Thermodynamic and structural analysis of complexes of self-complementary deoxyhexanucleotides 5 -d(GpCpApTpGpC) and 5 -d(GpCpTpApGpC) with anthracycline antibiotic daunomycin
Keywords:
deoxyhexanucleotide, d(GCAТGC), d(GCТAGC), daunomycin, hydrophobic interactions, NMR spectroscopy, molecular dynamics
Abstract
The investigation of the complexation of the anthracycline antibiotic daunomycin with the self-complementary deoxyhexanucleotides d(GCATGC) and d(GCTAGC) in aqueous solution is studied by one- and two-dimensional 1H NMR spectroscopy and molecular dynamics simulations. The equilibrium thermodynamic parameters of the complex formation and the spatial structures of the complexes are obtained. It was found that the antibiotic affinity to d(GCATGC) is higher that to d(GCATGC). Comparative analysis of the thermodynamic and conformational parameters of the hexamer complexes with the antibiotic enabled to conclude on the possible reasons of different affinities of daunomycin with the duplex forms of the deoxyhexanucleotide sequences studied.
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References
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Neidle S, Abraham Z. Structural and sequence-dependent aspects of drug intercalation into nucleic acids. CRC Crit Rev Biochem. 1984;17(1):73-121.
Chaires JB. Studies on the interaction of daunomycin with deoxypolynucleotides. Biochemistry. 1983;22(18):4204-211.
Chaires JB, Dattagupta N, Crothers D. Studies on interaction of anthracycline antibiotics and deoxyribonucleic acid: equilibrium binding studies on interaction of daunomycin with deoxyribonucleic acid. Biochemistry. 1982;21:3933-940.
Chaires JB, Fox KR, Herrera JE, Britt M, Waring MJ. Site and sequence specificity of the daunomycin - DNA interaction. Biochemistry. 1987;27:8227-36.
Newlin DD, Miller KJ, Pilch DF. Interactions of molecules with nucleic acids. Biopolymers. 1984;23(1):139-58.
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.
Veselkov AN, Iton RDzh, Pakhomov VI, Dymant LN, Devis DB. Strukturnyi i termodinamicheskii analiz sviazyvaniia antibiotika daunomitcina s dezoksigeksanukleotidmi razlichnoi posledovatelnosti osnovanii v tcepi metodom IaMR spektroskopii. Zhurn. struktur. khimii. 2001;42(2):236-50. (in Russian)
Iton RDzh, Veselkov DA, Pakhomov VI, Baranovskii SF, Bolotin PA, Osetrov SG, et al. Issledovanie sikvens-spetcifichnosti kompleksoobrazovaniia antibiotika daunomitcina s izomernymi dezoksitetranukleotidami metodom IaMR-spektroskopii. Molekuliar. biologiia. 1999;33(5):803-13. (in Russian)
Veselkov AN, Iton RDzh, Baranovskii SF, Osetrov SG, Bolotin PA, Dymant LN, et al. Kompleksoobrazovanie antibiotika daunomitcina s dezoksitetraribonukleozidtrifosfatom v vodnom rastvore. Zhurn. struktur. khimii. 1999;40:276-86. (in Russian)
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. Str. Dyn. 2000;17(5):887-901.
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.
Frederick CA, Williams LD, Ughetto G, van der Marel GA, van Boom JH, Rich A, Wang AH. Structural comparison of anticancer drug-DNA complexes: Adriamycin and daunomycin. Biochemistry. 1990;29(10): 2538-49.
Nunn CM, Van Meervelt L, Zhang S, Moore MH, Kennard O. DNA-drug interactions-the crystal structures of d(TGTACA) complexed with daunomycin. J. Mol. Biol. 1991;22(2):167-77.
Pahomov VI, Rogova OV, Volynkin VS, Veselkov KA, Hernandez Santiago AA, Semanin AV, et al. Distinctive features of complexation of anthracycline antibiotic daunomycin with deoxyhexanucl d(GCATGC) in aqueous solution: 1D- and 2D-NMR analysis. SPIE Proceeding. 2004;5507:333-41.
Chaires JB, Dattagupta N, Crothers D. Self-association of daunomycin. Biochemistry. 1982;21:3927-32.
Ravishanker G, Auffinger P, Langley DR, Jayaram B, Young MA, Beveridge DL. Treatment of Counterions in Computer Simulations of DNA. Rev. in Comp. Chem. 1997;11:317-72.
Cieplak P, Rao SN, Grootenhuis PDJ, Kollman PA. Free Energy Calculation on Base Specificity of Drug-DNA Interaction: Application to Daunomycin and Acridine Intercalation into DNA. Biochemistry. 1990;29:717-27.
Wijmendga SS, Mooten MW, Hilbers SW. NMR of nucleic acids: from spectrum to structure. NMR of macromolecules. A practical approach. Oxford: IRL Press; 1993. 437 p.
Veselkov AN, Karawajew L, Davies DB. 1H NMR Structural analysis of Ethidium Bromide Complexation with Self- Complementary Deoxytetranucleotides 5'-d(ApCpGpT), 5'-d(ApGpCpT) and 5'-(TpGpCpA) in Aqueous Solution. Biopolymers. 1996;38:745-57.
Ts'o POP. Bases, nucleosides, and nucleotides. In Basic Principles of Nucleic Acid Chemistry. N.Y.: Academic Press; 1974. P. 454-584.
Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Mayer E, Liedi KR. Daunomycin Intercalation Stabilizes Distinct Backbone Conformations of DNA. J. Biomol. Struct. Dyn. 2004;21(5):713-23.
Kopka ML, Fratini AV, Drew HR, Dickerson RE. Ordered water structure around a B-DNA dodecamer. A quantitative study. J. Mol. Biol. 1983;163:129-46.
Published
2007-06-05
Cited
How to Cite
Kostjukov, V. V., Rogova, O. V., & Evstigneev, M. P. (2007). Thermodynamic and structural analysis of complexes of self-complementary deoxyhexanucleotides 5 -d(GpCpApTpGpC) and 5 -d(GpCpTpApGpC) with anthracycline antibiotic daunomycin. Biophysical Bulletin, 1(17), 15-23. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/12840
Section
Molecular biophysics
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