Rational Design of Riboswitches: papers to read

Wachsmuth, et al - De novo design of a synthetic riboswitch that regulates transcription termination

• engineered switch terminates transcription in the absence of theophylline (6.5 fold induction in presence of theophylline)
• model folding of many candidate switches in steps of 5-10 nt (to simulate different elongation speeds) using RNAfold
• find distribution of MFE in shuffled sequences to characterize those structures more/less stable than expected by chance

Beisel and Smolke - Design Principles for Riboswitch Function

Dixon, et al - Reengineering Orthogonally Selective Riboswitches

Rieder, et al (referenced by Dixon)- Ligand-Induced Folding of the Adenosine Deaminase A-Riboswitch and Implications on Riboswitch Translational Control

Ceres, Trausch and Batey (Dec 2013) - Engineering modular ‘ON’ RNA switches using biological components

Perdizet, et al - Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

Ceres, et al (Mar 2013) - Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices