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Unformatted text preview: Possible Answer #2: Among ribozymes, known catalytic RNAs which yield a 5 phosphate and a 3 hydroxyl are group I and II introns and ribonuclease P (RNase P).1 The mechanism is also given by Kirsebom: Figure 6.1: from Kirsebom(2009)1 In this proposed mechanism, RNAs coordinate a metal (most likely Mg+2 or Mn+2) which complexes with a water molecule (shown in violet). The water is activated such that it acts as a nucleophile, attacking the phosphorous of the phosphate group and thus cleaving the 5 to 3 phosphodiester bond. Although a paper was found (Harris 2008) describing a small (67-74nt) group I intron, I did not choose to use this.2 Introns typically are spliced out of a larger transcript and I was almost certain that this exceeded the 100 nt requirement. In answering this question, I surveyed the RNase P RNAs (RPRs) of several species. The basic idea is to find a minimally catalytically active subset of a ribonuclease P ribozyme (sans protein) and a minimal subset of a targeted substrate it cleaves. These RNAs would then be considered to be a single or composite RNA, thus satisfying the auto-cleaving requirement of the question. RNase Ps which were soley protein or which required complete protein interaction to be catalytically functional were no considered. While the typical unmatured tRNA (with a 5 leader needing the be cleaved) would typically be in excess of 80nt, Forster and Altman (1990) investigated smaller subsets of the unmatured tRNA called external guide sequences.3 With these, one could hope to achieve a smaller footprint for the resultant RNA....
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- Spring '11