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Methods Mol Biol. 2014;1111:209-20. doi: 10.1007/978-1-62703-755-6_15.

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

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  • 1Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.


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.

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