| Autor: |
Angel F. Cisneros, Francois D. Rouleau, Carla Bautista, Pascale Lemieux, Nathan Dumont-Leblond |
| Jazyk: |
angličtina |
| Rok vydání: |
2023 |
| Předmět: |
|
| Zdroj: |
PeerJ Physical Chemistry, Vol 5, p e28 (2023) |
| Druh dokumentu: |
article |
| ISSN: |
2689-7733 |
| DOI: |
10.7717/peerj-pchem.28 |
| Popis: |
Synthetic biology aims to engineer biological circuits, which often involve gene expression. A particularly promising group of regulatory elements are riboswitches because of their versatility with respect to their targets, but early synthetic designs were not as attractive because of a reduced dynamic range with respect to protein regulators. Only recently, the creation of toehold switches helped overcome this obstacle by also providing an unprecedented degree of orthogonality. However, a lack of automated design and optimization tools prevents the widespread and effective use of toehold switches in high throughput experiments. To address this, we developed Toeholder, a comprehensive open-source software for toehold design and in silico comparison. Toeholder takes into consideration sequence constraints from experimentally tested switches, as well as data derived from molecular dynamics simulations of a toehold switch. We describe the software and its in silico validation results, as well as its potential applications and impacts on the management and design of toehold switches. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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