Angel F. Cisneros, François D. Rouleau, Carla Bautista, Pascale Lemieux, Nathan Dumont-LeblondPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
<p>Abstract: 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 benchmarking. Toeholder takes into consideration sequence constraints 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.</p>
Toehold switch, Riboswitches, Molecular switch, Expression regulation
