Difference between revisions of "Rational Design of Riboswitches: papers to read"

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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