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

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        <a href="https://2017.igem.org/Team:Fudan/Demonstrate"><img class="align" id="align-1" src='https://static.igem.org/mediawiki/2017/9/93/T--Fudan--synNotch.png' /></a>
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        <a href="https://2017.igem.org/Team:Fudan/Basic_Part"><img class="align" id="align-4" src='https://static.igem.org/mediawiki/2017/2/24/T--Fudan--hccOrange.png' /></a>
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        <a href="https://2017.igem.org/Team:Fudan/Composite_Part"><img class="align" id="align-3" src='https://static.igem.org/mediawiki/2017/6/66/T--Fudan--synTF.png' /></a>
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        <a href="https://2017.igem.org/Team:Fudan/Part_Collection"><img class="align" id="align-2" src='https://static.igem.org/mediawiki/2017/0/0c/T--Fudan--stripe.png' /></a>
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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</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://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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</div>
 
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<div class="block main-text sub-title  dark-blue">
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  <h class="sup-title dark-blue">Part Collection</h>
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<h2> </h2>
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<div class="block main-text main-text">
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  <p>As a team focusing on real-world problem, we found it is hard to obtain sufficient mammalian Biobricks on the Registry of Standard Biological Parts comparing to the convenience for project in bacteria. In synthetic biology, one central route is to construct a controllable biological network, and electing suitable transcription factor and corresponding promoter is vital.
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</p>
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<p>
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The best way to predict the future is to invent it. As we couldn’t find Biobricks that were completely satisfying to us, we just invent it.
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</p>
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<p>
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For this year’s iGEM competition, we present an approach to design customized mammalian synthetic transcription factor (SynTF) - synthetic promoter (SynPro) pairs. This set is a powerful toolbox to construct customized and orthogonal transcriptional network.
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</p>
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</div>
  
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<div class="block main-text main-text">
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  <h class="highlight-title dark-blue" id="Antigen"></br></br>How to design SynTF-SynPro</h><h2> </h2>
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  <p>SynTFs enable binding to user-specified DNA sequences, response element (REs), on SynPros then silencing or activating their transcription. The SynTFs we designed were in an unified style containing three core domains from N-terminal to C-terminal: DNA binding domain (DBD), nuclear location sequence (NLS), transcription regulating domain. We chose (G4S) as linker to be added between DBD and SV40 NLS for region flexibility. We could choose KRAB or VP64 as transcription regulating domain to construct silencing- or activating-form SynTFs (SynTF(S)s and SynTF(A)s). The structures of their corresponding silencing- or activating-form SynPros (SynPro(S)s and SynPro(A)s) were pSV40-N*RE or N*RE-minCMV.
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<div align="center">
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<img src="https://static.igem.org/mediawiki/2017/c/ca/T--Fudan--PCFigure.jpg">
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  <p>The critical step to find optional SynTF group is to find enough differently specific and orthogonal DBDs. We applied two approaches to achieve this. Firstly, we widely investigated those commonly used DBD originating from different species. Secondly, we devised a platform based on artificial zinc-finger (ZF). For the first idea, we chose Gal4DBD, PIP, ZFHD1 from a large number of candidates. For the second idea, we utilized a modified 3-tendem Cys2-His2 ZF as protein chassis. By replacing the DNA-interactional amino residues on ZF modules, we can generate RE-specific mammalian synthetic ZF (SynZF).
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<div class="column full_size">
 
  
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<h1> Part Collection </h1>
 
  
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<div class="block main-text main-text">
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  <h class="highlight-title dark-blue" id="Antigen"></br></br>The advantages of SynTF-SynPro</h><h2> </h2>
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<p>
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1. It is a unified design for applying both natural DBDs and artificial SynZFs as DBDs on SynTFs.
 +
</p>
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<p>
 +
2. It is a tunable design as you can adjust the silencing or activating fold by different repeats of REs.
 +
</p>
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<p>
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3. It is a universal design because ZF is a highly modular motif. You can design more than 4<sup>9</sup> specific SynZF–RE pairs theoretically.
 +
</p>
 +
 +
</div>
  
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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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<div class="block main-text main-text">
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  <h class="highlight-title dark-blue" id="Antigen"></br></br>Attention</h><h2> </h2>
 
<p>
 
<p>
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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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Cause the following reasons, actually functional SynZFs are much less than 4<sup>9</sup>: </p><p>
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1. one unit SynZF motif cannot recognize all the permutation of 3 consecutive bases.  </p><p>
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2. SynTF are probably not all complete orthogonal to each other. </p><p>
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3. RE repeats on SynPro can influence the function of chassis promoters. </p><p>
 +
Thus, before you applying our idea into your project. A pilot test is strongly needed.
 
