Biomod/2014/UCR/Breaking RNA: Difference between revisions

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<h1> Breaking RNA </h1>
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[http://openwetware.org/index.php?title=Biomod/2014/UCR/Breaking_RNA&action=edit EDIT]
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<h2> Content </h2>
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[[Image:RNA_Animation_v4.gif|center|500px]]
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<h3><u>A Synthetic Oscillatory System using Enzyme Aptamers</u></h3>
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  <p>In this topology, E1 and E2 are enzymes, while R1,R2,R3, and R4 represent RNA strands. Our aim is to develop an oscillatory system, where E1 would inhibit E2, and E2 would activate E1. The negative feedback loop of E1 is essential for the current model to oscillate, while the positive feedback loop may serve to improve the oscillations observed.</p>
<h1>RNA Clocks & Switches</h1>
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[[Image:RNA_Animation_v7.gif|center|800px]]


<h3><u>The Model</u></h3>
<h3><u>Abstract</u></h3>
  <p>Biomolecular clocks and toggle switches are circuits with important roles in biological systems; for instance, oscillators direct circadian rhythms, and bistable circuits control many developmental pathways. We are building simple synthetic transcriptional in vitro oscillatory and bistable circuits using RNA aptamers. Similar circuits have been constructed in the past; however, our systems are the first to utilize RNA aptamers. These RNA aptamers regulate bacterial RNA polymerases’ activity to generate positive and negative feedback loops. We built numerical models, which show our systems exhibit the expected behaviors. Experimentally, we have shown that RNA polymerases can be inhibited and reactivated by the binding and removal of the aptamers through strand displacement. This is an important step towards experimentally validating our circuits. The simplicity of our design allows it to be easily built upon, thus, paving the way for new biological circuits where RNA aptamers are powerful, programmable tools for designing dynamic interactions.</p>
 
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RNA Clocks & Switches


Abstract

Biomolecular clocks and toggle switches are circuits with important roles in biological systems; for instance, oscillators direct circadian rhythms, and bistable circuits control many developmental pathways. We are building simple synthetic transcriptional in vitro oscillatory and bistable circuits using RNA aptamers. Similar circuits have been constructed in the past; however, our systems are the first to utilize RNA aptamers. These RNA aptamers regulate bacterial RNA polymerases’ activity to generate positive and negative feedback loops. We built numerical models, which show our systems exhibit the expected behaviors. Experimentally, we have shown that RNA polymerases can be inhibited and reactivated by the binding and removal of the aptamers through strand displacement. This is an important step towards experimentally validating our circuits. The simplicity of our design allows it to be easily built upon, thus, paving the way for new biological circuits where RNA aptamers are powerful, programmable tools for designing dynamic interactions.

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