Nonhomologous end joining of complex DNA double-strand breaks with proximal thymine glycol and interplay with base excision repair.

•Thymine glycol (Tg) at the 3′-terminal or penultimate position of a DNA double-strand break impairs nonhomologous end joining.•Tg at the third position from a 3′ terminus has little effect on end joining•In general, ligation precedes Tg excision and replacement in these substrates.•Base excision repair of Tg at the fifth position from a 3′ terminus interferes with end joining.•The extent of processing for 3′ proximal Tg lesions reflects the intrinsic specificity of hNTH.