Reversible Photo-regulation of a Hammerhead Ribozyme Using a Diffusible Effector

Lee, Hyun-Wu; Robinson, Stephen G.; Bandyopadhyay, Subhajit; Mitchell, Reginald H.; Sen, Dipankar

doi:10.1016/j.jmb.2007.06.042

Cited by 36 publications

(22 citation statements)

References 36 publications

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“…Using the so-called ''UG module'', they obtained an allosteric ribozyme that was almost as active as an unmodified hammerhead ribozyme in the presence of the ''closed-ring'' form of their dihydropyrene, while it was almost completely inactive with the ''open-ring'' form. Analysis of the initial rates of hammerhead ribozyme cleavage revealed an impressive switching factor of 900, thereby demonstrating that in this system, an RNA receptor was able to transmit the sensing of a photon to a significant change in (ribo)enzymatic activity [18]. It should be noted that all three photoswitchable systems are far from ideal for applications inside biological systems.…”

Section: Aptamers and Ribozymes That Respond To Photoisomerizable Smamentioning

confidence: 89%

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Genetically encoded RNA photoswitches as tools for the control of gene expression

Jäschke¹

2012

FEBS Letters

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a b s t r a c tAn important goal in chemical and synthetic biology is controlling the expression of defined sets of genes by external stimuli, and one of the most attractive stimuli is light. Current approaches to the photocontrol of biological processes utilize photoresponsive proteins. In this article, I will illustrate the prospects of synthetic systems in which the receptor is a photoresponsive nucleic acid, and will review the different tools already in place to develop photoresponsive systems based on RNA. A particular focus is on genetically encoded photoswitches that can be expressed in prokaryotic or eukaryotic cells, and respond to photoisomerizable, cell-permeable small molecules.

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Section: Aptamers and Ribozymes That Respond To Photoisomerizable Smamentioning

confidence: 89%

“…These prototypes are RNA aptamers selected in vitro against three different photoisomerizable small molecules (see below). In one case, transmission of the signal from the sensor domain to a catalytic effector domain could be demonstrated [18].…”

Section: Photoresponsive Nucleic Acids -Current Statusmentioning

confidence: 99%

Genetically encoded RNA photoswitches as tools for the control of gene expression

Jäschke¹

2012

FEBS Letters

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“…In addition to natural riboswitches, this modular character has been exploited by RNA engineers to create aptamerbased allosteric ribozymes (e.g., Lee et al 2007;Link et al 2007) and gene control systems (e.g., Kim et al 2005;Topp and Gallivan 2007;Weigand and Suess 2007) with increasing diversity and complexity. These findings demonstrate that some RNA aptamers of a single structural class are robust structural and functional modules that can be used in different contexts to create precision molecular sensors.…”

Section: Introductionmentioning

confidence: 99%

Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteineThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

Wang

Breaker

2008

Biochem. Cell Biol.

105

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Numerous riboswitches have been discovered that specifically recognize metabolites and modulate gene expression. Each riboswitch class is defined either by the consensus sequence and structural features of its metabolite-binding aptamer domain, or by the distinct metabolite that the aptamer recognizes. Several distinct classes of riboswitches that respond to S-adenosylmethionine (SAM or AdoMet) have been discovered. Representatives of these classes have been shown to strongly discriminate against S-adenosylhomocystenine (SAH or AdoHcy), which is the metabolic byproduct produced when SAM is used as a cofactor for methylation reactions. However, a distinct class of riboswitches that selectively binds SAH, and strongly discriminates against SAM, also has been discovered. Herein we compare the features of SAM and SAH riboswitches, which help showcase the enormous structural diversity that RNA can harness to form precision genetic switches for compounds that are critical for fundamental metabolic processes.

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“…Similarly, an RNA aptamer that specifically binds to one isomerization state of spiropyran has been identified . In another interesting example, a light‐controlled dihydropyrene isomer–aptamer interaction has been used to reversibly regulate the catalytic efficiency of a hammerhead ribozyme …”

Section: Realizing Light‐regulated Rnas Using Photoswitchable Small Mmentioning

confidence: 99%

Designing optogenetically controlled RNA for regulating biological systems

Meng

Jaffrey

2015

Annals of the New York Academy of Sciences

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Light-responsive proteins have been used in the field of optogenetics to control cellular functions. However, surprisingly, analogous approaches to regulate and alter the functions of RNA molecules by light remain underdeveloped. RNA aptamers and RNA devices can perform diverse intracellular functions and are important tools in synthetic biology. This report explores the challenges of and potential strategies for engineering light regulation into functional RNAs in cells. We discuss approaches for using existing light-regulated proteins and small molecules to control RNA function in living cells. Additionally, applications of light-regulated RNAs for synthetic biology and for studying functions of endogenously expressed RNAs are discussed.

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Reversible Photo-regulation of a Hammerhead Ribozyme Using a Diffusible Effector

Cited by 36 publications

References 36 publications

Genetically encoded RNA photoswitches as tools for the control of gene expression

Genetically encoded RNA photoswitches as tools for the control of gene expression

Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteineThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

Designing optogenetically controlled RNA for regulating biological systems

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