Knot your average RNA: The Chlorella virus pyrimidine dimer‐specific glycosylase intron

Abstract

In vitro transcriptions of the 98‐nucleotide intron found in the Chlorella virus pdg locus always produce at least one slower‐migrating species (as ~10–20% of the total transcription yield) in addition to the expected transcripts. Extensive characterization of these slower‐migrating products suggests that they are knotted RNA molecules, which we call knRNAs, previously observed only by the ligation of synthetic ribo‐oligonucleotides. An RNA with knot‐forming interactions would display physical properties unique to this topology. The observation that knotting cannot be induced upon renaturation of the full length intron argues that the co‐transcriptional folding pathway that allows knotting is inaccessible during post‐transcriptional folding. We propose that knotting is the result of co‐transcriptional mis‐folding that allows the 3′‐end of an intron to become threaded through an internal loop during formation of its pseudoknotted structure, resulting in an open knot. Because it occurs during a biologically relevant process, this phenomenon may occur in vivo as well.