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Sensors 2017, 17(9), 1990; https://doi.org/10.3390/s17091990

Design of Artificial Riboswitches as Biosensors

1,2,3
,
4
,
1,3,4,* , 4,* and 1,3,5,6,7,8,9
1
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16–18, 04107 Leipzig, Germany
2
Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, University of Vienna, Währingerstraße 29, A-1090 Vienna, Austria
3
Faculty of Chemistry, Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
4
Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
5
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
6
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany
7
Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, 04103 Leipzig, Germany
8
Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg , Denmark
9
Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
*
Authors to whom correspondence should be addressed.
Received: 8 August 2017 / Revised: 23 August 2017 / Accepted: 25 August 2017 / Published: 30 August 2017
(This article belongs to the Special Issue Aptasensors 2016)
Full-Text   |   PDF [564 KB, uploaded 31 August 2017]   |  

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. View Full-Text
Keywords: aptamer; RNA structure; ligand binding; refolding; thermodynamics; rational design; folding kinetics aptamer; RNA structure; ligand binding; refolding; thermodynamics; rational design; folding kinetics
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Findeiß, S.; Etzel, M.; Will, S.; Mörl, M.; Stadler, P.F. Design of Artificial Riboswitches as Biosensors. Sensors 2017, 17, 1990.

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