Team:MIT

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<a href="http://bacolicio.us/http://2012.igem.org/Team:MIT/Motivation">
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<a href="http://2012.igem.org/Team:MIT/Motivation#s2">
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   <img src="http://2012.igem.org/wiki/images/4/44/Mithomepage1.png" alt="What is strand displacement?" style="border:1px solid black" width="250"/>
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   <img src="http://2012.igem.org/wiki/images/4/44/Mithomepage1.png" alt="Why make logic circuits with strand displacement?" style="border:1px solid black" width="250"/>
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<a href="http://2012.igem.org/Team:MIT/ResultsFoundational#exciting">
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<a href="http://2012.igem.org/Team:MIT/Motivation">
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   <img src="http://2012.igem.org/wiki/images/5/52/Mithomepage3.png" alt="We successfully showed strand displacement to work in vivo!" style="border:1px solid black" width="250"/>
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   <img src="http://2012.igem.org/wiki/images/5/52/Mithomepage3.png" alt="How does strand displacement work?" style="border:1px solid black" width="250"/>
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<a href="http://2012.igem.org/Team:MIT/HumanPractices">
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<a href="http://2012.igem.org/Team:MIT/TheKeyReaction#SDbio">
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   <img src="http://2012.igem.org/wiki/images/d/dd/Mithomepage5.png" alt="Read about our synthetic biology outreach projects!" style="border:1px solid black" width="250"/><br/>
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   <img src="http://2012.igem.org/wiki/images/d/dd/Mithomepage5.png" alt="Strand displacement reactions work in vivo!" style="border:1px solid black" width="250"/>
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<a href="http://2012.igem.org/Team:MIT/ResultsSensing">
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<a href="http://2012.igem.org/Team:MIT/Sensing#sensing1bio">
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   <img src="http://2012.igem.org/wiki/images/8/81/Mithomepage4.png" alt="Sensing / We made strand displacement circuitry compatible with mRNAs as inputs!" style="border:1px solid black" width="250"/>
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   <img src="http://2012.igem.org/wiki/images/8/81/Mithomepage4.png" alt="Sensing mRNA Levels using Strand Displacement" style="border:1px solid black" width="250"/>
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<a href="http://2012.igem.org/Team:MIT/ResultsProcessing">
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<a href="http://2012.igem.org/Team:MIT/NOTGate#NOTgate_designbio">
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   <img src="http://2012.igem.org/wiki/images/b/b7/Mithomepage6.png" alt="Processing / We designed a NOT gate and tested hammerhead ribozymes as part of building our circuitry!" style="border:1px solid black" width="250"/>
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   <img src="http://2012.igem.org/wiki/images/b/b7/Mithomepage6.png" alt="Strand Displacement NOT Gate Design" style="border:1px solid black" width="250"/>
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<a href="http://2012.igem.org/Team:MIT/ResultsActuation">
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<a href="http://2012.igem.org/Team:MIT/CircuitProduction#shortRNAbio">
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   <img src="http://2012.igem.org/wiki/images/b/b0/Mithomepage2.png" alt="Actuation / We designed and tested a circuit showing production of short RNAs which can regulate protein levels!" style="border:1px solid black" width="250"/><br/>
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   <img src="http://2012.igem.org/wiki/images/b/b0/Mithomepage2.png" alt="Making short RNAs in vivo to use in circuits" style="border:1px solid black" width="250"/><br/>
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<h3>Project Description</h3>
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<h3>In Vivo Molecular Computation Using RNA Strand Displacement in Mammalian Cells</h3>
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Imagine being able to diagnose and destroy diseased cells using RNA. This can be accomplished by using RNA strand displacement cascades that recognize certain mammalian cell-specific biomarkers, such as characteristic mRNA strands or metabolites, use these as abstract inputs to digital logic gates, and then yield a wide array of desired outputs.
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<p>The limited availability of promoters, genes, and repressors, along with the difficulty in assembling and delivering large DNA plasmids bottleneck advances in sophistication of genetic circuits in mammalian systems. In contrast, sophistication of <i>in vitro</i> synthetic DNA circuits has grown exponentially through the mechanism of <a href="http://2012.igem.org/Team:MIT/Motivation">toehold-mediated strand displacement</a>. These circuits demonstrate digital logic with reliable, modular, and scalable behaviors and maintain a small base-pair footprint. </p> <p>
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The raw processing power of these strand displacement circuits has been trapped in the test tube, sequestered from the traditional protein-based sensing, processing, and actuation method of synthetic biology. With the adaptation of strand displacement-based information processing, the application space of synthetic biology circuits will become larger and more accessible. </p>
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We propose a new method of implementing the paradigms of sensing, processing, and actuation inside mammalian cells by applying the mechanism of DNA strand displacement from the field of nucleic acid computation to RNA. Traditional synthetic biology approaches seem to have hit a barrier in terms of the number of regulatory components that can be used predictably and reliably, limiting the complexity of cellular circuits.
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Our project leverages strand displacement to create a processing technology that supports multi-input <b>sensing</b>, sophisticated <b>information processing</b>, and precisely-regulated <b>actuation</b> in mammalian cells. We designed and tested a novel <a href="http://2012.igem.org/Team:MIT/NOTGate">fully-functioning DNA NOT gate</a>, which enables complete logic operation. In addition, we used RNA strand displacement to <a href="http://2012.igem.org/Team:MIT/Sensing">sense cellular mRNA</a>. We also demonstrated our ability to <a href="http://2012.igem.org/Team:MIT/CircuitProduction#shortRNAbio">produce short RNAs</a> <i>in vivo</i>.
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On the other hand, the strand displacement method of molecular computing within mammalian cells is highly modular, scalable, and orthogonal. We have demonstrated that RNA can be used as a processing medium, and have proposed novel in vivo NOT gates, which along with AND and OR gates can directly be produced inside mammalian cells. Currently, we are developing modeling platforms to explore kinetics of strand displacement reactions in vivo, as well as designing actuation systems that allow the RNA logic to interface with a variety of protein outputs.
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Most importantly, we demonstrated that toehold-mediated strand displacement in RNA can occur in mammalian cells. This, combined with our feasibility studies outlined in the above paragraph, shows that <a href="http://2012.igem.org/Team:MIT/TheKeyReaction#iteration_2_invivo"><b>strand displacement is a viable information-processing technology</b></a>. We envision <i>in vivo</i> RNA strand displacement as a new foundation for scaling up complexity in engineered biological systems, with applications in biosynthesis, biomedical diagnostics and therapeutics.
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Our integrated approach can fundamentally impact the fields of biological engineering, biomedical engineering, and medical diagnostics.
 
