Title: Stability of RNA structural motifs and its influence on editing efficiency by adenosine deaminases

Authors: Vinhthuy Phan, Allen Thomas, Kriangsiri Malasri, Carrie Hayes Sutter

Addresses: Department of Computer Science, University of Memphis, Memphis, TN 38152, USA. ' Bioinformatics Program, University of Memphis, Memphis, TN 38152, USA. ' Department of Computer Science, University of Memphis, Memphis, TN 38152, USA. ' Department of Biology, University of Memphis, Memphis, TN 38152, USA

Abstract: We propose a novel method to estimate editing efficiency by adenosine deaminases that act on RNA (ADARs). The method employs the notion of stability of secondary structure in the vicinity of edited sites during transcription. Such an analysis of |dynamic| structural motifs of RNA is important because as a pre-spliced RNA is being transcribed and elongated, its entire structure, and thus its local structures, may change drastically. Our simulation showed that the stability of structures in the vicinity of edited sites correlates moderately highly with editing efficiency of edited sites recently established in laboratory experiments.

Keywords: RNA editing; ADAR; RNA motif; structural motifs; dynamic motifs; edited site prediction; editing efficiency; adenosine deaminases; bioinformatics; stability.

DOI: 10.1504/IJBRA.2010.031290

International Journal of Bioinformatics Research and Applications, 2010 Vol.6 No.1, pp.21 - 36

Received: 22 May 2008
Accepted: 12 Mar 2009
Published online: 27 Jan 2010 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article