Team:ZJU-China/project.htm

From 2012.igem.org

(Difference between revisions)
Line 146: Line 146:
   align: justify;
   align: justify;
}
}
-
 
+
b.orange{
 +
  color: #FF8000;
 +
  font-style:italic;
 +
}
h5{
h5{
Line 338: Line 341:
<!--Content Goes Here-->
<!--Content Goes Here-->
-
<p align="justify">In cells, engineered multi-enzyme pathways are common and are often physically and spatially organized, thus leading to the high output efficiency. But engineered synthetic pathways utilizing non-homologous enzymes often suffer from low efficiency of production caused by relative lack of spatial organization. RNA scaffold is designed to co-localize enzymes through interactions between binding domains on the scaffold and target peptides fused to each enzyme in engineered biological pathways <i>in vivo</i>. The scaffold allows efficient channeling of substrates to products over several enzymatic steps by limiting the diffusion of intermediates thus providing a bright future for solving the problem.</p>
+
<p align="justify">In cells, engineered multi-enzyme pathways are common and are often physically and spatially organized, thus leading to the high output efficiency. But engineered synthetic pathways utilizing non-homologous enzymes often suffer from low efficiency of production caused by relative lack of spatial organization. <b class="orange">RNA scaffold is designed to co-localize enzymes through interactions between binding domains on the scaffold and target peptides fused to each enzyme in engineered biological pathways <i>in vivo</i></b>. The scaffold allows <b class="orange">efficient channeling of substrates to products</b> over several enzymatic steps by <b class="orange">limiting the diffusion of intermediates</b> thus providing a bright future for solving the problem.</p>
<p align="justify">&nbsp;</p>
<p align="justify">&nbsp;</p>
-
<p align="justify">ZJU-China aims to design and realize tunable RNA scaffolds to accelerate biological pathways and control them on and off. In order to achieve the object, we added an aptamer structure on RNA scaffold as a switch to regulate biological pathways by micromolecular ligands. Then we can control the all-or-none binding relationship between the enzymes and the scaffold by the absence and the presence of a special ligand. </p>
+
<p align="justify">ZJU-China aims to design and realize tunable RNA scaffolds to accelerate biological pathways and control them on and off. In order to achieve the object, we added an aptamer structure on RNA scaffold as a switch to regulate biological pathways by micromolecular ligands. Then we can <b class="orange">control the all-or-none binding relationship</b> between the enzymes and the scaffold by the absence and the presence of a special ligand. </p>
<p align="justify">&nbsp;</p>
<p align="justify">&nbsp;</p>
<p align="justify">We demonstrated RNA scaffold do make the split GFPs get closer and fluoresce. As was expected, the riboscaffold with a theophylline aptamer can be regulated by theophylline in the range of 0-0.5mM IPTG. A scaffold library was also desired. By changing the sequence of MS2 aptamer binding site, we made the fluorescent decreased. The mutations with different arm length decrease the fluorescent intensity of split GPF by extending the distance between two split GFP parts FA and FB. It provides a series of half-on scaffolds. </p>
<p align="justify">We demonstrated RNA scaffold do make the split GFPs get closer and fluoresce. As was expected, the riboscaffold with a theophylline aptamer can be regulated by theophylline in the range of 0-0.5mM IPTG. A scaffold library was also desired. By changing the sequence of MS2 aptamer binding site, we made the fluorescent decreased. The mutations with different arm length decrease the fluorescent intensity of split GPF by extending the distance between two split GFP parts FA and FB. It provides a series of half-on scaffolds. </p>
Line 355: Line 358:
<!--Content Goes Here-->
<!--Content Goes Here-->
-
<p align="justify">In cells, engineered multi-enzyme pathways are common and are often physically and spatially organized, thus leading to the high output efficiency. But engineered synthetic pathways utilizing non-homologous enzymes often suffer from low efficienty of production caused by relative lack of spatial organization. Thus important issue lies in the method to increase the efficiency of the multi-enzyme pathways. </p>
+
<p align="justify">In cells, engineered multi-enzyme pathways are common and are often physically and spatially organized, thus leading to the high output efficiency. But engineered synthetic pathways utilizing non-homologous enzymes often suffer from low efficienty of production caused by relative lack of spatial organization. Thus important issue lies in the method to <b class="orange">increase the efficiency of the multi-enzyme pathways</b>. </p>
<p align="justify">&nbsp;</p>
<p align="justify">&nbsp;</p>
-
<p align="justify">Protein scaffolds can be designed to make enzymes closed through interactions between binding domains on the scaffold and target peptides fused to each enzyme. However, protein scaffold is usually large, has limit binding sites, and is hard to be engineered in architecture. DNA can be designed to self-assemble in vitro into many and varied nanostructures. However, DNA scaffold is hard to be controlled and might cause some potential problems <i>in vivo</i>. By contrast, RNA scaffold shows great advantages. For instance, RNA is more flexible, whose structures are varied, thus leading to their ease to splice. RNA scaffold is able to be controlled and has a satisfactory regulating efficiency. RNA scaffold works fast, because it doesn’t need translation like protein scaffold. Camille J. Delebecque and his colleagues have designed and assembled RNA structures and used them to speed up the reaction of hydrogen production. And that is what our project based on.</p>
+
<p align="justify">Protein scaffolds can be designed to make enzymes closed through interactions between binding domains on the scaffold and target peptides fused to each enzyme. However, protein scaffold is usually large, has limit binding sites, and is hard to be engineered in architecture. DNA can be designed to self-assemble in vitro into many and varied nanostructures. However, DNA scaffold is hard to be controlled and might cause some potential problems <i>in vivo</i>. By contrast, RNA scaffold shows great advantages. For instance, <b class="orange">RNA is more flexible</b>, whose structures are varied, thus leading to their ease to splice. RNA scaffold is able <b class="orange">to be controlled</b> and has a satisfactory regulating efficiency</b>. RNA scaffold <b class="orange">works fast</b>, because it doesn’t need translation like protein scaffold. Camille J. Delebecque and his colleagues have designed and assembled RNA structures and used them to speed up the reaction of hydrogen production. And that is what our project based on.</p>
<p align="justify">&nbsp;</p>
<p align="justify">&nbsp;</p>
<img src="https://static.igem.org/mediawiki/2012/b/b7/Zju_Backround_syn_and_bio.png" width="700px" />
<img src="https://static.igem.org/mediawiki/2012/b/b7/Zju_Backround_syn_and_bio.png" width="700px" />

Revision as of 23:59, 26 October 2012

PROJECT

01 ABSTRACT

02 BACKGROUND

03 S0: BASIC RNA SCAFFOLD

04 S1: ALLOSCAFFOLD

05 S2: SCAFFOLD LIBRARY

06 S3: BIOSYNTHESIS OF IAA

07 S4: POLYSCAFFOLD

08 PARTS

09 PERSPECTIVES