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]


<h2> Content </h2>
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[[Image:RNA_Animation_v4.gif|center|500px]]
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                  <p style="padding-bottom: 0pt; padding-top: 0pt; " class="Free_Form">University of California, Riverside</p>
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<h3><u>A Synthetic Oscillatory System using Enzyme Aptamers</u></h3>
  <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>


<h3><u>The Model</u></h3>
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                  <p style="padding-top: 0pt; " class="paragraph_style">Oscillators, nature’s biological clocks, have important applications ranging from maintaining a circadian rhythm to regulating hormonal levels. We are constructing a synthetic in vitro oscillatory network. In vitro oscillators have been constructed in the past; however, our system is the first to utilize RNA aptamers that allow for a simpler, yet robust oscillator. Our theoretical model for this oscillatory scheme shows that it is capable of having robust oscillations. On the experimental front, we have shown that our RNA polymerase enzymes can be inhibited and reactivated by the binding and removal of the aptamers respectively. This would be an important step towards our goal of experimentally validating the oscillatory scheme. We hope that the simplicity of our system allows it to be easily built upon, thus, paving the way for a new set of biological circuits and this would introduce RNA aptamers as a powerful tool for programmable, synthetic circuits.<br /></p>
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                  <p style="padding-bottom: 0pt; padding-top: 0pt; " class="paragraph_style_1">A Synthetic Oscillatory System</p>
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Revision as of 16:25, 29 September 2014

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                 <p style="padding-top: 0pt; " class="paragraph_style">Oscillators, nature’s biological clocks, have important applications ranging from maintaining a circadian rhythm to regulating hormonal levels. We are constructing a synthetic in vitro oscillatory network. In vitro oscillators have been constructed in the past; however, our system is the first to utilize RNA aptamers that allow for a simpler, yet robust oscillator. Our theoretical model for this oscillatory scheme shows that it is capable of having robust oscillations. On the experimental front, we have shown that our RNA polymerase enzymes can be inhibited and reactivated by the binding and removal of the aptamers respectively. This would be an important step towards our goal of experimentally validating the oscillatory scheme. We hope that the simplicity of our system allows it to be easily built upon, thus, paving the way for a new set of biological circuits and this would introduce RNA aptamers as a powerful tool for programmable, synthetic circuits.<br /></p>
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