Difference between revisions of "Rational Design of Riboswitches: papers to read"
(Created page with "Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]") |
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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] | ||
| + | * engineered switch terminates '''transcription''' in the absence 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 | ||
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Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function] | Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function] | ||
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| + | Dixon, et al - [http://www.pnas.org/content/107/7/2830.full#ref-19 Reengineering Orthogonally Selective Riboswitches] | ||
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| + | 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] | ||
| + | |||
| + | Ceres, Trausch and Batey (Dec 2013) - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905868/ Engineering modular ‘ON’ RNA switches using biological components] | ||
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| + | 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] | ||
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| + | 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] | ||
Revision as of 14:28, 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
- 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
