252-6.
[89] Reddy CK, Das A, Jayaram B. Do water molecules mediate protein-DNA recognition? J Mol Biol. 2001;314(3):619-32.