Abstract
Acidobasic properties of purine and pyrimidine bases (adenine, cytosine) and relevant nucleosides (adenosine, cytidine) were studied by means of glass-electrode potentiometry and the respective dissociation constants were determined under given experimental conditions (I = 0.1 M (NaCl), t = (25.0 ± 0.1) °C): adenine (pK HL = 9.65 ± 0.04, pK H2L = 4.18 ± 0.04), adenosine (pK H2L = 3.59 ± 0.05), cytosine (pK H2L = 4.56 ± 0.01), cytidine (pK H2L = 4.16 ± 0.02). In addition, thermodynamic parameters for bases: adenine (ΔH 0 = (−17 ± 4) kJ mol−1, ΔS 0 = (23 ± 13) J K−1 mol−1), cytosine (ΔH 0 = (−22 ± 1) kJ mol−1, ΔS 0 = (13 ± 5) J K−1 mol−1) were calculated. Acidobasic behavior of oligonucleotides (5′CAC-CAC-CAC3′ = (CAC)3, 5′AAA-CCC-CCC3′ = A3C6, 5′CCC-AAA-CCC3′ = C3A3C3) was studied under the same experimental conditions by molecular absorption spectroscopy. pH-dependent spectral datasets were analyzed by means of advanced chemometric techniques (EFA, MCR-ALS) and the presence of hemiprotonated species concerning (C+-C) a non-canonical pair (i-motif) in titled oligonucleotides was proposed in order to explain experimental data obtained according to literature.
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References
Burger, K. (Ed.) (1990). Biocoordination chemistry: Coordination equilibria in biologically active systems. Chichester: Ellis Horwood.
Cantor, C. R., Warshaw, M. M., & Shapiro, H. (1970). Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides. Biopolymers, 9, 1059–1103. DOI: 10.1002/bip.1970.360090909.
Casassas, E., Tauler, R., & Marqués, I. (1994). Interactions of H+ and Cu(II) ions with poly(adenylic acid): Study by factor analysis. Macromolecules, 27, 1729–1737. DOI: 10.1021/ma00085a010.
Casassas, E., Gargallo, R., Izquierdo-Ridorsa, A., & Tauler, R. (1995). Application of a multivariate curve resolution procedure for the study of the acid-base and copper(II) complexation equilibria of polycytidylic acid. Reactive and Functional Polymers, 27, 1–14. DOI: 10.1016/1381-5148(95)00025-B.
Gampp, H., Maeder, M., Meyer, C. J., & Zuberbühler, A. D. (1985). Calculation of equilibrium constants from multiwavelength spectroscopic data — II. SPECFIT: two user-friendly programs in BASIC and standard FORTRAN 77. Talanta, 32, 251–264. DOI: 10.1016/0039-9140(85)80077-1.
Gargallo, R., Cuesta-Sánchez, F., Izquierdo-Ridorsa, A., & Massart, D. L. (1996a). Application of Eigenstructure tracking analysis and SIMPLISMA to the study of the protonation equilibria of cCMP and several polynucleotides. Analytical Chemistry, 68, 2241–2247. DOI: 10.1021/ac950596m.
Gargallo, R., Tauler, R., & Izquierdo-Ridorsa, A. (1996b). Influence of selectivity and polyelectrolyte effects on the performance of soft-modelling and hard-modelling approaches applied to the study of acid-base equilibria of polyelectrolytes by spectrometric titrations. Analytica Chimica Acta, 331, 195–205. DOI: 10.1016/0003-2670(96)00205-X.
Gargallo, R., Tauler, R., & Izquierdo-Ridorsa, A. (1997a). Application of a multivariate curve resolution procedure to the analysis of second-order melting data of synthetic and natural polynucleotides. Analytical Chemistry, 69, 1785–1792. DOI: 10.1021/ac960809n.
Gargallo, R., Trauler, R., & Izquierdo-Ridorsa, A. (1997b). Acid-base and copper(II) complexation equilibria of poly(inosinic)-poly(cytidylic) acid. Biopolymers, 42, 271–283. DOI: 10.1002/(SICI)1097-0282(199709)42:3〈271::AID-BIP1〉3.0.CO;2-J.
Gargallo, R., Sotriffer, C. A., Liedl, K. R., & Rode, B. M. (1999). Application of multivariate analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pK a prediction for nucleic acids components. Journal of Computer-Aided Molecular Design, 13, 611–623. DOI: 10.1023/A:1008005522776.
