Difference between revisions of "Rational Design of Riboswitches: papers to read"
| Line 9: | Line 9: | ||
Rieder, et al (referenced by Dixon)- [http://onlinelibrary.wiley.com/doi/10.1002/cbic.200700057/full Ligand-Induced Folding of the Adenosine Deaminase A-Riboswitch and Implications on Riboswitch Translational Control] | Rieder, et al (referenced by Dixon)- [http://onlinelibrary.wiley.com/doi/10.1002/cbic.200700057/full Ligand-Induced Folding of the Adenosine Deaminase A-Riboswitch and Implications on Riboswitch Translational Control] | ||
| − | |||
| − | |||
Perdizet, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295289/ Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch] | Perdizet, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295289/ Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch] | ||
Ceres, et al (Mar 2013) - [http://pubs.acs.org/doi/ipdf/10.1021/sb4000096 Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices] | Ceres, et al (Mar 2013) - [http://pubs.acs.org/doi/ipdf/10.1021/sb4000096 Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices] | ||
| + | * OFF switches | ||
| + | |||
| + | Ceres, Trausch and Batey (Dec 2013) - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905868/ Engineering modular ‘ON’ RNA switches using biological components] | ||
Revision as of 14:37, 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
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
- OFF switches
Ceres, Trausch and Batey (Dec 2013) - Engineering modular ‘ON’ RNA switches using biological components
