ACID-BASE PROPERTIES OF CYTOSINE-CONTAINING OLIGONUCLEOTIDES

• Authors: HOLUBOVÁ Sylvie; BALCAROVÁ Zdeňka; LUBAL Přemysl; TRNKOVÁ Libuše
• Year of publication: 2011
• Type: Conference abstract
• MU Faculty or unit: Faculty of Science
• Description: The protonation equilibria1 of short-chain cytosine homo-oligodeoxyribonucleotides (ODNs) were studied by means of voltammetry and UV-Vis spectra. The work was aimed at ssDNA fragments with different length of the ODN chain. The shortest and longest ODNs were dC3 and dC18, respectively. In order to know the thermodynamic stability of ODNs, the effect of temperature and ionic strength was studied. The protonation constants were calculated by using a hard model (OPIUM or EQUISPEC) 2,3. It was found that the prolongation of the ODN chain supports the formation of more non-canonical bonds in the hemiprotonated (C+-C) pair (“i-motif”). While the exothermic protonation of nucleotides (CMP or dCMP) does not differ, the thermodynamic parameters change for ODNs as a consequence of the existence of an “i-motif” confirmed also by elimination voltammetry with linear scan (EVLS)4. These facts are important for the knowledge of the secondary structure of ODNs containing C nucleobase.

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