Difference between revisions of "Team:Fudan-TSI/Part Collection"

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This html document is created by Tian Huang for Team Fudan iGEM 2018.
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We make it compatible on laptop and mobile devices by using Materialize 1.0.0-rc.2.
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<h3>★  ALERT! </h3>
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    <link rel="stylesheet" href="https://2018.igem.org/wiki/index.php?title=Template:Fudan/materialize.css&action=raw&ctype=text/css">
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<p>This page is used by the judges to evaluate your team for the <a href="https://2019.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2019.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2019.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1> Part Collection </h1>
 
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<p>Did your team make a lot of great parts? Is there a theme that ties all your parts together? Do you have more than 10 parts in this collection? Did you make a CRISPR collection, a MoClo collection, or a collection of awesome pigment parts? Describe your parts collection on this page, so the judges can evaluate you for the Best Part Collection award.</p>
 
  
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<p>
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        /** 重置表单元素 **/
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While you should put all the characterization information for your parts on the Registry, you are encouraged to explain how all your parts form a collection on this page.
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    <title>2019 Team:Fudan -Part_Collection</title>
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</head>
  
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<h3>Note</h3>
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<div id="FudanWrapper" class="white">
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<p>This page should list all the parts in the collection your team made during your project and include direct links to your Parts main pages on the Registry. <b>You must add all characterization information for your parts on Parts Main Page on the Registry.</b> You should <b>not</b> put characterization information on this page.
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<h3>Best Part Collection Special Prize</h3>
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            <!-- Dropdown and List elements in navigation bar -->
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<p> To be eligible for this award, each part in the collection <b>must be well documented on the part's Main Page on the Registry</b>. If you have a collection of parts you wish to nominate your team for this <a href="https://2019.igem.org/Judging/Awards">special prize</a>, make sure you add your part numbers to your <a href="https://2019.igem.org/Judging/Judging_Form">judging form</a> and delete the alert box at the top of this page.</p>
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                    <div class="col s12 m6 valign-wrapper hide-on-med-and-up">
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                        <h1>Part collection</h1>
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                    </div>
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                    <div class="col s12 m6 valign-wrapper hide-on-med-and-up">
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                        <span>Our parts collection provides an extensive toolbox for researchers to construct their own transmembrane logic gates in mammalian cells.</span>
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                    </div>
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                </div>
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                <div id="figureBannerTitle" class="hide-on-small-only">
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                    <h1>Part collection</h1>
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                    <p><span>Our parts collection provides an extensive toolbox for researchers to construct their own transmembrane logic gates in mammalian cells.</span></p>
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                </div>
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                <div class="hide-on-small-only">
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                    <img src="https://static.igem.org/mediawiki/2018/e/e7/T--Fudan--title_partscollection.jpg">
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            <!-- main content of the page -->
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            <div class="container">
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                <!-- side navigator of page content -->
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                <ul id="pageContentNav" class="hide-on-med-and-down z-depth-0">
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                    <li><a href="/Team:Fudan-TSI/Basic_Part">Basic parts</a></li>
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                    <li><a href="/Team:Fudan-TSI/Composite_Part">Composite parts</a></li>
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                    <li><a href="/Team:Fudan-TSI/Optimization">Optimization</a></li>
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                    <li>Part collection</li>
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                    <li class="onThisPageNav"><a href="#section1">SynNotch receptors set</a></li>
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                    <li class="onThisPageNav"><a href="#section2">Transcriptional amplifiers set</a></li>
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                    <li class="onThisPageNav"><a href="#section3">Amplifiers & combiners</a></li>
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                    <li class="onThisPageNav"><a href="#section4">ENABLE</a></li>
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                    <li><a href="/Team:Fudan-TSI/Improve">Parts improvement</a></li>
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                    <li><a href="/Team:Fudan-TSI/Measurement">Quantification</a></li>
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                </ul>
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                <main>
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                    <div class="section container">
 +
                        <p>Our parts collection provides an extensive toolbox for researchers to construct their own transmembrane logic gates in mammalian cells. These parts were made as BioBricks, and are NOT ready for transfecting mammalian cells. Plasmids with these parts in eukaryotic expression backbone are available upon request.
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                        </p>
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                        <p>Our parts collection contains <b>all essential components</b> of our ENABLE toolbox, that could also be divided into several sets, enabling others to readily utilize them to improve their existing genetic circuits.
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                        </p>
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                        <p>Following our 3-layer design principle, all ENABLE components have been well characterized, including our SynNotch receptors, Amplifiers and Combiners. In the collection, we have provided 7 versions of SynNotch receptors with (1) different combinations of extracellular domains which can bind to different antigens with different affinities, (2) transmembrane domains with varying cleavage efficiency and (3) intracellular domains executing diverse transcriptional amplifications.
 +
                        </p>
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                        <p>We have provided a set of transcriptional amplifiers including zinc finger-based, TEV protease-based and split intein-based ones, allowing others to <b>build their own genetic circuits</b>, preferably through transcription (we have tested), but not limited to (we have not tested). Besides, a set of combiners with different copies of response elements are provided, which makes it <b>easy for others to tune the activation or repression threshold</b>. This feature was experimental confirmed previously and mathematically <a href="/Team:Fudan-TSI/Model#Transcriptional_Amplifier" target="_blank">modeled</a> in our 3-layer design again this year. Our modeling process could be used by others to predict their own genetic circuits before any wet-lab experiments.
 +
                        </p>
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                        <p>
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                            Each part (sometimes two combined) constitutes one of our ENABLE module, which has its unique function. Yet they consolidate together to create all the 16 transmembrane binary logic gates for mammalian cells.
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                        </p>
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                    </div>
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                    <div id="section1" class="section container scrolSpy">
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                        <h2>SynNotch receptors set</h2>
