Difference between revisions of "Team:Fudan/Parts Collection"

Line 313: Line 313:
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>tTA advance</td>
 
                                     <td>tTA advance</td>
−
                                     <td><a href="" target="_blank">016.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--016_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">016.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 321: Line 321:
 
                                     <td>mouse Notch1 extended core</td>
 
                                     <td>mouse Notch1 extended core</td>
 
                                     <td>tTA advance</td>
 
                                     <td>tTA advance</td>
−
                                     <td><a href="" target="_blank">017.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--017_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">017.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 329: Line 329:
 
                                     <td>mouse Notch1 extended core</td>
 
                                     <td>mouse Notch1 extended core</td>
 
                                     <td>tTA advance</td>
 
                                     <td>tTA advance</td>
−
                                     <td><a href="" target="_blank">018.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--018_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">018.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 337: Line 337:
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>tTA advance</td>
 
                                     <td>tTA advance</td>
−
                                     <td><a href="" target="_blank">019.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--019_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">019.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 345: Line 345:
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>Gal4-VP64</td>
 
                                     <td>Gal4-VP64</td>
−
                                     <td><a href="" target="_blank">020.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--020_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">020.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 353: Line 353:
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>Gal4-VP64</td>
 
                                     <td>Gal4-VP64</td>
−
                                     <td><a href="" target="_blank">021.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--021_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">021.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 361: Line 361:
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>mouse Notch1 core</td>
 
                                     <td>Gal4-VP64</td>
 
                                     <td>Gal4-VP64</td>
−
                                     <td><a href="" target="_blank">022.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--022_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">022.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                             </table>
 
                             </table>
Line 385: Line 385:
 
                                     <td>ZF21.16</td>
 
                                     <td>ZF21.16</td>
 
                                     <td>activation</td>
 
                                     <td>activation</td>
−
                                     <td><a href="" target="_blank">023.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--023_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">023.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 392: Line 392:
 
                                     <td>ZF42.10</td>
 
                                     <td>ZF42.10</td>
 
                                     <td>activation</td>
 
                                     <td>activation</td>
−
                                     <td><a href="" target="_blank">024.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--024_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">024.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 399: Line 399:
 
                                     <td>ZF43.8</td>
 
                                     <td>ZF43.8</td>
 
                                     <td>activation</td>
 
                                     <td>activation</td>
−
                                     <td><a href="" target="_blank">025.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--025_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">025.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 436: Line 436:
 
                                     <td> 4*ZF21.16-minCMV-2*ZF43.8</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>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="" target="_blank">032.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--032_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">032.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 442: Line 442:
 
                                     <td> 6*ZF21.16-minCMV-2*ZF43.8</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>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="" target="_blank">033.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--033_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">033.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 448: Line 448:
 
                                     <td> 8*ZF21.16-minCMV-2*ZF43.8</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>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="" target="_blank">034.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--034_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">034.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 477: Line 477:
 
                                     <td> 8*ZF21.16-minCMV</td>
 
                                     <td> 8*ZF21.16-minCMV</td>
 
                                     <td>8 copies of RE for ZF21.16 transcriptional activator to bind</td>
 
                                     <td>8 copies of RE for ZF21.16 transcriptional activator to bind</td>
−
                                     <td><a href="" target="_blank">026.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--026_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">026.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 483: Line 483:
 
                                     <td> 8*ZF42.10-minCMV</td>
 
                                     <td> 8*ZF42.10-minCMV</td>
 
                                     <td>8 copies of RE for ZF42.10 transcriptional activator to bind</td>
 
                                     <td>8 copies of RE for ZF42.10 transcriptional activator to bind</td>
−
                                     <td><a href="" target="_blank">027.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--027_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">027.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 489: Line 489:
 
                                     <td> 8*ZF43.8-minCMV</td>
 
                                     <td> 8*ZF43.8-minCMV</td>
 
                                     <td>8 copies of RE for ZF43.8 transcriptional activator to bind</td>
 
                                     <td>8 copies of RE for ZF43.8 transcriptional activator to bind</td>
−
                                     <td><a href="" target="_blank">028.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--028_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">028.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 495: Line 495:
 
                                     <td> 8*ZF21.16-CMV</td>
 
                                     <td> 8*ZF21.16-CMV</td>
 
                                     <td>8 copies of RE for ZF21.16 transcriptional activator to bind</td>
 
                                     <td>8 copies of RE for ZF21.16 transcriptional activator to bind</td>
−
                                     <td><a href="" target="_blank">029.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--029_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">029.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 501: Line 501:
 
