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Team:MIT/Motivation
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<h1>Background and Motivation</h1> | <h1>Background and Motivation</h1> | ||
| - | In the near future, biological circuits will be much more <b>modular</b> and <b>sophisticated</b> than they are now, with a ten-fold <b>smaller nucleotide footprint</b>. | + | <h4>In the near future, biological circuits will be much more <b>modular</b> and <b>sophisticated</b> than they are now, with a ten-fold <b>smaller nucleotide footprint</b>. </h4> |
<h3>The Enabling Technology: Toehold-Mediated Strand Displacement</h3> | <h3>The Enabling Technology: Toehold-Mediated Strand Displacement</h3> | ||
| - | <center><img src="https://static.igem.org/mediawiki/2012/e/ef/MIT_Strand_Displacement_Cartoon.png" | + | <center><br/><img src="https://static.igem.org/mediawiki/2012/e/ef/MIT_Strand_Displacement_Cartoon.png"/><br/><br/></center> |
| - | A <b>gate strand</b> and <b>output strand</b> exist as a complex that is <b>partially bound</b> through complementary Watson-Crick base-pairing within the S2 binding domain. The gate strand also contains an <b>open, unbound domain</b> called a <b>toehold</b> region, T*. An input strand with a free complementary toehold region, T, can bind to the toehold region on the gate strand, and subsequently displace the output strand to yield an input-gate complex. This is called a <b>toehold-mediated strand displacement</b> | + | A <b>gate strand</b> and <b>output strand</b> exist as a complex that is <b>partially bound</b> through complementary Watson-Crick base-pairing within the S2 binding domain. The gate strand also contains an <b>open, unbound domain</b> called a <b>toehold</b> region, T*. An input signal strand with a free complementary toehold region, T, can bind to the toehold region on the gate strand, and subsequently displace the output strand to yield an input-gate complex and a free output signal strand. This is called a <b>toehold-mediated strand displacement reaction</b>. The output signal strand can be used as an input signal for a downstream gate-output complex, enabling sophisticated interactions which yield full logic circuits. |
<h3>Background</h3> | <h3>Background</h3> | ||
| - | Qian and Winfree (<i>Science</i> 2011) utilized DNA computation to create AND and OR logic gates <i>in vitro</i>. They constructed a sophisticated binary square root circuit using these gates: | + | <a href="http://www.sciencemag.org/content/332/6034/1196.abstract">Qian and Winfree (<i>Science</i> 2011)</a> utilized DNA computation to create AND and OR logic gates <i>in vitro</i>. They constructed a sophisticated binary square root circuit using these gates: |
| - | <center><img src="https://static.igem.org/mediawiki/2012/4/4a/MIT_Curly_strands_square_root_circuit.png" width=570/></center> | + | <center> |
| - | + | <img src="https://static.igem.org/mediawiki/2012/4/4a/MIT_Curly_strands_square_root_circuit.png" width=570/> | |
| - | Each of these: | + | <div style="text-align: right; margin-right: 8em;"><em>Image courtesy of Lulu Qian.</em></div> |
| + | </div> | ||
| + | </center> | ||
| + | </br> | ||
| + | </br>Each of these: | ||
</br><img src="https://static.igem.org/mediawiki/2012/6/6c/MIT_Curly_strand_1.png" height=30> <img src="https://static.igem.org/mediawiki/2012/3/36/MIT_Curly_strand_2.png" height=15> | </br><img src="https://static.igem.org/mediawiki/2012/6/6c/MIT_Curly_strand_1.png" height=30> <img src="https://static.igem.org/mediawiki/2012/3/36/MIT_Curly_strand_2.png" height=15> | ||
</br>undergoes the same <b>toehold-mediated strand displacement reaction</b>. These reactions are fully modular and can be scaled to circuits of any degree of sophistication. | </br>undergoes the same <b>toehold-mediated strand displacement reaction</b>. These reactions are fully modular and can be scaled to circuits of any degree of sophistication. | ||
| - | <h3>Motivation for Bringing Strand Displacement to Mammalian Synthetic Biology</h3> | + | <h3 id="s2">Motivation for Bringing Strand Displacement to Mammalian Synthetic Biology</h3> |
<ul> | <ul> | ||
<li><b>More sophisticated circuits with smaller nucleotide footprint</b> | <li><b>More sophisticated circuits with smaller nucleotide footprint</b> | ||
| - | </br> | + | <center><img src="https://static.igem.org/mediawiki/2012/b/bc/MIT_Transcription_versus_strand_displacement_circuits.png" width=350></center> |
| + | </br> Sophistication of traditional transcription-translational circuits has grown linearly over the past 10 years, while sophistication of strand-displacement circuits has grown nearly exponentially. | ||
<li><b>Simple combinatorial design space</b> | <li><b>Simple combinatorial design space</b> | ||
| - | </br>With 4 | + | </br>With 4 nucleotides, we can create a nearly infinite number of orthogonal sequences leading to orthogonal parts. |
<li><b>Ease of composition</b> | <li><b>Ease of composition</b> | ||
</br>The input motif matches the output motif allowing for modular cascading reactions. | </br>The input motif matches the output motif allowing for modular cascading reactions. | ||
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An information processing system is of limited use without dynamic production. RNA is a good medium because it can be continually produced from a few initial DNA parts. As in nature, DNA acts as the information-storage medium, and RNA acts as the information-processing medium. We can transfect DNA parts into mammalian cells to co-opt existing cellular machinery to produce our RNA parts. | An information processing system is of limited use without dynamic production. RNA is a good medium because it can be continually produced from a few initial DNA parts. As in nature, DNA acts as the information-storage medium, and RNA acts as the information-processing medium. We can transfect DNA parts into mammalian cells to co-opt existing cellular machinery to produce our RNA parts. | ||
| - | + | </br> | |
| - | </br>Our RNA parts can then interact with the cell through sensing and actuation. Endogenous cellular RNAs can act as inputs, and we can actuate by knocking down endogenous cellular RNAs. | + | </br>Our RNA parts can then interact with the cell through <a href="https://2012.igem.org/Team:MIT/Sensing">sensing</a> and <a href="https://2012.igem.org/Team:MIT/Actuation">actuation</a>. Endogenous cellular RNAs can act as inputs, and we can actuate by knocking down endogenous cellular RNAs. |
Latest revision as of 03:55, 27 October 2012
Background and Motivation
In the near future, biological circuits will be much more modular and sophisticated than they are now, with a ten-fold smaller nucleotide footprint.
The Enabling Technology: Toehold-Mediated Strand Displacement
Background
Qian and Winfree (Science 2011) utilized DNA computation to create AND and OR logic gates in vitro. They constructed a sophisticated binary square root circuit using these gates:
Image courtesy of Lulu Qian.
undergoes the same toehold-mediated strand displacement reaction. These reactions are fully modular and can be scaled to circuits of any degree of sophistication.
Motivation for Bringing Strand Displacement to Mammalian Synthetic Biology
- More sophisticated circuits with smaller nucleotide footprint
- Simple combinatorial design space With 4 nucleotides, we can create a nearly infinite number of orthogonal sequences leading to orthogonal parts.
- Ease of composition The input motif matches the output motif allowing for modular cascading reactions.
- Tunability We can set arbitrary digital signal thresholds by varying the concentration of circuit species. We can also achieve signal amplification by including a fuel molecule.
