Biopolym. Cell. 2004; 20(6):479-492.
Структура та функції біополімерів
Особливості процесу самоасоціації дезоксигексануклеотиду 5'- d(GpCpApTpGp) і його комплексоутворення з антрацикліновим антибіотиком дауноміцином у водному розчині
1Веселков О. Н., 2Ітон Р. Дж., 1Пахомов В. І., 1Рогова О. В., 1Волинкін В. С., 1Семанін О. В., 1Димант Л. Н., 2Девіс Д. Б.
  1. Севастопольський національний технічний университет
    вул. Університетська, 33, Севастополь, Україна, 99053
  2. Беркбек колледж Лондонского университета
    Малет-стрит, Лондон WC1E 7НХ, Великобритания

Abstract

Методами одно- і двовимірної кореляційної 1Н-ЯМР спектро­скопи (2M-TOCSY і 2M-NOESY) досліджено самоасоціацію самокомплементарного дезоксигексануклеотиду 5'-d(GpCpApTpGp) і його комплексоутворення з протипухлинним ан­тибіотиком дауноміцином у водному розчині. Визначено кон­центраційні і температурні залежності хімічних зсувів необмінних протонів дезоксигексануклеотиду і дауноміцину, за якими розраховано рівноважні константи і термодинамічні параметри (ΔН і ΔS) реакцій утворення дуплексу d(GCATGC) і комплексів гексамеру з антибіотиком. На основі аналізу змін протонних хімічних зсувів гексамеру в області низьких концентрацій і при порівняно невисоких температурах зроблено припущення про формування послідовністю d(GCATGC) ком­пактної структури (наприклад, подібній до шпильки) у водно­му розчині. Побудовано просторові структури итильки та інтеркаляцийного комплексу дауноміцину з дуплексом гексаме­ру d(GCATGC) методами молекулярної механіки з використанням програми X-PLOR. Проведено порівняльний аналіз параметрів утворення комплексів антибіотика дауноміцину з дезоксигексануклеотидами різної послідовності основ у лан­цюзі.

References

[1] Arcamone F., Penco S. Anthracyclines and anthracenedionebased anticancer agents, Ed. J. W. Lown. New York: Elsevier 1988 p. 125.
[2] Martin B, Vaquero A, Priebe W, Portugal J. Bisanthracycline WP631 inhibits basal and Sp1-activated transcription initiation in vitro. Nucleic Acids Res. 1999;27(17):3402-9.
[3] Monneret C. Recent developments in the field of antitumour anthracyclines. Eur J Med Chem. 2001;36(6):483-93.
[4] Kellogg GE, Scarsdale JN, Fornari FA Jr. Identification and hydropathic characterization of structural features affecting sequence specificity for doxorubicin intercalation into DNA double-stranded polynucleotides. Nucleic Acids Res. 1998;26(20):4721-32.
[5] Garbesi A, Bonazzi S, Zanella S, Capobianco ML, Giannini G, Arcamone F. Synthesis and binding properties of conjugates between oligodeoxynucleotides and daunorubicin derivatives. Nucleic Acids Res. 1997;25(11):2121-8.
[6] Arcamone F, Cassinelli G. Biosynthetic anthracyclines. Curr Med Chem. 1998;5(5):391-419.
[7] Gewirtz DA. A critical evaluation of the mechanisms of action proposed for the antitumor effects of the anthracycline antibiotics adriamycin and daunorubicin. Biochem Pharmacol. 1999;57(7):727-41.
[8] Rabbani A, Iskandar M, Ausio J. Daunomycin-induced unfolding and aggregation of chromatin. J Biol Chem. 1999;274(26):18401-6.
[9] Kiyomiya K, Satoh J, Horie H, Kurebe M, Nakagawa H, Matsuo S. Correlation between nuclear action of anthracycline anticancer agents and their binding affinity to the proteasome. Int J Oncol. 2002;21(5):1081-5.
[10] Froelich-Ammon SJ, Osheroff N. Topoisomerase poisons: harnessing the dark side of enzyme mechanism. J Biol Chem. 1995;270(37):21429-32.
[11] Guano F, Pourquier P, Tinelli S, Binaschi M, Bigioni M, Animati F, Manzini S, Zunino F, Kohlhagen G, Pommier Y, Capranico G. Topoisomerase poisoning activity of novel disaccharide anthracyclines. Mol Pharmacol. 1999;56(1):77-84.
[12] Pigram WJ, Fuller W, Hamilton LD. Stereochemistry of intercalation: interaction of daunomycin with DNA. Nat New Biol. 1972;235(53):17-9.
[13] Neidle S, Taylor G. Nucleic acid binding drugs. Part IV. The crystal structure of the anti-cancer agent daunomycin. Biochim Biophys Acta. 1977;479(4):450-9.
