Toeholder: a software for automated design and in silico validation of toehold riboswitches

• Published in: PeerJ Physical Chemistry
• Main Authors: Angel F. Cisneros, Francois D. Rouleau, Carla Bautista, Pascale Lemieux, Nathan Dumont-Leblond
• Format: Article
• Language: English
• Published: PeerJ Inc. 2023-06-01
• Subjects: Toehold switch; Riboswitch; Molecular switch; Expression regulation; Software; Detection
• Online Access: https://peerj.com/articles/pchem-28.pdf

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.