</p>
 
</p>
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<br>
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</div>
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<h3>Best Part Collection Special Prize</h3>
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<p>Did your team make a lot of great parts? Is there a team 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? Tell the judges you should be evaluated for the Best Parts Collection award! To be eligible for this award, these parts must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts.
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<br><br>
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If you have a collection of parts you wish to nominate your team for this <a href="https://2017.igem.org/Judging/Awards">special prize</a>, make sure you add your part numbers to your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.</p>
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<br>
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<div class="block main-text main-text">
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  <h class="highlight-title dark-blue" id="Antigen"></br></br>See More</h><h2> </h2>
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<p>
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Integrated information about Part Collection posted on <a href="https://2017.igem.org/Team:Fudan/Demonstrate">Demonstrate</a>: Wiring orthogonal and tunable SynTF-SynPro repertoire. You cannot miss it.
 +
</p>
 +
<p>
  
 +
We listed Biobricks belong to Part Collection below.
  
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<div class="highlight">
 
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<h4>Note</h4>
 
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<p>This page should list all the parts in the collection your team made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page.</p>
 
  
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<table class="tg" width="60%" style="border-collapse:separate; border-spacing:2px 10px;">
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  <tr>
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    <th colspan="2"><b>SynTFs</b></th>
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    <th colspan="2"><b>SynPros</b></th>
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  </tr>
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  <tr>
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    <td>Gal4-KRAB(TF-KRAB-1)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446037”>(BBa_K2446037)</a></td>
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    <td>Sv40-UAS(Sv40-UAS)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446036”>(BBa_K2446036)</a></td>
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  </tr>
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    <td rowspan="3">ZF_PIP_KRAB(TF-KRAB-2)</td>
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    <td rowspan="3"><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446045”>(BBa_K2446045)</a></td>
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    <td>SV40_2_PIP</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446033”>(BBa_K2446033)</a></td>
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  </tr>
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  <tr>
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    <td>SV40_4_PIP</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446034”>(BBa_K2446034)</a></td>
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  </tr>
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  <tr>
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    <td>SV40_8_PIP</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446035”>(BBa_K2446035)</a></td>
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  </tr>
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  <tr>
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    <td>ZF_21-16KRAB(TF-KRAB-3)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446039”>(BBa_K2446039)</a></td>
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    <td>SV40_8_ZF_21-16</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446030”>(BBa_K2446030)</a></td>
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    <td>ZF_42-10_KRAB(TF-KRAB-4)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446040”>(BBa_K2446040)</a></td>
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    <td>SV40_8_ZF_42-10</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446025”>(BBa_K2446025)</a></td>
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  </tr>
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  <tr>
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    <td rowspan="3">ZF_43-8_KRAB(TF-KRAB-5)</td>
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    <td rowspan="3"><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446041”>(BBa_K2446041)</a></td>
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    <td>SV40_2_ZF_43-8</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446026”>(BBa_K2446026)</a></td>
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  </tr>
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  <tr>
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    <td>SV40_4_ZF_43-8</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446027”>(BBa_K2446027)</a></td>
 +
  </tr>
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  <tr>
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    <td>SV40_8_ZF_43-8</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446028”>(BBa_K2446028)</a></td>
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  </tr>
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  <tr>
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    <td>ZF_54-8_KRAB(TF-KRAB-6)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446042”>(BBa_K2446042)</a></td>
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    <td>SV40_8_ZF_54-8</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446029”>(BBa_K2446029)</a></td>
 +
  </tr>
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  <tr>
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    <td>ZFHD1_KRAB(TF-KRAB-7)</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446043”>(BBa_K2446043)</a></td>
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    <td>SV40_4_ZFHD1</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446032”>(BBa_K2446032)</a></td>
 +
  </tr>
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</table>
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{{Fudan/PageFooter}}

Latest revision as of 23:47, 1 November 2017
Part Collection

As a team focusing on real-world problem, we found it is hard to obtain sufficient mammalian Biobricks on the Registry of Standard Biological Parts comparing to the convenience for project in bacteria. In synthetic biology, one central route is to construct a controllable biological network, and electing suitable transcription factor and corresponding promoter is vital.