[14] Barthwal R, Mujeeb A, Srivastava N, Sharma U. A proton nuclear magnetic resonance investigation of the conformation of daunomycin. Chem Biol Interact. 1996;100(2):125-39.
[15] Wang AH, Ughetto G, Quigley GJ, Rich A. Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-A resolution. Biochemistry. 1987;26(4):1152-63.
[16] Nunn CM, Van Meervelt L, Zhang SD, Moore MH, Kennard O. DNA-drug interactions. The crystal structures of d(TGTACA) and d(TGATCA) complexed with daunomycin. J Mol Biol. 1991;222(2):167-77.
[17] Qu X, Trent JO, Fokt I, Priebe W, Chaires JB. Allosteric, chiral-selective drug binding to DNA. Proc Natl Acad Sci U S A. 2000;97(22):12032-7.
[18] Moore MH, Hunter WN, d'Estaintot BL, Kennard O. DNA-drug interactions. The crystal structure of d(CGATCG) complexed with daunomycin. J Mol Biol. 1989;206(4):693-705.
[19] Ren J, Chaires JB. Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry. 1999;38(49):16067-75.
[20] Chen KX, Gresh N, Pullman B. A theoretical investigation on the sequence selective binding of daunomycin to double-stranded polynucleotides. J Biomol Struct Dyn. 1985;3(3):445-66.
[21] Pullman B. Molecular mechanisms of specificity in DNA-antitumour drug interactions.Adv Drug Res. 1989; 18:1-113.
[22] Chaires JB, Herrera JE, Waring MJ. Preferential binding of daunomycin to 5'ATCG and 5'ATGC sequences revealed by footprinting titration experiments. Biochemistry. 1990;29(26):6145-53.
[23] Neidle S., Sanderson, M. The interaction of daunomycin and adriamycin with nucleic acids. Mol. Aspects of Anti-Cancer Drug Action, Eds S. Neidle, M. J. Waring.-London: Macmillan 1983 pp. 35-57.
[24] Veselkov A. N., Eaton R. J., Baranovsky S. F., Osetrov S. G., Pahomov V. I., Bolotin P. A., Djimant L. N., Davies D. B. NMR analysis of the interaction of antibiotic daunomycin with deoxytetranucleotide, 5'-d(TpGpCpA), in aqueous solution. Biopolym Cell. 1999; 15(2):154-162.
[25] Davies DB, Eaton RJ, Baranovsky SF, Veselkov AN. NMR investigation of the complexation of daunomycin with deoxytetranucleotides of different base sequence in aqueous solution. J Biomol Struct Dyn. 2000;17(5):887-901.
[26] Davies DB, Karawajew L, Veselkov AN. 1H-NMR structural analysis of ethidium bromide complexation with self-complementary deoxytetranucleotides 5'-d(ApCpGpT), 5'-d(ApGpCpT), and 5'-d(TpGpCpA) in aqueous solution. Biopolymers. 1996;38(6):745-57.
[27] Davies D.B., Veselkov A.N. Structural and thermodynamical analysis of molecular complexation by 1H NMR spectroscopy: Intercalation of ethidium bromide with the isomeric deoxytetranucleoside triphosphates 5'-d(GpCpGpC) and 5'-d(CpGpCpG) in aqueous solution. Journal of the Chemical Society - Faraday Transactions. 1996; 92 (19):3545-3557.
[28] Veselkov AN, Iton PDzh, Pakhomov VI, Dymant LN, Devis DB. Structural and thermodynamic analysis of the binding of the antibiotic daunomycin dezoksigeksanukleotidami with different base sequences in the chain by NMR spectroscopy. Zhurn. Struktur. khimii. 2001. 42(2):236-50.
[29] Veselkov AN, Eaton RJ, Pakhomov VI, Semanin AV, Baranovskii SF, Dymant LN, Davies DB. Analysis of complex formation of daunomycin with the deoxyhexanucleotide 5'-d(TpApCpGpTpA) in an aqueous solution from NMR-spectroscopy data. Mol Biol (Mosk). 2001;35(5):868-78
[30] 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.
[31] Veselkov A. N., Osetrov S. G., Pahomov V. I., Veselkova N. V., Davies D. B. Self-association of deoxyoligonucleotide d(GpApCpApTpGpTpC) in aqueous solution: 1H-NMR thermodynamical analysis of the octamer duplex formation. Biopolym. Cell. 1998; 14(3):184-190.
[32] SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A. 1998;95(4):1460-5.
[33] Chou SH, Chin KH, Wang AH. Unusual DNA duplex and hairpin motifs. Nucleic Acids Res. 2003;31(10):2461-74.
[34] Lane AN, Jenkins TC. Thermodynamics of nucleic acids and their interactions with ligands. Q Rev Biophys. 2000;33(3):255-306.
