ISSN print edition: 0366-6352 ISSN electronic edition: 1336-9075 Registr. No.: MK SR 9/7 Published monthly

Spectroscopic study of protonation of oligonucleotides containing adenine and cytosine

Terézia Vojtylová, Dana Dospivová, Olga Třísková, Iveta Pilařová, Přemysl Lubal, Marta Farková, Libuše Trnková, and Petr Táborský

Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic

E-mail: lubal@chemi.muni.cz

Received: 26 November 2008  Revised: 6 April 2009  Accepted: 20 April 2009

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.

Keywords: oligonucleotides - adenine - cytosine - protonation - thermodynamics - chemometrics

Full paper is available at www.springerlink.com.

DOI: 10.2478/s11696-009-0077-8

Chemical Papers 63 (6) 731–737 (2009)