Design of Artificial Riboswitches as Biosensors
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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2017-08-01
|
| Series: | Sensors |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1424-8220/17/9/1990 |
| _version_ | 1798040039685357568 |
|---|---|
| author | Sven Findeiß Maja Etzel Sebastian Will Mario Mörl Peter F. Stadler |
| author_facet | Sven Findeiß Maja Etzel Sebastian Will Mario Mörl Peter F. Stadler |
| author_sort | Sven Findeiß |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T22:02:00Z |
| format | Article |
| id | doaj.art-2cf4c4f8f8894591a0126c4816bfa464 |
| institution | Directory Open Access Journal |
| issn | 1424-8220 |
| language | English |
| last_indexed | 2024-04-11T22:02:00Z |
| publishDate | 2017-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Sensors |
| spelling | doaj.art-2cf4c4f8f8894591a0126c4816bfa4642022-12-22T04:00:52ZengMDPI AGSensors1424-82202017-08-01179199010.3390/s17091990s17091990Design of Artificial Riboswitches as BiosensorsSven Findeiß0Maja Etzel1Sebastian Will2Mario Mörl3Peter F. Stadler4Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16–18, 04107 Leipzig, GermanyInstitute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, GermanyBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16–18, 04107 Leipzig, GermanyInstitute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, GermanyBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16–18, 04107 Leipzig, GermanyRNA 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.https://www.mdpi.com/1424-8220/17/9/1990aptamerRNA structureligand bindingrefoldingthermodynamicsrational designfolding kinetics |
| spellingShingle | Sven Findeiß Maja Etzel Sebastian Will Mario Mörl Peter F. Stadler Design of Artificial Riboswitches as Biosensors Sensors aptamer RNA structure ligand binding refolding thermodynamics rational design folding kinetics |
| title | Design of Artificial Riboswitches as Biosensors |
| title_full | Design of Artificial Riboswitches as Biosensors |
| title_fullStr | Design of Artificial Riboswitches as Biosensors |
| title_full_unstemmed | Design of Artificial Riboswitches as Biosensors |
| title_short | Design of Artificial Riboswitches as Biosensors |
| title_sort | design of artificial riboswitches as biosensors |
| topic | aptamer RNA structure ligand binding refolding thermodynamics rational design folding kinetics |
| url | https://www.mdpi.com/1424-8220/17/9/1990 |
| work_keys_str_mv | AT svenfindeiß designofartificialriboswitchesasbiosensors AT majaetzel designofartificialriboswitchesasbiosensors AT sebastianwill designofartificialriboswitchesasbiosensors AT mariomorl designofartificialriboswitchesasbiosensors AT peterfstadler designofartificialriboswitchesasbiosensors |