Differential Destabilization of the DNA Oligonucleotide Double Helix by a T·G Mismatch, 3,N4-Ethenocytosine, 3,N4-Ethanocytosine, or an 8-(Hydroxymethyl)-3,N4-ethenocytosine Adduct Incorporated into the Same Sequence Contexts

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Abstract
The T·G mismatch and the exocyclic adduct 3,N4-ethenocytosine (εC) are repaired by the same enzyme, the human G/T(U) mismatch-DNA glycosylase (TDG). This enzyme removes the T, U, or εC base from duplex DNA. The rate of cleavage was found to differ with the lesion and was also affected by neighbor sequences [Hang, B., Medina, M., Fraenkel-Conrat, H., and Singer, B. (1998) Proc. Natl. Acad. Sci. U.S.A.95, 13561−13566]. Since sequence influences duplex stability, we determined the thermodynamic stability of T·G and εC-containing 15-mer duplexes in which the bases flanking the lesion were systematically varied. The duplexes contained central 5‘-TTXTT, 5‘-AAXAA, 5‘-CCXCC, or 5‘-GGXGG sequences, where X is T, εC, or two closely related structural derivatives of εC: 3,N4-ethanocytosine (EC) and 8-(hydroxymethyl)-εC (8-HM-εC). Each of the four lesions, incorporated opposite G, decreased both the thermal (Tm) and thermodynamic stability (ΔG°37) of the 15-mer control duplexes. On the basis of the Tm and ΔG°37 values, the order of destabilization of the TTXTT sequence in 15-mer duplexes was as follows: 8-HM-εC > EC > εC > T·G. The ΔTm values range from −15.8 to −9.5 °C when Ct = 8 μM. Duplexes with flanking AA or TT neighbors were more destabilized, by an average of 2 °C, than those with flanking GG or CC neighbors. The base opposite the modified base also influenced duplex stability. Within the TT context, of the four changed bases opposite the adducts, C had the greatest destabilizing effect, up to −18.4 °C. In contrast, a G opposite an adduct was generally the least destabilizing, and the smallest value was −3.0 °C. Destabilizations were enthalpic in origin. Thus, this work shows that independently changing the modified base, the sequence, or the base opposite the lesion each affects the stability of the duplex, to significantly varying extents. The potential contribution of the thermodynamic stability to repair efficiency is discussed.