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   <li><a href="http://www.alnylam.com"><img src='http://2012.igem.org/wiki/images/1/16/ALYNYAM.jpg' style = "width:175px;"'></a></li>
   <li><a href="http://www.alnylam.com"><img src='http://2012.igem.org/wiki/images/1/16/ALYNYAM.jpg' style = "width:175px;"'></a></li>
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Latest revision as of 19:41, 25 June 2013

iGEM 2012
Why make logic circuits with strand displacement? How does strand displacement work? Strand displacement reactions work in vivo!
Sensing mRNA Levels using Strand Displacement Strand Displacement NOT Gate Design Making short RNAs in vivo to use in circuits

Project Description

The limited availability of promoters, genes, and repressors, along with the difficulty in assembling and delivering large DNA plasmids bottleneck advances in sophistication of genetic circuits in mammalian systems. In contrast, sophistication of in vitro synthetic DNA circuits has grown exponentially through the mechanism of toehold-mediated strand displacement. These circuits demonstrate digital logic with reliable, modular, and scalable behaviors and maintain a small base-pair footprint.

The raw processing power of these strand displacement circuits has been trapped in the test tube, sequestered from the traditional protein-based sensing, processing, and actuation method of synthetic biology. With the adaptation of strand displacement-based information processing, the application space of synthetic biology circuits will become larger and more accessible.

Our project leverages strand displacement to create a processing technology that supports multi-input sensing, sophisticated information processing, and precisely-regulated actuation in mammalian cells. We designed and tested a novel fully-functioning DNA NOT gate, which enables complete logic operation. In addition, we used RNA strand displacement to sense cellular mRNA. We also demonstrated our ability to produce short RNAs in vivo.

Most importantly, we demonstrated that toehold-mediated strand displacement in RNA can occur in mammalian cells. This, combined with our feasibility studies outlined in the above paragraph, shows that strand displacement is a viable information-processing technology. We envision in vivo RNA strand displacement as a new foundation for scaling up complexity in engineered biological systems, with applications in biosynthesis, biomedical diagnostics and therapeutics.



Sponsors