Enhanced Cleavage at Abasic Sites within Clustered Lesions in Nucleosome Core Particles

Clustered lesions are a hallmark of γ-radiolysis, but are produced by other damaging agents as well. Bistranded clustered lesions are precursors to double-strand breaks and are challenging to repair, thus making them an especially deleterious form of DNA damage. An abasic site (AP) is an alkaline-labile lesion frequently present in clustered lesions. Strand scission at an AP site is accelerated ≈100-fold in nucleosome core particles (NCPs). We examined how AP reactivity was affected within clustered lesions in NCPs. The rate constant of strand scission is increased as much as 2.5-fold in the presence of a proximal abasic site or thymidine glycol in the complementary strand. A proximal mispair has a similar effect on AP reactivity. Increased AP reactivity within a clustered lesion correlates with decreased UV melting temperatures of the corresponding duplexes compared to one containing an isolated abasic site. However, the thermodynamics of duplex melting do not correlate with AP reactivity within different clustered lesions. Overall, increased AP reactivity within clustered lesions is attributed to greater access of histone proteins to the lesion due to decreased duplex stability.