Ultraviolet-Driven Self-Repair in Chimeric d(GAUU) Outcompetes Damage Formation

Abstract

The stability of nucleic acids under intense ultraviolet (UV) irradiation was key to the persistence of life on Earth. Among the canonical nucleobases, pyrimidines are most susceptible to UV photodamage, yielding cyclobutane pyrimidine dimers (CPDs) that distort nucleic acid conformation and interfere with function. Prior to the emergence of enzymatic CPD repair, e.g. via photolyases, intrinsic processes like UV-induced self-repair may have influenced the perseverance of ancient nucleic acids in high-UV early Earth environments. Our previous work reported self-repair quantum yields for the canonical CPD-containing RNA sequence GAU=U (0.23%), and the DNA sequence d(GAT=T) (0.44%), but the origin of the disparity is unclear. Here, we address this missing link experimentally by measuring the self-repair of the chimeric CPD-containing sequence d(GAU=U) to d(GAUU) using UV/Vis spectroscopy and HPLC analysis. Upon irradiation at 285 nm, its repair quantum yield (1.16%) exceeded the repair yields of GAU=U, d(GAT=T) and T=TAG, as well as the reported CPD formation yields in d(TT) and UU. We then measured damage formation in d(UU) and found a damage quantum yield of 0.74%, demonstrating that d(GAUU), to our knowledge, is the first reported oligonucleotide in which the self-repair quantum yield exceeds the measured net damage quantum yield under identical irradiation conditions. These results highlight the combined importance of backbone conformation and nucleobase identity in governing self-repair and suggest that chimeric sequences could have been especially UV-resistant precursors to canonical DNA. The enhanced repair of dU-containing DNA implies that replacement of dU with T in primordial DNA may have required the prior evolution of efficient enzymatic repair of UV photodamage.