title: Synthesis, stability, and protonation studies of a self-complementary dodecamer containing the modified nucleoside 2'-deoxyzebularine.
abstract: 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 (50 degrees C 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 37 degrees C were studied by means of spectroscopically monitored titrations. For the K nucleoside, a pK(a) value of 3.13 +/- 0.09 was obtained. For the dodecamer, four acid-base species were found in the pH range 2-12, with pK(a) 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.
authors.affiliation: Department of Analytical Chemistry, University of Barcelona, Martí i Franqués, 1-11, E-08028 Barcelona, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Vives
authors.forename: R
authors.initials: R
authors.lastname: Eritja
authors.forename: R
authors.initials: R
authors.lastname: Tauler
authors.forename: V E
authors.initials: VE
authors.lastname: Marquez
authors.forename: R
authors.initials: R
authors.lastname: Gargallo
mesh_terms: D002851:Chromatography, High Pressure Liquid; D003562:Cytidine / Q000031:analogs & derivatives; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D013058:Mass Spectrometry; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011522:Protons; D011741:Pyrimidine Nucleosides / Q000138:chemical synthesis* / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013696:Temperature; D013997:Time Factors
chemical_list: D009838:Oligodeoxyribonucleotides; D011522:Protons; D011741:Pyrimidine Nucleosides; D003562:Cytidine; C009131:pyrimidin-2-one beta-ribofuranoside; D004247:DNA