Sequence-structure relations of pseudoknot RNA.

Fenix Wd Huang,Linda Ym Li,Christian M Reidys

doi:10.1186/1471-2105-10-s1-s39

Abstract

BackgroundThe analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two mutually crossing bonds (3-noncrossing). These structures are folded by a novel, ab initio prediction algorithm, cross, capable of searching all 3-noncrossing RNA structures. The algorithm outputs the minimum free energy structure.ResultsAfter giving some background on RNA pseudoknot structures and providing an outline of the folding algorithm being employed, we present in this paper various, statistical results on the mapping from RNA sequences into 3-noncrossing RNA pseudoknot structures. We study properties, like the fraction of pseudoknot structures, the dominant pseudoknot-shapes, neutral walks, neutral neighbors and local connectivity. We then put our results into context of molecular evolution of RNA.ConclusionOur results imply that, in analogy to RNA secondary structures, 3-noncrossing pseudoknot RNA represents a molecular phenotype that is well suited for molecular and in particular neutral evolution. We can conclude that extended, percolating neutral networks of pseudoknot RNA exist.

Highlights

The analysis of sequence-structure relations of ribunucleic acid (RNA) is based on a specific notion and folding of RNA structure
While cross is an exponential time algorithm it allows to fold sequences of length 100 with an average folding time of 4.5 minutes. While it is beyond the scope of this paper to present the algorithm cross in detail, the objective of this section is first to sketch its key organization and second to discuss some basic properties of RNA pseudoknot structures
First we describe our findings with respect to the statistics of pseudoknot RNA structures and second we present our data with respect to the particular organization of the sequences in neutral networks

Summary

Introduction

The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two mutually crossing bonds (3noncrossing). These structures are folded by a novel, ab initio prediction algorithm, cross, capable of searching all 3-noncrossing RNA structures. On one hand RNA is described by its primary sequence, a linear string composed of the nucleotides A, G, U and C. The primary sequence embodies the genotypic legislative. RNA, being less structurally constrained than its chemical relative DNA, does fold into 3D-structures, representing the phenotypic executive.

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Conclusion