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                        <p>We have provided 7 versions of SynNotch receptors. Each of them can transduce signal from out of the cell via a contact-dependent antigen-stimulated cleavage process. When expressing two SynNotch receptors with two different extracellular domains recognizing two types of antigens, the cell is able to accept dual inputs. The chosen nanobodies are highly specific against their antigens, and the chosen intracellular domains are transcriptionally orthogonal. For more specific details, please refer to our parts listed below.</p>
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                        <div class="tableHolder">
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                            <table class="striped">
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                                <tr>
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                                    <th> BioBrick ID</th>
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                                    <th>Protein Name</th>
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                                    <th>Recognized Antigen (affinity)</th>
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                                    <th>Transmembrane Domain</th>
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                                    <th>Intracellular Domain</th>
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                                    <th>Sequence Verification</th>
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                                </tr>
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                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549016" target="_blank">BBa_K2549016</a></td>
 +
                                    <td> LaG17-mN1c-tTAA</td>
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                                    <td>GFP (low)</td>
 +
                                    <td>mouse Notch1 core</td>
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                                    <td>tTA advance</td>
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                                    <td><a href="https://2018.igem.org/File:T--Fudan--016_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">016.ab1</a></td>
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                                </tr>
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                                <tr>
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                                    <td><a href="http://parts.igem.org/Part:BBa_K2549017" target="_blank">BBa_K2549017</a></td>
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                                    <td> LaG17-mN1ce-tTAA</td>
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                                    <td>GFP (low)</td>
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                                    <td>mouse Notch1 extended core</td>
 +
                                    <td>tTA advance</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--017_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">017.ab1</a></td>
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                                </tr>
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                                <tr>
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                                    <td><a href="http://parts.igem.org/Part:BBa_K2549018" target="_blank">BBa_K2549018</a></td>
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                                    <td> LaG16-mN1ce-tTAA</td>
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                                    <td>GFP (high)</td>
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                                    <td>mouse Notch1 extended core</td>
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                                    <td>tTA advance</td>
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                                    <td><a href="https://2018.igem.org/File:T--Fudan--018_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">018.ab1</a></td>
 +
                                </tr>
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                                <tr>
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                                    <td><a href="http://parts.igem.org/Part:BBa_K2549019" target="_blank">BBa_K2549019</a></td>
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                                    <td> LaG16-2-mN1c-tTAA</td>
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                                    <td>GFP (ultrahigh)</td>
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                                    <td>mouse Notch1 core</td>
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                                    <td>tTA advance</td>
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                                    <td><a href="https://2018.igem.org/File:T--Fudan--019_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">019.ab1</a></td>
 +
                                </tr>
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                                <tr>
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                                    <td><a href="http://parts.igem.org/Part:BBa_K2549020" target="_blank">BBa_K2549020</a></td>
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                                    <td> LaG16-2-mN1c-GV2</td>
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                                    <td>GFP (ultrahigh)</td>
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                                    <td>mouse Notch1 core</td>
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                                    <td>Gal4-VP64</td>
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                                    <td><a href="https://2018.igem.org/File:T--Fudan--020_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">020.ab1</a></td>
 +
                                </tr>
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                                <tr>
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                                    <td><a href="http://parts.igem.org/Part:BBa_K2549021" target="_blank">BBa_K2549021</a></td>
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                                    <td> &alpha;CD19-mN1c-tTAA</td>
 +
                                    <td>CD19</td>
 +
                                    <td>mouse Notch1 core</td>
 +
                                    <td>Gal4-VP64</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--021.abl.zip" target="_blank">021.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549022" target="_blank">BBa_K2549022</a></td>
 +
                                    <td> &alpha;CD19-mN1c-GV2</td>
 +
                                    <td>CD19</td>
 +
                                    <td>mouse Notch1 core</td>
 +
                                    <td>Gal4-VP64</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--022_TGCCACCTGACGTCTAAGAA_added.abl.zip" target="_blank">022.ab1</a></td>
 +
                                </tr>
 +
                            </table>
 +
                        </div>
 +
                    </div>
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                    <div id="section2" class="section container scrolSpy">
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                        <h2>Transcriptional amplifiers set</h2>
 +
                        <p>Last year, we have constructed <a href="https://2017.igem.org/Team:Fudan/Part_Collection" target="_blank">3 zinc finger-based transcription repressors</a>. This year, we have expanded our zinc finger-based transcription factors library by adding 3 more zinc finger-based transcription activators.</p>
 +
                        <p>
 +
                            Although we prefer to use eight copies of response elements (RE) for a balance between not-too-hard molecular cloning and sufficient signal-to-noise ratio, we have provided 4 promotors with different repeats of response elements, <b>allowing others to explore and tune their own transcriptional amplifiers</b>. <a href="/Team:Fudan-TSI/Model#Transcriptional_Amplifer" target="_blank">Latest modeling</a> strongly supports our experimental preference, showing that eight copies of response elements can render the best result in line with our needs.</p>
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                        <div class="tableHolder">
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                            <table class="striped">
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                                <tr>
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                                    <th> BioBrick ID</th>
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                                    <th>Protein Name</th>
 +
                                    <th>DNA Binding Domain</th>
 +
                                    <th>Transcriptional</th>
 +
                                    <th>Sequence Verification</th>
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                                </tr>
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                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549023" target="_blank">BBa_K2549023</a></td>
 +
                                    <td> ZF21.16-VP64</td>
 +
                                    <td>ZF21.16</td>
 +
                                    <td>activation</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--023_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">023.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549024" target="_blank">BBa_K2549024</a></td>
