Abstract
RNA aptamers readily recognize small organic molecules, polypeptides, as well as other nucleic acids in a highly specific manner. Many such aptamers have evolved as parts of regulatory systems in nature. Experimental selection techniques such as SELEX have been very successful in finding artificial aptamers for a wide variety of natural and synthetic ligands. Changes in structure and/or stability of aptamers upon ligand binding can propagate through larger RNA constructs and cause specific structural changes at distal positions. In turn, these may affect transcription, translation, splicing, or binding events. The RNA secondary structure model realistically describes both thermodynamic and kinetic aspects of RNA structure formation and refolding at a single, consistent level of modelling. Thus, this framework allows studying the function of natural riboswitches in silico. Moreover, it enables rationally designing artificial switches, combining essentially arbitrary sensors with a broad choice of read-out systems. Eventually, this approach sets the stage for constructing versatile biosensors.
Highlights
Non-protein-coding RNAs regulate diverse cellular processes, including the fundamental steps of protein production transcription and translation [1]
We focus on thermodynamic and kinetic aspects to de novo design or further investigate riboswitches in silico
A typical riboswitch consists of a sensory domain that is linked to a regulatory domain
Summary
Sven Findeiß 1,2,3 , Maja Etzel 4 , Sebastian Will 1,3 , Mario Mörl 4, * and Peter F. Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, University of Vienna, Währingerstraße 29, A-1090 Vienna, Austria. Faculty of Chemistry, Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany. Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany. Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, 04103 Leipzig, Germany
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