Difference between revisions of "Part:BBa K1859015"
 
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<br>
 
<br>
  
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<p>BBa_K1859015 can let mRNA circularize efficiently in E. coli by combining it with
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<p>[BBa_K1859015] can let mRNA circularize efficiently in E. coli by combining it with
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  <a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > BBa_K1859016 </a>.
+
  <a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > [BBa_K1859016] </a>.
 
  </p>
 
  </p>
 +
<p>
 +
Circular Parts, the 3'side of the intron
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332005" > [BBa_K1332005] </a>
 +
and the 5'side of the intron
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332003" > [BBa_K1332003] </a>
 +
, is what use sequence subcloned ribozyme involved self‐splicing in T4 Phage.
 +
 +
By associating Circular Parts on both ends of optional sequence, you can circularize mRNA making its DNA. </p>
  
 
<p>As for details of circular mRNA, refer to  
 
<p>As for details of circular mRNA, refer to  
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<br>
 
<br>
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<p>We improved the 5´side of the intron
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<p>We improved the 3´side of the intron
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332003" > [BBa_K1332003]
+
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332005" > [BBa_K1332005]
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  </a> in iGEM2014 and made BBa_K1859015.
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  </a> of iGEM2014 and made [BBa_K1859015].
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Circular parts, the 3'side of the intron
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Circular parts of iGEM2014 are cloned only sequence of ribozyme involved the splicing from td intron in T4 phage.
 +
However, [BBa_K1859015] is cloned the sequence except the ribozyme extra in addition to
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332005" > [BBa_K1332005]
 +
</a>
 +
.
 +
</p>
 +
 
 +
<p>
 +
We attached this part[BBa_K1859015] to 5'sides of  
 +
His-RFP without stop codon
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332002" > [BBa_K1332002]
 +
</a>.
 +
Then, it was connected to 5'sides of
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > [BBa_K1859016]
 +
</a>.
 +
In addition,Lacl
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_R0010" >[BBa_R0010] </a>
 +
, RBS
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_B0034" >[BBa_B0034] </a>
 +
and DT
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_B0015" >[BBa_B0015] </a>
 +
was conbined with it, making
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859026" >[BBa_K1859026] </a>
 +
.
 +
 
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859026" >[BBa_K1859026] </a>
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is the generator to improve circular efficiency of mRNA.
 +
The sequence that cloned extra in [BBa_K1859015] has complementarity with the sequence that cloned extra in
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > [BBa_K1859016]</a>.
 +
</p>
 +
<p>
 +
You can let mRNA circularize efficiently by using
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859026" > [BBa_K1859026] </a>
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([BBa_K1859015] and
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > [BBa_K1859016] </a>
 +
) than using the generator of 2014
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332011" > [BBa_K1332011] </a>
 +
(
 
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332005" > [BBa_K1332005] </a>  
 
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332005" > [BBa_K1332005] </a>  
−
and the 5'side of the intron
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and
 
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332003" > [BBa_K1332003] </a>
 
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332003" > [BBa_K1332003] </a>
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, in 2014 cloned only sequence of ribozyme involved splicing from td intron in T4 phage.
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).</p>
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However, BBa_K1859015 is cloned extra a part of intron adding the part in 2014.
+
−
A part of intron involved in BBa_K1859015 has complementarity with a part of intron involved in
+
−
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > BBa_K1859016</a>.
+
  
  
 +
This part is involved in the second step of the mechanism of the group I intron circularization.<br>
 +
Two exons are connected with each other in the circularization system; furthermore an exon can theoretically be circularized by the system. (shown below)<br>
 +
<img src="https://static.igem.org/mediawiki/2014/a/a1/PIEGIFU3.png" width="650px"></img><br><br>
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<img src="https://static.igem.org/mediawiki/2014/d/d2/PIEGIFU2.png" width="600px"></img><br>
  
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<b>Fig. about circularization</b><br><br><br>
 +
 +
Circular parts of iGEM2014 were cloned only sequence of ribozyme involved the splicing from td intron in T4 phage.
 +
However, [BBa_K1859015] and [BBa_K1859016] were cloned the sequence extra in addition to the ribozyme. The secondary structure as the mRNA is shown below.<br>
 
</p>
 
</p>
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<p>When circular mRNA is produced using BBa_K1859015 and
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<center><img src="https://static.igem.org/mediawiki/2015/b/b9/Gifu_outside_1.png" width="380" height="" vspace="25" hspace="" align=""></img></center>
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > BBa_K1859016 </a>,
+
  
  
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  efficiency of circularising rises than parts of 2014.</p>
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<p>
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The generator is comprised of Circular parts improved to become complementary (
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859015" > [BBa_K1859015] </a>
 +
  and
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > [BBa_K1859016] </a>
 +
), His-RFP without stop codon
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332002" >[BBa_K1332002] </a>
 +
, Lacl
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_R0010" >[BBa_R0010] </a>
 +
, RBS
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_B0034" >[BBa_B0034] </a>
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and DT
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_B0015" >[BBa_B0015] </a>
 +
.
 +
</p>
 +
 