 +
                                    <td> ZF42.10-VP64</td>
 +
                                    <td>ZF42.10</td>
 +
                                    <td>activation</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--024_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">024.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549025" target="_blank">BBa_K2549025</a></td>
 +
                                    <td> ZF43.8-VP64</td>
 +
                                    <td>ZF43.8</td>
 +
                                    <td>activation</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--025_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">025.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2446039" target="_blank">BBa_K2446039</a></td>
 +
                                    <td> ZF21.16-KRAB</td>
 +
                                    <td>ZF21.16</td>
 +
                                    <td>repression</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--046.abl.zip" target="_blank">039.abl</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2446040" target="_blank">BBa_K2446040</a></td>
 +
                                    <td> ZF42.10-KRAB</td>
 +
                                    <td>ZF42.10</td>
 +
                                    <td>repression</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--047.abl.zip" target="_blank">040.abl</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2446041" target="_blank">BBa_K2446041</a></td>
 +
                                    <td> ZF43.8-KRAB</td>
 +
                                    <td>ZF43.8</td>
 +
                                    <td>repression</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--041p.abl.zip" target="_blank">041.abl</a></td>
 +
                                </tr>
 +
                            </table>
 +
                        </div>
 +
                        <div class="tableHolder">
 +
                            <table class="striped">
 +
                                <tr>
 +
                                    <th> BioBrick ID</th>
 +
                                    <th>DNA Name</th>
 +
                                    <th>Usage</th>
 +
                                    <th>Sequence Verification</th>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549032" target="_blank">BBa_K2549032</a></td>
 +
                                    <td> 4*ZF21.16-minCMV-2*ZF43.8</td>
 +
                                    <td>4 copies of RE for ZF21.16 transcriptional activator to bind, and 2 copies of RE for ZF43.8 transcriptional repressor to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--032_TGCCACCTGACGTCTAAGAA_added.abl.zip" target="_blank">032.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549033" target="_blank">BBa_K2549033</a></td>
 +
                                    <td> 6*ZF21.16-minCMV-2*ZF43.8</td>
 +
                                    <td>6 copies of RE for ZF21.16 transcriptional activator to bind, and 2 copies of RE for ZF43.8 transcriptional repressor to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--033_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">033.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549034" target="_blank">BBa_K2549034</a></td>
 +
                                    <td> 8*ZF21.16-minCMV-2*ZF43.8</td>
 +
                                    <td>8 copies of RE for ZF21.16 transcriptional activator to bind, and 2 copies of RE for ZF43.8 transcriptional repressor to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--034_TGCCACCTGACGTCTAAGAA_added.abl.zip" target="_blank">034.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549035" target="_blank">BBa_K2549035</a></td>
 +
                                    <td> 8*ZF21.16-minCMV-8*ZF43.8</td>
 +
                                    <td>8 copies of RE for ZF21.16 transcriptional activator to bind, and 8 copies of RE for ZF43.8 transcriptional repressor to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--035.abl.zip" target="_blank">035.ab1</a></td>
 +
                                </tr>
 +
                            </table>
 +
                        </div>
 +
                        <p>As is stated above, we have provided three types of transcriptional-based Amplifiers, including zinc finger-based, TEV protease-based and split intein-based. These Amplifiers must be used with our Combiners to execute designed binary logic function.</p>
 +
                    </div>
 +
                    <div id="section3" class="section container scrolSpy">
 +
                        <h2>Amplifiers and Combiners work together to execute binary computation</h2>
 +
                        <h3>Zinc finger-based</h3>
 +
                        <p>For simple binary logic function, such as A gate, NOT A gate, OR gate, NOR gate, and NIMPLY gate, placing response elements upstream and downstream of the promoter is sufficient. For more details, please visit our <a href="/Team:Fudan-TSI/Results" target=”_blank”>results page</a>.
 +
                        </p>
 +
                        <div class="tableHolder">
 +
                            <table class="striped">
 +
                                <tr>
 +
                                    <th> BioBrick ID</th>
 +
                                    <th>Combiner Name</th>
 +
                                    <th>Usage</th>
 +
                                    <th>Sequence Verification</th>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549026" target="_blank">BBa_K2549026</a></td>
 +
                                    <td> 8*ZF21.16-minCMV</td>
 +
                                    <td>8 copies of RE for ZF21.16 transcriptional activator to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--026_TGCCACCTGACGTCTAAGAA_added.abl.zip" target="_blank">026.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549027" target="_blank">BBa_K2549027</a></td>
 +
                                    <td> 8*ZF42.10-minCMV</td>
 +
                                    <td>8 copies of RE for ZF42.10 transcriptional activator to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--027_TGCCACCTGACGTCTAAGAA_added.abl.zip" target="_blank">027.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549028" target="_blank">BBa_K2549028</a></td>
 +
                                    <td> 8*ZF43.8-minCMV</td>
 +
                                    <td>8 copies of RE for ZF43.8 transcriptional activator to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--028_TGCCACCTGACGTCTAAGAA_added.abl.zip" target="_blank">028.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank">BBa_K2549029</a></td>
 +
                                    <td> 8*ZF21.16-CMV</td>
 +
                                    <td>8 copies of RE for ZF21.16 transcriptional activator to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--029_TGCCACCTGACGTCTAAGAA_added.abl.zip" target="_blank">029.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549030" target="_blank">BBa_K2549030</a></td>
 +
                                    <td> 8*ZF42.10-CMV</td>
 +
                                    <td>8 copies of RE for ZF42.10 transcriptional activator to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--030_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">030.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549031" target="_blank">BBa_K2549031</a></td>
 +
                                    <td> 8*ZF43.8-CMV</td>
 +
                                    <td>8 copies of RE for ZF43.8 transcriptional activator to bind</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--031_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">031.ab1</a></td>
 +
                                </tr>
 +
                            </table>
 +
                        </div>
 +
                        <h3> TEV protease-based</h3>
 +
                        <p>For IMPLY gate, we placed TEV protease-controlled destroyable nuclear localization sequence between zinc finger DNA binding domain (DBD) and transcription factor (TF). In the presence of intracellular TEV protease, DBD-TF would be cleaved, thus destroying its transcriptional regulation function and efficiently blocking its signal. For more details, please visit our <a href="/Team:Fudan-TSI/Results" target=”_blank”>results page</a>.</p>
 +
                        <div class="tableHolder">
 +
                            <table class="striped">
 +
                                <tr>
 +
                                    <th> BioBrick ID</th>
 +
                                    <th>Protein Name</th>
 +
                                    <th>Sequence Verification</th>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549039" target="_blank">BBa_K2549039</a></td>
 +
                                    <td> VP64-dNLS-ZF21.16</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--039_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">039.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549040" target="_blank">BBa_K2549040</a></td>
 +
                                    <td> KRAB-dNLS-ZF21.16</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--040_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">040.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549041" target="_blank">BBa_K2549041</a></td>
 +
                                    <td> NLS-TEVp</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--041.abl.zip" target="_blank">041.ab1</a></td>
 +
                                </tr>
 +
                            </table>
 +
                        </div>
 +
                        <h3>Split intein-based</h3>
 +