                                     <td> 8*ZF42.10-CMV</td>
 
                                     <td> 8*ZF42.10-CMV</td>
 
                                     <td>8 copies of RE for ZF42.10 transcriptional activator to bind</td>
 
                                     <td>8 copies of RE for ZF42.10 transcriptional activator to bind</td>
−
                                     <td><a href="" target="_blank">030.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--030_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">030.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 507: Line 507:
 
                                     <td> 8*ZF43.8-CMV</td>
 
                                     <td> 8*ZF43.8-CMV</td>
 
                                     <td>8 copies of RE for ZF43.8 transcriptional activator to bind</td>
 
                                     <td>8 copies of RE for ZF43.8 transcriptional activator to bind</td>
−
                                     <td><a href="" target="_blank">031.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--031_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">031.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                             </table>
 
                             </table>
Line 523: Line 523:
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549039" target="_blank">BBa_K2549039</a></td>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549039" target="_blank">BBa_K2549039</a></td>
 
                                     <td> VP64-dNLS-ZF21.16</td>
 
                                     <td> VP64-dNLS-ZF21.16</td>
−
                                     <td><a href="" target="_blank">039.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--039_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">039.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549040" target="_blank">BBa_K2549040</a></td>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549040" target="_blank">BBa_K2549040</a></td>
 
                                     <td> KRAB-dNLS-ZF21.16</td>
 
                                     <td> KRAB-dNLS-ZF21.16</td>
−
                                     <td><a href="" target="_blank">040.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--040_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">040.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
Line 549: Line 549:
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549036" target="_blank">BBa_K2549036</a></td>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549036" target="_blank">BBa_K2549036</a></td>
 
                                     <td> VP64-ZF21.16N-CfaN</td>
 
                                     <td> VP64-ZF21.16N-CfaN</td>
−
                                     <td><a href="" target="_blank">036.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--036_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">036.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549037" target="_blank">BBa_K2549037</a></td>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549037" target="_blank">BBa_K2549037</a></td>
 
                                     <td> KRAB-ZF21.16N-CfaN</td>
 
                                     <td> KRAB-ZF21.16N-CfaN</td>
−
                                     <td><a href="" target="_blank">037.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--037_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">037.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                                 <tr>
 
                                 <tr>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549038" target="_blank">BBa_K2549038</a></td>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549038" target="_blank">BBa_K2549038</a></td>
 
                                     <td> CfaC-ZF21.16C-NLS</td>
 
                                     <td> CfaC-ZF21.16C-NLS</td>
−
                                     <td><a href="" target="_blank">038.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--038_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">038.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
<tr>
 
<tr>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_BBa_K2549042" target="_blank">BBa_K2549042</a></td>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_BBa_K2549042" target="_blank">BBa_K2549042</a></td>
 
                                     <td>NLS-TEVpN-CfaN</td>
 
                                     <td>NLS-TEVpN-CfaN</td>
−
                                     <td><a href="" target="_blank">042.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--042_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">042.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
<tr>
 
<tr>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549043" target="_blank">BBa_K2549043</a></td>
 
                                     <td><a href="http://parts.igem.org/Part:BBa_K2549043" target="_blank">BBa_K2549043</a></td>
 
                                     <td>CfaC-TEVpC</td>
 
                                     <td>CfaC-TEVpC</td>
−
                                     <td><a href="" target="_blank">043.ab1</a></td>
+
                                     <td><a href="https://2018.igem.org/File:T--Fudan--043_TGCCACCTGACGTCTAAGAA.abl.zip" target="_blank">043.ab1</a></td>
 
                                 </tr>
 
                                 </tr>
 
                             </table>
 
                             </table>

Revision as of 10:18, 15 October 2018

Parts collection

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

Parts collection

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

Our parts collection has provided 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.

Followed 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, allowing others to build their own genetic circuits, preferably through transcription (we have test), but not limited to (we have not test). 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(需要对应链接) 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 exprssing two SynNotch receptors with two different extracellular domains recognizing two types of antigens, the cell is able to accept dual inputs. The chosen nanobodies(需要对应链接) are highly specific against their antigens, and the chosen intracellular domains are transcriptional orthogonality. 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 additional 3 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(需要对应链接) strongly supports our experimental preference, and others could just BBa_K2549035, e.g.

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
BBa_K2446040 ZF42.10-KRAB ZF42.10 repression
BBa_K2446041 ZF43.8-KRAB ZF43.8 repression
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, the cleavage between DBD-TF would destroy the transcriptional regulation function of DBD-TF. 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 complex binary logic gates, including XOR gate and XNOR gate, using split intein-based Amplifers, still following 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 SynNotch Intracellular Domain Amplifier 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-8*ZF43.8-d2EGFP
B NIMPLY A tTAA + Gal4-VP64 4*UAS-minCMV-ZF21.16-VP64
TRE3GV-ZF43.8-KRAB		 8*ZF21.16-minCMV-8*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

Abstract

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.