 +
<br clear="all">
 +
<b>About the complementary sequences at outside of both splicing sites</b><br>
 +
&nbsp;&nbsp;  There are the complementary sequences inside the splicing site in this intron. We thought that the sequence brings one splicing site close to the other one and ensures the reaction takes place.<br>
 +
&nbsp;&nbsp; Therefore, we cloned splicing sites with complementary sequences in intron and made it into parts. Moreover, we made the device which express circular mRNA by using this part, and made its express in <i>E. coli</i>. Then, complementary sequences are included in outside of both splicing sites in RNA.
 +
</br>
 +
<p class="center"><img src="https://static.igem.org/mediawiki/2015/e/e1/About-at-autside.png" width="427" height="277" vspace="25" hspace="50"></img></p>
 +
<center><b>Fig2. Replacing the splicing site and parts constructed</b></center>
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<br>
 +
&nbsp;&nbsp; We used <a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859026"style="text-decoration:none;" >BBa_K1859026</a> for generator of outside complementarity.
 +
 
 +
<p>
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The RNA made by this generator [BBa_K1859026] was designed to bind outside of circular mRNA complementary.
 +
</p>
 +
 
 +
<p class="center">
 +
<img src="https://static.igem.org/mediawiki/2015/1/17/Bba1859026.png" width="800" height="236" vspace="10" hspace="40"></img></p>
 +
 
 +
 
 +
<p>
 +
We found that circular efficiency of [BBa_K1859026] was the best,  when we compared with the amount of circular mRNA made by these generators
 +
<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1332011" > [BBa_K1332011]</a>
 +
,
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859024" > [BBa_K1859024]</a>
 +
,
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<a href= "https://parts.igem.org/wiki/index.php?title=Part:BBa_K1859025" > [BBa_K1859025]</a>
 +
,[BBa_K1859026].
 +
</p>
 +
 
  
  
 
</html>
 
</html>

Latest revision as of 03:39, 25 September 2015

the 3´side of the intron[BBa_K1332005] +complementary seqence


[BBa_K1859015] can let mRNA circularize efficiently in E. coli by combining it with [BBa_K1859016] .

Circular Parts, the 3'side of the intron [BBa_K1332005] and the 5'side of the intron [BBa_K1332003] , is what use sequence subcloned ribozyme involved self‐splicing in T4 Phage. By associating Circular Parts on both ends of optional sequence, you can circularize mRNA making its DNA.

As for details of circular mRNA, refer to ‘iGEM Gifu 2014' .


We improved the 3´side of the intron [BBa_K1332005] of iGEM2014 and made [BBa_K1859015]. Circular parts of iGEM2014 are cloned only sequence of ribozyme involved the splicing from td intron in T4 phage. However, [BBa_K1859015] is cloned the sequence except the ribozyme extra in addition to [BBa_K1332005] .

We attached this part[BBa_K1859015] to 5'sides of His-RFP without stop codon [BBa_K1332002] . Then, it was connected to 5'sides of [BBa_K1859016] . In addition,Lacl [BBa_R0010] , RBS [BBa_B0034] and DT [BBa_B0015] was conbined with it, making [BBa_K1859026] . [BBa_K1859026] is the generator to improve circular efficiency of mRNA. The sequence that cloned extra in [BBa_K1859015] has complementarity with the sequence that cloned extra in [BBa_K1859016].

You can let mRNA circularize efficiently by using [BBa_K1859026] ([BBa_K1859015] and [BBa_K1859016] ) than using the generator of 2014 [BBa_K1332011] ( [BBa_K1332005] and [BBa_K1332003] ).

This part is involved in the second step of the mechanism of the group I intron circularization.
Two exons are connected with each other in the circularization system; furthermore an exon can theoretically be circularized by the system. (shown below)



Fig. about circularization


Circular parts of iGEM2014 were cloned only sequence of ribozyme involved the splicing from td intron in T4 phage. However, [BBa_K1859015] and [BBa_K1859016] were cloned the sequence extra in addition to the ribozyme. The secondary structure as the mRNA is shown below.

The generator is comprised of Circular parts improved to become complementary ( [BBa_K1859015] and [BBa_K1859016] ), His-RFP without stop codon [BBa_K1332002] , Lacl [BBa_R0010] , RBS [BBa_B0034] and DT [BBa_B0015] .


About the complementary sequences at outside of both splicing sites
   There are the complementary sequences inside the splicing site in this intron. We thought that the sequence brings one splicing site close to the other one and ensures the reaction takes place.
   Therefore, we cloned splicing sites with complementary sequences in intron and made it into parts. Moreover, we made the device which express circular mRNA by using this part, and made its express in E. coli. Then, complementary sequences are included in outside of both splicing sites in RNA.

Fig2. Replacing the splicing site and parts constructed

   We used BBa_K1859026 for generator of outside complementarity.

The RNA made by this generator [BBa_K1859026] was designed to bind outside of circular mRNA complementary.

We found that circular efficiency of [BBa_K1859026] was the best, when we compared with the amount of circular mRNA made by these generators [BBa_K1332011] , [BBa_K1859024] , [BBa_K1859025] ,[BBa_K1859026].