                        <p>We built the more complex binary logic gates, such as XOR and XNOR gate, using split intein-based Amplifiers. Utilizing intein's ability to fuse the split ends of a transcription factor together, we're able to present these logic gates consistent with our 3-layer design principle. For more details, please visit our <a href="/Team:Fudan-TSI/Results" target=”_blank”>results page</a>.</p>
 +
                        <div class="tableHolder">
 +
                            <table class="striped">
 +
                                <tr>
 +
                                    <th> BioBrick ID</th>
 +
                                    <th>Protein Name</th>
 +
                                    <th>Sequence Verification</th>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549036" target="_blank">BBa_K2549036</a></td>
 +
                                    <td> VP64-ZF21.16N-CfaN</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--036_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">036.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549037" target="_blank">BBa_K2549037</a></td>
 +
                                    <td> KRAB-ZF21.16N-CfaN</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--037_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">037.ab1</a></td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549038" target="_blank">BBa_K2549038</a></td>
 +
                                    <td> CfaC-ZF21.16C-NLS</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--038_TGCCACCTGACGTCTAAGAA_added.abl.zip" target="_blank">038.ab1</a></td>
 +
                                </tr>
 +
<tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549042" target="_blank">BBa_K2549042</a></td>
 +
                                    <td>NLS-TEVpN-CfaN</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--042_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">042.ab1</a></td>
 +
                                </tr>
 +
<tr>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549043" target="_blank">BBa_K2549043</a></td>
 +
                                    <td>CfaC-TEVpC</td>
 +
                                    <td><a href="https://2018.igem.org/File:T--Fudan--043_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">043.ab1</a></td>
 +
                                </tr>
 +
                            </table>
 +
                        </div>
 +
                    </div>
 +
                    <div id="section4" class="section container scrolSpy">
 +
                        <h2>ENABLE - 16 logic gates for transmembrane signaling</h2>
 +
<div class="tableHolder">
 +
                            <table class="striped">
 +
                                <tr>
 +
                                    <th> Gate</th>
 +
                                    <th>Intracellular Domain of the Receptor</th>
 +
                                    <th>the Amplifier</th>
 +
                                    <th>the Combiner</th>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> TRUE</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>/</td>
 +
                                    <td>CMV-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> FALSE</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>/</td>
 +
                                    <td>/</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> A</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549023" target="_blank">ZF21.16-VP64</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549026" target="_blank">8*ZF21.16-minCMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> B</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>4*UAS-<a href="http://parts.igem.org/Part:BBa_K2549023" target="_blank">ZF21.16-VP64</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549026" target="_blank">8*ZF21.16-minCMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> NOT&nbsp;A</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2446039" target="_blank">ZF21.16-KRAB</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank">8*ZF21.16-CMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> NOT&nbsp;B</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>4*UAS-<a href="http://parts.igem.org/Part:BBa_K2446039" target="_blank">ZF21.16-KRAB</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank">8*ZF21.16-CMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> OR</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549023" target="_blank">ZF21.16-VP64</a><div class="divider"></div>
 +
                                        4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2549023" target="_blank">ZF21.16-VP64</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549026" target="_blank">8*ZF21.16-minCMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> NOR</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2446039" target="_blank">ZF21.16-KRAB</a><div class="divider"></div>
 +
                                        4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2446039" target="_blank">ZF21.16-KRAB</a></td>
 +
                                    <td>8*ZF21.16-CMV<a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank"></a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> XOR</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549039" target="_blank">VP64-dNLS-ZF21.16</a>-T2A-<a href="http://parts.igem.org/Part:BBa_K2549042" target="_blank">NLS-TEVpN-CfaN</a><div class="divider"></div>
 +
                                        4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2549043" target="_blank">CfaC-TEVpC</a>-T2A-<a href="http://parts.igem.org/Part:BBa_K2549039" target="_blank">VP64-dNLS-ZF21.16</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549026" target="_blank">8*ZF21.16-minCMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> AND</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549036" target="_blank">VP64-ZF21.16N-CfaN</a><div class="divider"></div>
 +
                                        4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2549038" target="_blank">CfaC-ZF21.16C-NLS</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549026" target="_blank">8*ZF21.16-minCMV</a>-d2EGFP </td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> NAND</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549037" target="_blank">KRAB-ZF21.16N-CfaN</a><div class="divider"></div>
 +
                                        4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2549038" target="_blank">CfaC-ZF21.16C-NLS</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank">8*ZF21.16-CMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> A&nbsp;IMPLY&nbsp;B</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549040" target="_blank">KRAB-dNLS-ZF21.16</a><div class="divider"></div>
 +
                                        4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2549041" target="_blank">NLS-TEVp</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank">8*ZF21.16-CMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> B&nbsp;IMPLY&nbsp;A</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>4*UAS-minCMV-<a href="http://parts.igem.org/Part::BBa_K254904" target="_blank">KRAB-dNLS-ZF21.16</a><div class="divider"></div>
 +
                                        TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549041" target="_blank">NLS-TEVp</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank">8*ZF21.16-CMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> A&nbsp;NIMPLY&nbsp;B</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549023" target="_blank">ZF21.16-VP64</a><div class="divider"></div>
 +
                                        4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2446041" target="_blank">ZF43.8-KRAB</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549035" target="_blank">8*ZF21.16-minCMV-2*ZF43.8</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> B&nbsp;NIMPLY&nbsp;A</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2549023" target="_blank">ZF21.16-VP64</a><div class="divider"></div>
 +
                                        TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2446041" target="_blank">ZF43.8-KRAB</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549035" target="_blank">8*ZF21.16-minCMV-2*ZF43.8</a>-d2EGFP</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td> XNOR</td>
 +
                                    <td>tTAA + Gal4-VP64</td>
 +
                                    <td>TRE3GV-<a href="http://parts.igem.org/Part:BBa_K2549040" target="_blank">KRAB-dNLS-ZF21.16</a>-T2A-<a href="http://parts.igem.org/Part:BBa_K2549042" target="_blank">NLS-TEVpN-CfaN</a><div class="divider"></div>
 +
                                        4*UAS-minCMV-<a href="http://parts.igem.org/Part:BBa_K2549043" target="_blank">CfaC-TEVpC</a>-T2A-<a href="http://parts.igem.org/Part:BBa_K2549040" target="_blank">KRAB-dNLS-ZF21.16</a></td>
 +
                                    <td><a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank">8*ZF21.16-CMV</a>-d2EGFP</td>
 +
                                </tr>
 +
                            </table>
 +
                        </div>
 +
<p>Here is our 3-layer design of transmembrane binary logic gates. On the left lying a truth table which indicates the inputs and outputs of the according logic computation. What is set on the right is how it works. The double crossline on the top represents the plasma membrane. A and B signify the signal input, which are surface-expressed EGFP and surface-expressed CD19 in our system. What are embed on the membrane are our SynNotch receptors, the intracellular domain of which are transcriptional activators, which are  tTAA and GV2 in our assay. The large rectangle represents the nucleus. The elongated rectangle with an array before represents the genetic circuit that are under control of the transcriptional factors. Squares in groups of three represent transcriptional factors that are amplified by the amplifier layer. You can swipe the bar to detect other gates by yourself.</p>
 +
 