[35] Huang YM, Phillips DR. Thermodynamics of the interaction of daunomycin with DNA. Biophys Chem. 1977;6(3):363-8.
[36] Chaires JB, Dattagupta N, Crothers DM. Self-association of daunomycin. Biochemistry. 1982;21(17):3927-32.
[37] Veselkov AN, Dymant LN, Bolotin PA, Baranovsky SF, Parkes HG, Davies DB. Investigation of the interaction of ethidium bromide with tetradeoxyribonucleotide 5'-d(GpCpGpC) by 1H NMR spectroscopy. Mol Biol (Mosk). 1995; 29(2):326-338.
[38] Davies DB, Pahomov VI, Veselkov AN. NMR determination of the conformational and drug binding properties of the DNA heptamer d(GpCpGpApApGpC) in aqueous solution. Nucleic Acids Res. 1997;25(22):4523-31.
[39] Wijmenga S.S., Mooten M.W., Hilbers C.W. NMR of macromolecules. A practical approach, London: Oxford Univ. press 1993 p. 217.
[40] Nilges M, Clore GM, Gronenborn AM, Brunger AT, Karplus M, Nilsson L. Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry. 1987;26(12):3718-33.
[41] Searle MS, Hall JG, Denny WA, Wakelin LP. NMR studies of the interaction of the antibiotic nogalamycin with the hexadeoxyribonucleotide duplex d(5'-GCATGC)2. Biochemistry. 1988;27(12):4340-9.
[42] Thorpe JH, Teixeira SC, Gale BC, Cardin CJ. Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution. Nucleic Acids Res. 2003;31(3):844-9.
[43] Petersheim M, Turner DH. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 1983;22(2):256-63.
[44] Veselkov AN, Dymant LN, Kodintsev VV, Lisiutin VA, Parkes H, Davies D. Self-association of deoxytetraribonucleoside triphosphates d(TpGpCpA) in an aqueous solution by 1H NMR spectroscopy. Biofizika. 1995;40(2):283-92.
[45] Roy S, Weinstein S, Borah B, Nickol J, Appella E, Sussman JL, Miller M, Shindo H, Cohen JS. Mechanism of oligonucleotide loop formation in solution. Biochemistry. 1986;25(23):7417-23.
[46] Eaton RJ, Veselkov DA, Baranovskiy SF, Osetrov CG, Dymant LN, Devis DB, Veselkov AN. Investigation of self-assembly of molecules anthracycline antibiotic in an aqueous solution by 1H NMR. Khimicheskaya fizika. 2000; 19(2):98-104.
[47] Brunger A.T. X-PLOR, a system for X-ray crystallography and NMR. Yale: Univ. press 1992, 382p.
[48] Parkinson G, Vojtechovsky J, Clowney L, Br?nger AT, Berman HM. New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr D Biol Crystallogr. 1996;52(Pt 1):57-64.
[49] Kale L., Skeel R., Bhandarkar M., Brunner R., Gursoy A., Krawetz N., Phillips J., Shinozaki A, Varadarajan K, Schulten, K. NAMD2: Greater Scalability for Parallel Molecular Dynamics J Comput Phys. 1999; 151 (1):283-312.
[50] MacKerell Jr. A.D., Banavali N.K. All-Atom Empirical Force Field for Nucleic Acids: II. Application to Molecular Dynamics Simulations of DNA and RNA in Solution. J Comput Chem 2000; 21 (2):105-120.
[51] Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. Comparison of simple potential functions for simulating liquid water. J Chem Phys; 1983; 79 (2):926-935.
[52] Kleywegt G.J. Dictionaries for heteros. News from Uppsala Software Factory-5, 1998; p. 4.
[53] Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000;28(1):235-42.
[54] Berendsen H.J.C., Postma J.P.M., Van Gunsteren W.F., Dinola A., Haak J.R. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984; 81 (8):3684-3690.
[55] Humphrey W., Dalke A., Schulten K. VMD: Visual molecular dynamics. J Mol Graph 1996; 14 (1):33-8.
[56] Giessner-Prettre C, Pullman B. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q Rev Biophys. 1987;20(3-4):113-72.
[57] Poltev V.I., Teplukhin A.V. Conformational implication of some nucleotide sequences.Int. J. Quant. Chem., 1989; 35:91-102.
[58] Dickerson RE. Definitions and nomenclature of nucleic acid structure parameters. J Biomol Struct Dyn. 1989;6(4):627-34.
[59] Schuerman G.S., Van Meervelt L. Conformational flexibility of the DNA backbone. 2000; 122 (2):232-240.
[60] Howerton SB, Nagpal A, Williams LD. Surprising roles of electrostatic interactions in DNA-ligand complexes. Biopolymers. 2003;69(1):87-99.