Difference between revisions of "Part:BBa K313010"
Line 8: Line 8:
 
<br>We are SYSU-CHINA 2021 and this year we use circRNA to colocalize enzymes, which are fused to RNA binding proteins(RBP). We choose MS2 coat protein and PP7 coat protein as our RBP,and their aptamer on circRNA.For contribution, we predict its 2D and 3D structure,to present a visual impression.
 
<br>We are SYSU-CHINA 2021 and this year we use circRNA to colocalize enzymes, which are fused to RNA binding proteins(RBP). We choose MS2 coat protein and PP7 coat protein as our RBP,and their aptamer on circRNA.For contribution, we predict its 2D and 3D structure,to present a visual impression.
  
 +
__NOTOC__
 +
We are SYSU-CHINA 2021 and this year we use circRNA to colocalize enzymes, which are fused to RNA binding proteins(RBP). We choose MS2 coat protein and PP7 coat protein as our RBP,and their aptamer on circRNA.For contribution, we predict its 2D and 3D structure,to present a visual impression.
 +
 +
===Applications of BBa_K313010===
 +
We are SYSU-CHINA 2021 and this year we use circRNA to colocalize enzymes, which are fused to RNA binding proteins(RBP). We choose MS2 coat protein and PP7 coat protein as our RBP,and their aptamer on circRNA.For contribution, we predict its 2D and 3D structure,to present a visual impression.
 +
 +
===2D stucture===
 +
<!-- DON'T DELETE --><partinfo>BBa_K313010 StartReviews</partinfo>
 +
<!-- Template for a user review
 +
{|width='80%' style='border:1px solid gray'
 +
|-
 +
|width='10%'|
 +
<partinfo>BBa_K313010 AddReview number</partinfo>
 +
<I>Username</I>
 +
|width='60%' valign='top'|
 +
experimental data
 +
|};
 +
<!-- End of the user review template -->
 +
<!-- DON'T DELETE --><partinfo>BBa_K313010 EndReviews</partinfo>
 +
<br>We use RNAfold and StructureEditor to predict 2D structure of our circRNA, which contains MS2 aptamer.The results are below:
 +
[[Image:MS2_aptamer_on_the_circRNA_scaffold.png ‎ | border | center | 300px]]
 +
<font size="1"><center>Figure 1.2D stucture predicted by RNAfold</center></font><br/>
 +
[[Image:SYSU-CHINA_circRNA-1.png ‎ | border | center | 300px]]
 +
<font size="1"><center>Figure 2.2D stucture predicted by StructureEditor</center></font><br/>
 +
 +
===3D stucture===
 +
<!-- DON'T DELETE --><partinfo>BBa_K313010 StartReviews</partinfo>
 +
<!-- Template for a user review
 +
{|width='80%' style='border:1px solid gray'
 +
|-
 +
|width='10%'|
 +
<partinfo>BBa_K313010 AddReview number</partinfo>
 +
<I>Username</I>
 +
|width='60%' valign='top'|
 +
experimental data
 +
|};
 +
<!-- End of the user review template -->
 +
<!-- DON'T DELETE --><partinfo>BBa_K313010 EndReviews</partinfo>
 +
<br>We use this website:http://biophy.hust.edu.cn/new/3dRNA/create, to predict the 3D structure of our circRNA, which contains MS2 aptamer.The result lists below:
 +
<br>[[image:SYSU-CHINA circRNA-2.png |border|center|300px]]
 +
<br><font size="1"><center>Figure 3. 3D stucture of MS2 aptamer predicted by Xiaolab</center></font>
 +
 +
===MS2 binding mechanism===
 +
<!-- DON'T DELETE --><partinfo>BBa_K313010 StartReviews</partinfo>
 +
<!-- Template for a user review
 +
{|width='80%' style='border:1px solid gray'
 +
|-
 +
|width='10%'|
 +
<partinfo>BBa_K313010 AddReview number</partinfo>
 +
<I>Username</I>
 +
|width='60%' valign='top'|
 +
experimental data
 +
|};
 +
<!-- End of the user review template -->
 +
<!-- DON'T DELETE --><partinfo>BBa_K313010 EndReviews</partinfo>
 +
<br>[[Image:MS2 binding mechanism.png  | border | center | 300px]]
 +
<br><center><font size="1">Figure 4. MS2 binding mechanism</font></center>
 +
 +
<br>
 +
===split EGFP===
 +
<!-- DON'T DELETE --><partinfo>BBa_K313010 StartReviews</partinfo>
 +
<!-- Template for a user review
 +
{|width='80%' style='border:1px solid gray'
 +
|-
 +
|width='10%'|
 +
<partinfo>BBa_K313010 AddReview number</partinfo>
 +
<I>Username</I>
 +
|width='60%' valign='top'|
 +
experimental data
 +
|};
 +
<!-- End of the user review template -->
 +
<!-- DON'T DELETE --><partinfo>BBa_K313010 EndReviews</partinfo>
 +
<br>We are SYSU-CHINA,and this year we use this part as MS2 coat protein's aptamer to do a split EGFP experiment,for the proof of concept.Here we found a research article, which use liner RNA with MS2 and PP7 aptamer, to do the split EGFP experiment.Below are their experimental data.
 +
<br>[[Image:The_principle_of_spite_EGFP.png  | border | center | 300px]]
 +
<br><center><font size="1">Figure 3.the principle and experimental data of split EGFP</font>
  
