Difference between revisions of "Rational Design of Riboswitches: papers to read"
| Line 1: | Line 1: | ||
Wachsmuth, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575828/ De novo design of a synthetic riboswitch that regulates transcription termination] | Wachsmuth, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575828/ De novo design of a synthetic riboswitch that regulates transcription termination] | ||
| − | * engineered switch terminates '''transcription''' in the absence of theophylline | + | * 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 | * 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 | * find distribution of MFE in shuffled sequences to characterize those structures more/less stable than expected by chance | ||
Revision as of 14:33, 29 May 2014
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
