To knot or not to knot? Examination of 16S ribosomal RNA models

The presence of topological knots in large RNA structures is highly unlikel y given that 1) no RNA structures determined thus far contain topological k nots, 2) secondary structure maps for most RNA molecules are knot free, 3) there are no known RNA topoisomerases, and 4) it is difficult to imagine ho w knots could be formed specifically and uniquely during transcription. Sin ce native RNA structures probably lack topological knots, models of these R NA molecules should be free of knots as well. Therefore, we have examined f our existing models for the 30S ribosomal subunit to determine if any of th e three domains of the 16S rRNA molecule is knotted. We found that all but one model had at least one knotted domain. We conclude that models of large RNA molecules should be examined for knotting before publication.