Novel base pairing in nucleic acids: CH donor group mediated base pairing involving 3-methyluracil

Abstract

3-Methyluracil (3MU) has previously been shown in transcription and ribosome binding studies conducted in vitro to function like one or more of the canonical bases. Due to the presence of the 3-methyl “blocking group”, it was suggested that 3MU could not base pair with the normal bases. It is now shown that base-pairing trends obtained with a recently force-fit computational method are consistent with previously observed transcription and ribosome binding trends. The present work indicates the “blocked” Watson—Crick donor site on 3MU is capable of mediating recognition interactions occurring in the virtual absence of competition from classical hydrogen-bond donors. Thus the experimental trends are rationalized with base pairs containing one classical hydrogen bond and one non-classical hydrogen bond containing a CH donor group.