By Scott K. Silverman

This publication reports reports displaying that fascinating and worthy molecular-scale switches and sensors should be made from nucleic acids, via either man made and traditional capacity. the 1st element of the e-book is dedicated to synthetic nucleic acid switches and sensors. In moment part, 3 chapters express that nature has been as artful a molecular-scale engineer as any smooth scientist, within the evolution of average nucleic acid switches and sensors.

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Additional resources for Nucleic Acid Switches and Sensors (Molecular Biology Intelligence Unit )

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Sudarsan N, Wickiser JK, Nakamura S et al. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev 2003; 17:2688-2697 . 41. Mandai M, Lee M, Barrick JE et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 2004; 306:275-279. 42. Mandai M, Boese B, Barrick JE er al. Riboswirches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 2003; 113:577-586. 43. Mandai M, Breaker RR. Adenine riboswitches and gene activation by disruption of a transcriptional terminator .

Destabilized ribozymes and Maxizyrnes. 18•19 StemII of the hammerheadribozyme, which is criticalfor catalytic activity, has been reduced to a single G-C basepair and a loop. Addition of the oligonucleotide effector(dashedline) contributes to a lengthening and stabilization of stem II via the formation of a pseudo-half-knot. 29 A hammerhead ribozyrne motif is createdwith additional sequence dements that destabilize the catalytic core. Addition of the oligonucleotide eHector (dashedline),whichhybridizes to ponions ofthisadditionalsequence, reestablishes acompetentcatalyticcore.

The designs of these allosteric ribozymes involve oligonucleotide effectors that serve as either inducers or repressors, sometimes within the same deoxyribozyme construct. Figure 3C shows the design of the itANDi~DNOTi6 deoxyribozyme, which shows the "logic" behaviour of being turned on in the presence of both effectors i and ii (but not in the presence of only one) and being turned off by effector iii, regardless of the presence of effectors i and ii. The activation portions of the design of this deoxyribozyme echo the TRAP methodology, except that here the artenuaror sequence elements (defined by the it loop and its S' continuation as well as the i3loop and its 3' continuation) base-pair with and inactivate the substrate binding arms (rather than the catalytic core) of the deoxyribozyrne, with the it and i3loops acting as sensors.

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