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                            <div class="galleryActive">
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                            </div>
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                            <div class="galleryBtnLeft hide-on-small-only"><i class="fa fa-angle-left"></i></div>
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                        </div>
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                    </div>
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                </main>
 +
            </div>
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 +
            <!--Abstract on content page-->
 +
            <div id="abstractContent" class="z-depth-2">
 +
                <a href="#!"><img alt=alt="project summary" src="https://static.igem.org/mediawiki/2018/9/96/T--Fudan--X.svg"></a>
 +
                <div class="container">
 +
                    <h2 style="margin: 0;padding: 10px 0;">Project Summary</h2>
 +
                    <p style="margin: 0">Contact-dependent signaling is critical for multicellular biological
 +
                            events, yet customizing contact-dependent signal transduction between
 +
                            cells remains challenging. Here we have developed the ENABLE toolbox, a
 +
                            complete set of transmembrane binary logic gates. Each gate consists of
 +
                            3 layers: Receptor, Amplifier, and Combiner. We first optimized synthetic
 +
                            Notch receptors to enable cells to respond to different signals across the
 +
                            membrane reliably. These signals, individually amplified intracellularly by
 +
                            transcription, are further combined for computing. Our engineered zinc finger-based
 +
                            transcription factors perform binary computation and output designed products.
 +
                            In summary, we have combined spatially different signals in mammalian cells,
 +
                            and revealed new potentials for biological oscillators, tissue engineering,
 +
                            cancer treatments, bio-computing, etc. ENABLE is a toolbox for constructing
 +
                            contact-dependent signaling networks in mammals. The 3-layer design principle
 +
                            underlying ENABLE empowers any future development of transmembrane logic circuits,
 +
                            thus contributes a foundational advance to Synthetic Biology.
 +
                    </p>
 +
                </div>
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            </div>
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                            <h3 class="col s12" style="text-align: left; color: rgba(255, 255, 255, 0.8); font-size: 18px">ENABLE: making cells even smarter</h3>
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Revision as of 06:32, 29 August 2019

