Synthesis, stability, and protonation studies of a self-complementary dodecamer containing the modified nucleoside 2'-deoxyzebularine

17 pages, 6 figures, 1 scheme.-- PMID: 14691937 [PubMed].-- Available online Nov 3, 2003.The nucleoside 2'-deoxyzebularine (K) was incorporated into the self-complementary dodecamer 5-CGTACGKGTACG-3 by solid-phase 2-cyanoethylphosphoramidite chemistry using dimethoxytrityl (DMT) as the 5-hydroxyl protecting group. Standard synthesis cycles using trichloroacetic acid and short ammonia treatment (50ºC for 30 min) were found to be the optimal conditions to obtain the desired dodecamer with minimum acid and basic degradation of the acid- and base-sensitive 2-pyrimidinone residue. The protonation equilibria of the K nucleoside and of the dodecamer at 37ºC were studied by means of spectroscopically monitored titrations. For the K nucleoside, a pKa value of 3.13 0.09 was obtained. For the dodecamer, four acid-base species were found in the pH range 2-12, with pKa values of 9.60 0.07, 4.46 0.16, and 2.87 0.19. Melting experiments were carried out to confirm the proposed acid-base concentration profiles. Finally, kinetic experiments were also carried out at several pH values to evaluate the stability of the K nucleoside and of the dodecamer. An increased stability was shown by the K nucleoside when incorporated into the dodecamer. Multivariate methods based on both hard- and soft-modeling were applied for the analysis of spectroscopic data, allowing the estimation of concentration profiles and pure spectra.Ministerio de Educación y Cultura; Grant Number: MCYT BQ42000-0788, Generalitat de Catalunya; Grant Number: 2001SGR00056.Peer reviewe