Difference between revisions of "Team:Fudan/Part Collection"
Penicillin (Talk | contribs) |
Penicillin (Talk | contribs) |
||
| Line 59: | Line 59: | ||
<h class="sup-title dark-blue">Part Collection</h> | <h class="sup-title dark-blue">Part Collection</h> | ||
<h2> </h2> | <h2> </h2> | ||
| − | |||
</div> | </div> | ||
| Line 74: | Line 73: | ||
<div class="block main-text main-text"> | <div class="block main-text main-text"> | ||
| − | <h class="highlight-title dark-blue" id="Antigen"></br></br>How to design SynTF-SynPro</h> | + | <h class="highlight-title dark-blue" id="Antigen"></br></br>How to design SynTF-SynPro</h><h2> </h2> |
<p>SynTFs enable binding to user-specified DNA sequences, aka response element (REs), on SynPros then silencing or activating their transcription. The SynTFs we designed were in an elegant and unified style containing three core domains from N-terminal to C-terminal: DNA binding domain (DBD), linker and nuclear location sequence (NLS), transcription regulating domain. We chose (G4S) as linker to be added between DBD and SV40 NLS for providing 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. | <p>SynTFs enable binding to user-specified DNA sequences, aka response element (REs), on SynPros then silencing or activating their transcription. The SynTFs we designed were in an elegant and unified style containing three core domains from N-terminal to C-terminal: DNA binding domain (DBD), linker and nuclear location sequence (NLS), transcription regulating domain. We chose (G4S) as linker to be added between DBD and SV40 NLS for providing 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. | ||
</p> | </p> | ||
| Line 81: | Line 80: | ||
<div class="block main-text main-text"> | <div class="block main-text main-text"> | ||
| − | <h class="highlight-title dark-blue" id="Antigen"></br></br>The advantages of pSV40-ZF43-8;8*</h> | + | <h class="highlight-title dark-blue" id="Antigen"></br></br>The advantages of pSV40-ZF43-8;8*</h><h2> </h2> |
<p>The critical point for enlarging optional SynTF group is to find enough differently specific and orthogonal DBDs. We applied two ideas to achieve this. Firstlly, 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 aminol residues on ZF modules, we can generate RE-specific mammalian synthetic ZF (SynZF). | <p>The critical point for enlarging optional SynTF group is to find enough differently specific and orthogonal DBDs. We applied two ideas to achieve this. Firstlly, 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 aminol residues on ZF modules, we can generate RE-specific mammalian synthetic ZF (SynZF). | ||
</p> | </p> | ||
| Line 92: | Line 91: | ||
<div class="block main-text main-text"> | <div class="block main-text main-text"> | ||
| − | <h class="highlight-title dark-blue" id="Antigen"></br></br>The advantages of SynTF-SynPro</h> | + | <h class="highlight-title dark-blue" id="Antigen"></br></br>The advantages of SynTF-SynPro</h><h2> </h2> |
<p> | <p> | ||
| − | It is a unified design for applying both natural DBDs and artificial SynZFs as DBDs on SynTFs. | + | 1. It is a unified design for applying both natural DBDs and artificial SynZFs as DBDs on SynTFs. |
</p> | </p> | ||
<p> | <p> | ||
| − | It is a tunable design as you can adjust the silencing or activating fold by take different repeats of RES. | + | 2. It is a tunable design as you can adjust the silencing or activating fold by take different repeats of RES. |
</p> | </p> | ||
<p> | <p> | ||
| − | It is a universal design because ZF is a highly modular motif. You can design more than 49 specific SynZF–RE pairs theoretically. | + | 3. It is a universal design because ZF is a highly modular motif. You can design more than 49 specific SynZF–RE pairs theoretically. |
</p> | </p> | ||
| Line 107: | Line 106: | ||
<div class="block main-text main-text"> | <div class="block main-text main-text"> | ||
| − | <h class="highlight-title dark-blue" id="Antigen"></br></br>Attention:</h> | + | <h class="highlight-title dark-blue" id="Antigen"></br></br>Attention:</h><h2> </h2> |
<p> | <p> | ||
Cause the following reason, actually functional SynZFs are much less than 49: </br> | Cause the following reason, actually functional SynZFs are much less than 49: </br> | ||
| Line 118: | Line 117: | ||
<div class="block main-text main-text"> | <div class="block main-text main-text"> | ||
| − | <h class="highlight-title dark-blue" id="Antigen"></br></br>See More</h> | + | <h class="highlight-title dark-blue" id="Antigen"></br></br>See More</h><h2> </h2> |
<p> | <p> | ||
Integrated information about Part Collection posted on Demonstrate page: Wiring orthogonal and tunable SynTF-SynPro repertoire. You cannot miss it. | Integrated information about Part Collection posted on Demonstrate page: Wiring orthogonal and tunable SynTF-SynPro repertoire. You cannot miss it. | ||
Revision as of 00:46, 1 November 2017
|
|
|
|
As a team focusing on real-world problem in mammal, we found it hard to obtain criterial mammalian Biobricks on the Registr y of Standard Biological Parts comparing to the convenience for project in bacteria. In synthetic biology, one central route is to construct a controllable biology network, so 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.
SynTFs enable binding to user-specified DNA sequences, aka response element (REs), on SynPros then silencing or activating their transcription. The SynTFs we designed were in an elegant and unified style containing three core domains from N-terminal to C-terminal: DNA binding domain (DBD), linker and nuclear location sequence (NLS), transcription regulating domain. We chose (G4S) as linker to be added between DBD and SV40 NLS for providing 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 point for enlarging optional SynTF group is to find enough differently specific and orthogonal DBDs. We applied two ideas to achieve this. Firstlly, 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 aminol residues on ZF modules, we can generate RE-specific mammalian synthetic ZF (SynZF).
The silencing fold of SynPro(S)-ZF43-8;N* is tunable by choosing different N* RE repeats.
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 take 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.
Cause the following reason, 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 prom oters. Thus, before you want to apply our idea into your project. A test is strongly needed.
Integrated information about Part Collection posted on Demonstrate page: Wiring orthogonal and tunable SynTF-SynPro repertoire. You cannot miss it.
We listed biobricks belong to Part Collection here.
