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

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  <li class='active'><a href='http://openwetware.org/wiki/Biomod/2014/UCR/Breaking_RNA'><span>Home</span></a></li>
                  <p style="padding-bottom: 0pt; padding-top: 0pt; " class="Free_Form">University of California, Riverside</p>
  <li><a href='http://openwetware.org/wiki/Biomod/2014/UCR/Breaking_RNA/Motivation_&_Objectives'><span>Motivation & Objectives</span></a></li>
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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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<h1>RNA Clocks & Switches</h1>
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                  <p style="padding-bottom: 0pt; padding-top: 0pt; " class="paragraph_style_1">Abstract</p>
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<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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                  <p style="padding-bottom: 0pt; padding-top: 0pt; " class="paragraph_style_1">A Synthetic Oscillatory System</p>
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Latest revision as of 23:50, 25 October 2014

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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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