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Literature DB >> 24549622

In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP.

Kazuhiro Furukawa¹, Hongzhou Gu, Ronald R Breaker.

Abstract

Recently, a number of study have shown the ligand-dependent allosteric ribozymes can be harnessed as biosensors, high-throughput screening, and agents for the control of gene expression in vivo, called artificial riboswitches. In this chapter, we describe how in vitro selection can be used to create an allosteric ribozyme that senses bacterial second messenger cyclic-di-GMP (c-di-GMP). A hammerhead ribozyme was joined to a natural c-di-GMP class I riboswitch aptamer via communication modules. Both c-di-GMP-activating and -inhibiting ribozyme can be obtained by this approach.

Entities: Chemical Gene Species

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Year: 2014 PMID： 24549622 PMCID： PMC5325115 DOI： 10.1007/978-1-62703-755-6_15

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

22 in total

In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP.

1. Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site.

2. Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization.

3. Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector.

4. Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphate.

5. Kinetics of intermolecular cleavage by hammerhead ribozymes.

6. Structural basis of ligand binding by a c-di-GMP riboswitch.

7. Riboswitches in eubacteria sense the second messenger cyclic di-GMP.

8. Artificial ribozyme switches containing natural riboswitch aptamer domains.

9. An allosteric self-splicing ribozyme triggered by a bacterial second messenger.

10. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.

1. A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements.

Review 2. Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors.

3. Integration of an Expression Platform in the SELEX Cycle to Select DNA Aptamer Binding to a Disease Biomarker.

Review 4. Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors.