The incorporation of
ribonucleotides in
DNA has attracted considerable notice in recent years, since the pool of
ribonucleotides can exceed that of the
deoxyribonucleotides by at least 10-20-fold, and single
ribonucleotide incorporation by
DNA polymerases appears to be a common event. Moreover
ribonucleotides are potentially mutagenic and lead to
genome instability. As a consequence, errantly incorporated
ribonucleotides are rapidly repaired in a process dependent upon
RNase H enzymes. On the other hand, global genomic nucleotide excision repair (NER) in prokaryotes and eukaryotes removes damage caused by covalent modifications that typically distort and destabilize
DNA through the production of lesions derived from bulky chemical
carcinogens, such as
polycyclic aromatic hydrocarbon metabolites, or via crosslinking. However, a recent study challenges this lesion-recognition paradigm. The work of Vaisman et al. (2013) [34] reveals that even a single
ribonucleotide embedded in a
deoxyribonucleotide duplex is recognized by the bacterial NER machinery in vitro. In their report, the authors show that spontaneous mutagenesis promoted by a steric-gate pol V mutant increases in uvrA, uvrB, or uvrC strains lacking rnhB (encoding
RNase HII) and to a greater extent in an NER-deficient strain lacking both
RNase HI and
RNase HII. Using purified UvrA, UvrB, and UvrC
proteins in in vitro assays they show that despite causing little distortion, a single
ribonucleotide embedded in
a DNA duplex is recognized and doubly-incised by the NER complex. We present the hypothesis to explain the recognition and/or verification of this small lesion, that the critical 2'-OH of the
ribonucleotide - with its unique electrostatic and hydrogen bonding properties - may act as a signal through interactions with
amino acid residues of the prokaryotic NER complex that are not possible with
DNA. Such a mechanism might also be relevant if it were demonstrated that the eukaryotic NER machinery likewise incises an embedded
ribonucleotide in
DNA.