<script src="https://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.11.3.min.js"></script> 2019 Team:Fudan -Part_Collection

Part collection

Our parts collection provides an extensive toolbox for researchers to construct their own transmembrane logic gates in mammalian cells.

Part collection

Our parts collection provides an extensive toolbox for researchers to construct their own transmembrane logic gates in mammalian cells.

Our parts collection provides an extensive toolbox for researchers to construct their own transmembrane logic gates in mammalian cells. These parts were made as BioBricks, and are NOT ready for transfecting mammalian cells. Plasmids with these parts in eukaryotic expression backbone are available upon request.

Our parts collection contains all essential components of our ENABLE toolbox, that could also be divided into several sets, enabling others to readily utilize them to improve their existing genetic circuits.

Following our 3-layer design principle, all ENABLE components have been well characterized, including our SynNotch receptors, Amplifiers and Combiners. In the collection, we have provided 7 versions of SynNotch receptors with (1) different combinations of extracellular domains which can bind to different antigens with different affinities, (2) transmembrane domains with varying cleavage efficiency and (3) intracellular domains executing diverse transcriptional amplifications.

We have provided a set of transcriptional amplifiers including zinc finger-based, TEV protease-based and split intein-based ones, allowing others to build their own genetic circuits, preferably through transcription (we have tested), but not limited to (we have not tested). Besides, a set of combiners with different copies of response elements are provided, which makes it easy for others to tune the activation or repression threshold. This feature was experimental confirmed previously and mathematically modeled in our 3-layer design again this year. Our modeling process could be used by others to predict their own genetic circuits before any wet-lab experiments.

Each part (sometimes two combined) constitutes one of our ENABLE module, which has its unique function. Yet they consolidate together to create all the 16 transmembrane binary logic gates for mammalian cells.

SynNotch receptors set

We have provided 7 versions of SynNotch receptors. Each of them can transduce signal from out of the cell via a contact-dependent antigen-stimulated cleavage process. When expressing two SynNotch receptors with two different extracellular domains recognizing two types of antigens, the cell is able to accept dual inputs. The chosen nanobodies are highly specific against their antigens, and the chosen intracellular domains are transcriptionally orthogonal. For more specific details, please refer to our parts listed below.