  
Line 19: Line 94:
  
  
−
<!-- Uncomment this to enable Functional Parameter display
+
 
 
===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K313010 parameters</partinfo>
 
<partinfo>BBa_K313010 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Revision as of 09:45, 13 October 2021

loading sequence of RNA phage MS2

This sequence is necessary for loading of RNA into the capsid of RNA phage MS2. The coat proteins of phage MS2 is known to aggregate around this sequence.

Please see [http://2010.igem.org/Team:UT-Tokyo/Sudoku_assay_MS2 Phage MS2] assay page.

We are SYSU-CHINA 2021 and this year we use circRNA to colocalize enzymes, which are fused to RNA binding proteins(RBP). We choose MS2 coat protein and PP7 coat protein as our RBP,and their aptamer on circRNA.For contribution, we predict its 2D and 3D structure,to present a visual impression.


We are SYSU-CHINA 2021 and this year we use circRNA to colocalize enzymes, which are fused to RNA binding proteins(RBP). We choose MS2 coat protein and PP7 coat protein as our RBP,and their aptamer on circRNA.For contribution, we predict its 2D and 3D structure,to present a visual impression.

Applications of BBa_K313010

We are SYSU-CHINA 2021 and this year we use circRNA to colocalize enzymes, which are fused to RNA binding proteins(RBP). We choose MS2 coat protein and PP7 coat protein as our RBP,and their aptamer on circRNA.For contribution, we predict its 2D and 3D structure,to present a visual impression.

2D stucture

UNIQ605d625843bea27a-partinfo-00000001-QINU UNIQ605d625843bea27a-partinfo-00000002-QINU
We use RNAfold and StructureEditor to predict 2D structure of our circRNA, which contains MS2 aptamer.The results are below:

MS2 aptamer on the circRNA scaffold.png
Figure 1.2D stucture predicted by RNAfold

SYSU-CHINA circRNA-1.png
Figure 2.2D stucture predicted by StructureEditor

3D stucture

UNIQ605d625843bea27a-partinfo-00000003-QINU UNIQ605d625843bea27a-partinfo-00000004-QINU
We use this website:http://biophy.hust.edu.cn/new/3dRNA/create, to predict the 3D structure of our circRNA, which contains MS2 aptamer.The result lists below:


SYSU-CHINA circRNA-2.png

Figure 3. 3D stucture of MS2 aptamer predicted by Xiaolab

MS2 binding mechanism

UNIQ605d625843bea27a-partinfo-00000005-QINU UNIQ605d625843bea27a-partinfo-00000006-QINU


MS2 binding mechanism.png

Figure 4. MS2 binding mechanism


split EGFP

UNIQ605d625843bea27a-partinfo-00000007-QINU UNIQ605d625843bea27a-partinfo-00000008-QINU
We are SYSU-CHINA,and this year we use this part as MS2 coat protein's aptamer to do a split EGFP experiment,for the proof of concept.Here we found a research article, which use liner RNA with MS2 and PP7 aptamer, to do the split EGFP experiment.Below are their experimental data.


The principle of spite EGFP.png

Figure 3.the principle and experimental data of split EGFP


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Functional Parameters