Rational Design of Riboswitches: papers to read - Revision history

ToEckdahl at 14:26, 30 May 2014

2014-05-30T14:26:34Z

Laheyer at 14:37, 29 May 2014

2014-05-29T14:37:06Z

Laheyer at 14:33, 29 May 2014

2014-05-29T14:33:33Z

Laheyer at 14:28, 29 May 2014

2014-05-29T14:28:38Z

Laheyer: Created page with "Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]"

2014-05-29T13:54:00Z

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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Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]

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 Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]
+* In this paper they develop a kinetics model for riboswitches that function in any of three ways: translational repression, transcriptional termination, and mRNA destabilization.  The mathematical modelling involved differential equations to describe each step in the mechanism of transcription, ligand binding, translation, and RNA degradation.  They emphasized the importance of the relative rates of reversible steps such as RNA folding and ligand binding to irreversible steps such as transcription termination and RNA degradation.  They built theophylline riboswitches to confirm important aspects of their model.
 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]
 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]

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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
+* 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

← Older revision		Revision as of 14:28, 29 May 2014
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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
		+
	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]
		+
		+	Dixon, et al - [http://www.pnas.org/content/107/7/2830.full#ref-19 Reengineering Orthogonally Selective Riboswitches]
		+
		+	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]
		+
		+	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]