Izquierdo-Ridorsa, A., Casassas, E., Gargallo, R., Marqués, I., & Tauler, R. (1996). A comparative study of polyelectrolyte effects and conformation changes in several purine and pyrimidine homopolyribonucleotiedes. Reactive and Functional Polymers, 28, 127–137. DOI: 10.1016/1381-5148(95)00049-6.
Jaumot, J., Vives, M., & Gargallo, R. (2004). Application of multivariate resolution methods to the study of biochemical and biophysical processes. Analytical Biochemistry, 327, 1–13. DOI: 10.1016/j.ab.2003.12.028.
de Juan, A., Izquierdo-Ridorsa A., Gargallo, R., Tauler, R., Fonrondona, G., & Casassas, E. (1997). Three-way curve resolution applied to the study of solvent effects on the thermodynamic and conformational transitions related to the protonation of polycytidylic acid. Analytical Biochemistry, 249, 174–183. DOI: 10.1006/abio.1997.2175.
de Juan, A., Casassas, E., & Tauler, R. (2000). Soft modeling of analytical data. In R. A. Meyers (Ed.), Encyclopedia of analytical chemistry: Applications, theory and instrumentation (Vol. 11, pp. 9800–9837). New York: Wiley.
Kývala, M., Lubal, P., & Lukeš, I. (1998). Determination of equilibrium constants with the OPIUM computer program. In IX Spanish — Italian and Mediterranean Congress on Thermodynamics of Metal Complexes SIMEC’98, 2–5 June, 1998. Girona, Spain. http://www.natur.cuni.cz/~kyvala/opium. html
Lubal, P., & Havel, J. (1997a). Spectrophotometric and potentiometric study of uranyl hydrolysis in perchlorate medium. Is derivative spectrophotometry suitable for search of the chemical model? Chemical Papers, 51, 213–220.
Lubal, P., & Havel, J. (1997b). The study of complex equilibria of uranium(VI) with selenate. Talanta, 44, 457–466. DOI: 10.1016/S0039-9140(96)02103-0.
Martell, A. E., Smith, R. M., & Motekaitis, R. (2004). NIST Critically selected stability constants of metal complexes database, Version 8.0. Ghaitersburg, MD, USA: NIST.
Mikelová, R., Trnková, L., Jelen, F., Adam, V., & Kizek, R. (2007). Resolution of overlapped reduction signals in short hetero-oligonucleotides by elimination voltametry. Electroanalysis, 19, 348–355. DOI: 10.1002/elan.200603739.
Saenger, W. (1984). Principles of nucleic acid structure. New York: Springer Verlag.
Sigel, H., & Griesser, R. (2005). Nucleside 5′-triphosphates: self-association, acid-base, and metal-ion binding properties in solution. Chemical Society Reviews, 34, 875–900. DOI: 10.1039/b505986k.
Trnková, L., Jelen, F., & Postbieglová, I. (2003). Application of elimination voltametry to the resolution of adenine and cytosine signals in oligonucleotides. I. Homooligodeoxynucleotides dA9 and dC9. Electroanalysis, 15, 1529–1535. DOI: 10.1002/elan.200302719.
Trnková, L., Jelen, F., & Postbieglová, I. (2006). Application of elimination voltametry to the resolution of adenine and cytosine signals in oligonucleotides. II. Heterooligodeoxynucleotides with different sequences of adenine and cytosine nucleotides. Electroanalysis, 18, 662–669. DOI: 10.1002/elan.200503447.
Trnková, L., Mach, S., Mikelová, R., & Farková, M. (2009). Unpublished results.
Vorlíčková, M., Kypr, J., & Sklenář, V. (2005). Nucleic acids: Spectroscopic methods. In P. J. Worsfold, A. Townshend, and C. S. Poole (Eds.), Encyclopedia of analytical science (2nd Ed., Vol. 6, pp. 391–399). Oxford: Elsevier.
Warshaw, M. M., & Tinoco, I., Jr. (1966). Optical properties of sixteen dinucleoside phosphates. Journal of Molecular Biology, 20, 29–38. DOI: 10.1016/0022-2836(66)90115-X.
Zemánek, M., Kypr, J., & Vorlíčková, M. (2005). Conformational properties of DNA containing (CCA)n and (TGG)n trinucleotide repeats. International Journal of Biological Macromolecules, 36, 23–32. DOI: 10.1016/j.ijbiomac.2005.03.005.
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Vojtylová, T., Dospivová, D., Třísková, O. et al. Spectroscopic study of protonation of oligonucleotides containing adenine and cytosine. Chem. Pap. 63, 731–737 (2009). https://doi.org/10.2478/s11696-009-0077-8
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DOI: https://doi.org/10.2478/s11696-009-0077-8