The best way to predict the future is to invent it. As we couldn’t find Biobricks that were completely satisfying to us, we just invent it.

For this year’s iGEM competition, we present an approach to design customized mammalian synthetic transcription factor (SynTF) - synthetic promoter (SynPro) pairs. This set is a powerful toolbox to construct customized and orthogonal transcriptional network.



How to design SynTF-SynPro

SynTFs enable binding to user-specified DNA sequences, response element (REs), on SynPros then silencing or activating their transcription. The SynTFs we designed were in an unified style containing three core domains from N-terminal to C-terminal: DNA binding domain (DBD), nuclear location sequence (NLS), transcription regulating domain. We chose (G4S) as linker to be added between DBD and SV40 NLS for region flexibility. We could choose KRAB or VP64 as transcription regulating domain to construct silencing- or activating-form SynTFs (SynTF(S)s and SynTF(A)s). The structures of their corresponding silencing- or activating-form SynPros (SynPro(S)s and SynPro(A)s) were pSV40-N*RE or N*RE-minCMV.

The critical step to find optional SynTF group is to find enough differently specific and orthogonal DBDs. We applied two approaches to achieve this. Firstly, we widely investigated those commonly used DBD originating from different species. Secondly, we devised a platform based on artificial zinc-finger (ZF). For the first idea, we chose Gal4DBD, PIP, ZFHD1 from a large number of candidates. For the second idea, we utilized a modified 3-tendem Cys2-His2 ZF as protein chassis. By replacing the DNA-interactional amino residues on ZF modules, we can generate RE-specific mammalian synthetic ZF (SynZF).



The advantages of SynTF-SynPro

1. It is a unified design for applying both natural DBDs and artificial SynZFs as DBDs on SynTFs.

2. It is a tunable design as you can adjust the silencing or activating fold by different repeats of REs.

3. It is a universal design because ZF is a highly modular motif. You can design more than 49 specific SynZF–RE pairs theoretically.



Attention

Cause the following reasons, actually functional SynZFs are much less than 49:

1. one unit SynZF motif cannot recognize all the permutation of 3 consecutive bases.

2. SynTF are probably not all complete orthogonal to each other.

3. RE repeats on SynPro can influence the function of chassis promoters.

Thus, before you applying our idea into your project. A pilot test is strongly needed.



See More

Integrated information about Part Collection posted on Demonstrate: Wiring orthogonal and tunable SynTF-SynPro repertoire. You cannot miss it.

We listed Biobricks belong to Part Collection below.

SynTFs SynPros
Gal4-KRAB(TF-KRAB-1) (BBa_K2446037) Sv40-UAS(Sv40-UAS) (BBa_K2446036)
ZF_PIP_KRAB(TF-KRAB-2) (BBa_K2446045) SV40_2_PIP (BBa_K2446033)
SV40_4_PIP (BBa_K2446034)
SV40_8_PIP (BBa_K2446035)
ZF_21-16KRAB(TF-KRAB-3) (BBa_K2446039) SV40_8_ZF_21-16 (BBa_K2446030)
ZF_42-10_KRAB(TF-KRAB-4) (BBa_K2446040) SV40_8_ZF_42-10 (BBa_K2446025)
ZF_43-8_KRAB(TF-KRAB-5) (BBa_K2446041) SV40_2_ZF_43-8 (BBa_K2446026)
SV40_4_ZF_43-8 (BBa_K2446027)
SV40_8_ZF_43-8 (BBa_K2446028)
ZF_54-8_KRAB(TF-KRAB-6) (BBa_K2446042) SV40_8_ZF_54-8 (BBa_K2446029)
ZFHD1_KRAB(TF-KRAB-7) (BBa_K2446043) SV40_4_ZFHD1 (BBa_K2446032)