Degradation of Cytosine Radical Cations in 2'-Deoxycytidine and in i-Motif DNA: Hydrogen-Bonding Guided Pathways.

Radical cations of nucleobases are key intermediates causing genome mutation, among which cytosine C is of growing importance because the ensuing cytosine oxidation causes GC → AT transversions in DNA replication. Although the chemistry and biology of steady-state C oxidation products have been characterized, time-resolved study of initial degradation pathways of C is still at the preliminary stage. Herein, we choose i-motif, a unique C-quadruplex structure composed of hemiprotonated base pairs C(H):C, to examine C degradation in a DNA surrounding without interference of G bases. Comprehensive time-resolved spectroscopy were performed to track C dynamics in i-motif and in free base dC. The competing pathways of deprotonation (1.4 × 10 s), tautomerization (8.8 × 10 s), and hydration (5.3 × 10 s) are differentiated, and their rate constants are determined for the first time, underlining the strong reactivity of C. Distinct pathway is observed in i-motif compared with dC, showing the prominent features of C hydration forming C(5OH) and C(6OH). By further experiments of pH-dependence, comparison with single strand, and with Ag mediated i-motif, the mechanisms of C degradation in i-motif are disclosed. The hydrogen-bonding within C(H):C plays a significant role in guiding the reaction flux, by blocking the tautomerization of C(-H) and reversing the equilibrium from C(-H) to C. The C radicals in i-motif thus retain more cation character, and are mainly subject to hydration leading to lesion products that can induce disruption of i-motif structure and affect its critical roles in gene-regulation.