Design of RNA-Based Translational Repressors

The toehold switch is an RNA-based riboregulator that activates translation in response to a cognate trigger RNA and provides high ON/OFF ratios, excellent orthogonality, and logic capabilities. Riboregulators that provide the inverse function - turning off translation in response to a trigger RNA - are also versatile tools for sensing and efficiently implementing logic gates such as NAND or NOR. Toehold and three-way junction (3WJ) repressors are two de novo designed translational repressors devised to provide NOT functions with an easily programmable and intuitive structural design. Toehold and 3WJ repressors repress translation upon binding to cognate trigger RNAs by forming strong hairpin and three-way junction structures, respectively. These two translational repressors can be incorporated into multi-input NAND and NOR gates. This chapter provides methods for designing these translational repressors and protocols for in vivo characterization in E. coli.