BioBrick ID Protein Name Recognized Antigen (affinity) Transmembrane Domain Intracellular Domain Sequence Verification
BBa_K2549016 LaG17-mN1c-tTAA GFP (low) mouse Notch1 core tTA advance 016.ab1
BBa_K2549017 LaG17-mN1ce-tTAA GFP (low) mouse Notch1 extended core tTA advance 017.ab1
BBa_K2549018 LaG16-mN1ce-tTAA GFP (high) mouse Notch1 extended core tTA advance 018.ab1
BBa_K2549019 LaG16-2-mN1c-tTAA GFP (ultrahigh) mouse Notch1 core tTA advance 019.ab1
BBa_K2549020 LaG16-2-mN1c-GV2 GFP (ultrahigh) mouse Notch1 core Gal4-VP64 020.ab1
BBa_K2549021 αCD19-mN1c-tTAA CD19 mouse Notch1 core Gal4-VP64 021.ab1
BBa_K2549022 αCD19-mN1c-GV2 CD19 mouse Notch1 core Gal4-VP64 022.ab1

Transcriptional amplifiers set

Last year, we have constructed 3 zinc finger-based transcription repressors. This year, we have expanded our zinc finger-based transcription factors library by adding 3 more zinc finger-based transcription activators.

Although we prefer to use eight copies of response elements (RE) for a balance between not-too-hard molecular cloning and sufficient signal-to-noise ratio, we have provided 4 promotors with different repeats of response elements, allowing others to explore and tune their own transcriptional amplifiers. Latest modeling strongly supports our experimental preference, showing that eight copies of response elements can render the best result in line with our needs.

BioBrick ID Protein Name DNA Binding Domain Transcriptional Sequence Verification
BBa_K2549023 ZF21.16-VP64 ZF21.16 activation 023.ab1
BBa_K2549024 ZF42.10-VP64 ZF42.10 activation 024.ab1
BBa_K2549025 ZF43.8-VP64 ZF43.8 activation 025.ab1
BBa_K2446039 ZF21.16-KRAB ZF21.16 repression 039.abl
BBa_K2446040 ZF42.10-KRAB ZF42.10 repression 040.abl
BBa_K2446041 ZF43.8-KRAB ZF43.8 repression 041.abl
BioBrick ID DNA Name Usage Sequence Verification
BBa_K2549032 4*ZF21.16-minCMV-2*ZF43.8 4 copies of RE for ZF21.16 transcriptional activator to bind, and 2 copies of RE for ZF43.8 transcriptional repressor to bind 032.ab1
BBa_K2549033 6*ZF21.16-minCMV-2*ZF43.8 6 copies of RE for ZF21.16 transcriptional activator to bind, and 2 copies of RE for ZF43.8 transcriptional repressor to bind 033.ab1
BBa_K2549034 8*ZF21.16-minCMV-2*ZF43.8 8 copies of RE for ZF21.16 transcriptional activator to bind, and 2 copies of RE for ZF43.8 transcriptional repressor to bind 034.ab1
BBa_K2549035 8*ZF21.16-minCMV-8*ZF43.8 8 copies of RE for ZF21.16 transcriptional activator to bind, and 8 copies of RE for ZF43.8 transcriptional repressor to bind 035.ab1

As is stated above, we have provided three types of transcriptional-based Amplifiers, including zinc finger-based, TEV protease-based and split intein-based. These Amplifiers must be used with our Combiners to execute designed binary logic function.

Amplifiers and Combiners work together to execute binary computation

Zinc finger-based

For simple binary logic function, such as A gate, NOT A gate, OR gate, NOR gate, and NIMPLY gate, placing response elements upstream and downstream of the promoter is sufficient. For more details, please visit our results page.

BioBrick ID Combiner Name Usage Sequence Verification
BBa_K2549026 8*ZF21.16-minCMV 8 copies of RE for ZF21.16 transcriptional activator to bind 026.ab1
BBa_K2549027 8*ZF42.10-minCMV 8 copies of RE for ZF42.10 transcriptional activator to bind 027.ab1
BBa_K2549028 8*ZF43.8-minCMV 8 copies of RE for ZF43.8 transcriptional activator to bind 028.ab1
BBa_K2549029 8*ZF21.16-CMV 8 copies of RE for ZF21.16 transcriptional activator to bind 029.ab1
BBa_K2549030 8*ZF42.10-CMV 8 copies of RE for ZF42.10 transcriptional activator to bind 030.ab1
BBa_K2549031 8*ZF43.8-CMV 8 copies of RE for ZF43.8 transcriptional activator to bind 031.ab1

TEV protease-based

For IMPLY gate, we placed TEV protease-controlled destroyable nuclear localization sequence between zinc finger DNA binding domain (DBD) and transcription factor (TF). In the presence of intracellular TEV protease, DBD-TF would be cleaved, thus destroying its transcriptional regulation function and efficiently blocking its signal. For more details, please visit our results page.

BioBrick ID Protein Name Sequence Verification
BBa_K2549039 VP64-dNLS-ZF21.16 039.ab1
BBa_K2549040 KRAB-dNLS-ZF21.16 040.ab1
BBa_K2549041 NLS-TEVp 041.ab1

Split intein-based

We built the more complex binary logic gates, such as XOR and XNOR gate, using split intein-based Amplifiers. Utilizing intein's ability to fuse the split ends of a transcription factor together, we're able to present these logic gates consistent with our 3-layer design principle. For more details, please visit our results page.

