Article

Information, probability, and the abundance of the simplest RNA active sites

Department of Computer Science, University of Colorado at Boulder, 430 UCB, Boulder, CO 80309-0430, USA.
Frontiers in Bioscience (Impact Factor: 3.52). 02/2008; 13(16):6060-71. DOI: 10.2741/3137
Source: PubMed

ABSTRACT

The abundance of simple but functional RNA sites in random-sequence pools is critical for understanding emergence of RNA functions in nature and in the laboratory today. The complexity of a site is typically measured in terms of information, i.e. the Shannon entropy of the positions in a multiple sequence alignment. However, this calculation can be incorrect by many orders of magnitude. Here we compare several methods for estimating the abundance of RNA active-site patterns in the context of in vitro selection (SELEX), highlighting the strengths and weaknesses of each. We include in these methods a new approach that yields confidence bounds for the exact probability of finding specific kinds of RNA active sites. We show that all of the methods that take modularity into account provide far more accurate estimates of this probability than the informational methods, and that fast approximate methods are suitable for a wide range of RNA motifs.

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    • "By many kinds of calculations, RNA and ribozymes are likely to have played early roles in life on Earth (Atkins et al. 2011). However, even small known ribozymes can contain dozens of required ribonucleotides, making them statistically infrequent (Kennedy et al. 2008), unstable because adjacent nucleotides can be aligned for easy hydrolysis (Soukup and Breaker 1999), burdened with replication that is easily poisoned by chirally related sugars (Joyce et al. 1984b), and difficult to extricate from stable double-stranded replicative intermediates (Sievers and Von Kiedrowski 1994; Engelhart et al. 2013). "
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    • "The modeled route to this goal (Fig. 1) combines several straightforward ideas. Firstly, I have previously emphasized the value of molecular simplicity in making a structure accessible to primitive synthesis (Illangasekare and Yarus, 1999; Kennedy et al., 2008; Yarus, 2011b). Aminoacyl-RNA synthesis via a 5 nt ribozyme is a characterized experimental example (Yarus, 2011b); such a molecule would occur via untemplated RNA synthesis as soon as mildly activated nucleotides existed. "
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    • "Finally, the second loop in the Trp site has several specific implications. First, previous estimates of the probability of finding particular types of RNA sites (Knight and Yarus 2003; Knight et al. 2005; Kennedy et al. 2008) may be inflated by failing to take into account undetectable, but nonetheless important parts of the active site, such as those revealed here. Second, embedding the site in a random-sequence background provides an effective means for detecting such FIGURE 7. (A) A newly defined tryptophan binding site derived from selection, construction, mutagenesis, and massed sequence analysis of selected pools. "
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