BioBrick ID Protein Name Sequence Verification
BBa_K2549036 VP64-ZF21.16N-CfaN 036.ab1
BBa_K2549037 KRAB-ZF21.16N-CfaN 037.ab1
BBa_K2549038 CfaC-ZF21.16C-NLS 038.ab1
BBa_K2549042 NLS-TEVpN-CfaN 042.ab1
BBa_K2549043 CfaC-TEVpC 043.ab1

ENABLE - 16 logic gates for transmembrane signaling

Gate Intracellular Domain of the Receptor the Amplifier the Combiner
TRUE tTAA + Gal4-VP64 / CMV-d2EGFP
FALSE tTAA + Gal4-VP64 / /
A tTAA + Gal4-VP64 TRE3GV-ZF21.16-VP64 8*ZF21.16-minCMV-d2EGFP
B tTAA + Gal4-VP64 4*UAS-ZF21.16-VP64 8*ZF21.16-minCMV-d2EGFP
NOT A tTAA + Gal4-VP64 TRE3GV-ZF21.16-KRAB 8*ZF21.16-CMV-d2EGFP
NOT B tTAA + Gal4-VP64 4*UAS-ZF21.16-KRAB 8*ZF21.16-CMV-d2EGFP
OR tTAA + Gal4-VP64 TRE3GV-ZF21.16-VP64
4*UAS-minCMV-ZF21.16-VP64		 8*ZF21.16-minCMV-d2EGFP
NOR tTAA + Gal4-VP64 TRE3GV-ZF21.16-KRAB
4*UAS-minCMV-ZF21.16-KRAB		 8*ZF21.16-CMV-d2EGFP
XOR tTAA + Gal4-VP64 TRE3GV-VP64-dNLS-ZF21.16-T2A-NLS-TEVpN-CfaN
4*UAS-minCMV-CfaC-TEVpC-T2A-VP64-dNLS-ZF21.16		 8*ZF21.16-minCMV-d2EGFP
AND tTAA + Gal4-VP64 TRE3GV-VP64-ZF21.16N-CfaN
4*UAS-minCMV-CfaC-ZF21.16C-NLS		 8*ZF21.16-minCMV-d2EGFP
NAND tTAA + Gal4-VP64 TRE3GV-KRAB-ZF21.16N-CfaN
4*UAS-minCMV-CfaC-ZF21.16C-NLS		 8*ZF21.16-CMV-d2EGFP
A IMPLY B tTAA + Gal4-VP64 TRE3GV-KRAB-dNLS-ZF21.16
4*UAS-minCMV-NLS-TEVp		 8*ZF21.16-CMV-d2EGFP
B IMPLY A tTAA + Gal4-VP64 4*UAS-minCMV-KRAB-dNLS-ZF21.16
TRE3GV-NLS-TEVp		 8*ZF21.16-CMV-d2EGFP
A NIMPLY B tTAA + Gal4-VP64 TRE3GV-ZF21.16-VP64
4*UAS-minCMV-ZF43.8-KRAB		 8*ZF21.16-minCMV-2*ZF43.8-d2EGFP
B NIMPLY A tTAA + Gal4-VP64 4*UAS-minCMV-ZF21.16-VP64
TRE3GV-ZF43.8-KRAB		 8*ZF21.16-minCMV-2*ZF43.8-d2EGFP
XNOR tTAA + Gal4-VP64 TRE3GV-KRAB-dNLS-ZF21.16-T2A-NLS-TEVpN-CfaN
4*UAS-minCMV-CfaC-TEVpC-T2A-KRAB-dNLS-ZF21.16		 8*ZF21.16-CMV-d2EGFP

Here is our 3-layer design of transmembrane binary logic gates. On the left lying a truth table which indicates the inputs and outputs of the according logic computation. What is set on the right is how it works. The double crossline on the top represents the plasma membrane. A and B signify the signal input, which are surface-expressed EGFP and surface-expressed CD19 in our system. What are embed on the membrane are our SynNotch receptors, the intracellular domain of which are transcriptional activators, which are tTAA and GV2 in our assay. The large rectangle represents the nucleus. The elongated rectangle with an array before represents the genetic circuit that are under control of the transcriptional factors. Squares in groups of three represent transcriptional factors that are amplified by the amplifier layer. You can swipe the bar to detect other gates by yourself.

alt="project

Project Summary

Contact-dependent signaling is critical for multicellular biological events, yet customizing contact-dependent signal transduction between cells remains challenging. Here we have developed the ENABLE toolbox, a complete set of transmembrane binary logic gates. Each gate consists of 3 layers: Receptor, Amplifier, and Combiner. We first optimized synthetic Notch receptors to enable cells to respond to different signals across the membrane reliably. These signals, individually amplified intracellularly by transcription, are further combined for computing. Our engineered zinc finger-based transcription factors perform binary computation and output designed products. In summary, we have combined spatially different signals in mammalian cells, and revealed new potentials for biological oscillators, tissue engineering, cancer treatments, bio-computing, etc. ENABLE is a toolbox for constructing contact-dependent signaling networks in mammals. The 3-layer design principle underlying ENABLE empowers any future development of transmembrane logic circuits, thus contributes a foundational advance to Synthetic Biology.