Difference between revisions of "Part:BBa K3425017"
 
(7 intermediate revisions by the same user not shown)
Line 3: Line 3:
 
<partinfo>BBa_K3425017 short</partinfo>
 
<partinfo>BBa_K3425017 short</partinfo>
  
 +
<html>
 +
<p>This series of iGEM Type IIS templates present easy to use blueprints to design parts for this assembly standard. These parts provide ready-made sequences which contain the different fusion sites for a promoter, RBS, CDS and terminator part according to the following image*.</p>
 +
</html>
 +
<center>https://static.igem.org/mediawiki/parts/b/b7/PCR_for_pSB1C00.png</center>
 +
<html>
 +
<p>By adding the fusion and restriction sites by DNA synthesis or PCR, the part is ready to be cloned into the Type IIS universal acceptor </html>[[Part:pSB1C00|<partinfo>pSB1C00</partinfo>]]<html>. More information about this backbone can be found in its page. It can also be found, together with all our experience in this cloning method, in Team Uppsala 2020's <a href="https://2020.igem.org/Team:UofUppsala/Engineering#TypeIIS">iGEM Type IIS standard guidebook</a>.</p>
  
−
<!-- Add more about the biology of this part here
+
<p>*<b>Note:</b> This image was taken from the </html>[[Part:pSB1C00|<partinfo>pSB1C00</partinfo>]]<html> page to provide visual aid for the explanation without redirecting to another page.</p>
−
===Usage and Biology===
+
</html>
  
−
<!-- -->
+
This part is part of iGEM Uppsala 2020's <html><a href="https://parts.igem.org/Collections/iGEM_Type_IIS_Collections">iGEM Type IIS standard collection</a></html>.
−
<span class='h3bb'>Sequence and Features</span>
+
 
 +
===Usage and biology===
 +
<html>
 +
<p>This part is a promoter template, and it is used to clone promoter-type parts (such as </html>[[Part:J23119|<partinfo>J23119</partinfo>]]<html>) into </html>[[Part:pSB1C00|<partinfo>pSB1C00</partinfo>]]<html>, the first step towards assembling transcriptional units with iGEM Type IIS assembly. The template is flanked by fusion sites FS_a (GGAG) and FS_b (TACT), which will allow it to take the first position when using it for assembly to a Level 1 or pOdd plasmid (such as </html>[[Part:pSB1K01|<partinfo>pSB1K01</partinfo>]]<html>).</p>
 +
 
 +
<p>Follow these steps to use this template:</p>
 +
<ol>
 +
<li>Obtain the template sequence from "Sequence and features"</li>
 +
<li>Substitute the A homopolymer (annotated as Promoter template) by the desired promoter part </li>
 +
<li>Order the corresponding primers to anneal and extend*.</li>
 +
</ol>
 +
<p>For ease of use, we provide a .dna file which also contains example primers. This file can be found in Team Uppsala 2020's <a href="https://2020.igem.org/Team:UofUppsala/Parts#Collection">Parts page</a> </p>
 +
 
 +
 
 +
<p>*<b>Note:</b> These parts are short so they should be ordered as oligos and extended by PCR [1]. The Fw and Rv oligos should overlap by at least 20bp. If the entire part (including fusion sites and SapI sites) is less than 60bp long, each strand can be ordered as an oligo and then annealed directly.</p>
 +
 
 +
<p>The following table details the part numbers and names of the design templates.</p>
 +
<center>
 +
 
 +
<style>
 +
.parts-table {
 +
border: 3px solid #ccc;
 +
border-collapse: collapse;
 +
}
 +
 
 +
.parts-table td {
 +
padding: 5px;
 +
border: 1px solid #ccc;
 +
vertical-align: center;
 +
//border-collapse: collapse;
 +
}
 +
 
 +
.parts-table th {
 +
background-color: #464646;
 +
//border-collapse: collapse;
 +
border: 1px solid #ccc;
 +
padding: 5px;
 +
color: #f2f2f2;
 +
vertical-align: text-top;
 +
text-align: center;
 +
}
 +
</style>
 +
<table class="parts-table">
 +
<tr>
 +
<th>Registry Number</th>
 +
<th>Name</th>
 +
 
 +
</tr>
 +
<tr>
 +
<td></html>[[Part:BBa_K3425017|<partinfo>BBa_K3425017</partinfo>]]<html></td>
 +
<td>Promoter template</td>
 +
 
 +
</tr>
 +
<tr>
 +
<td></html>[[Part:BBa_K3425018|<partinfo>BBa_K3425018</partinfo>]]<html></td>
 +
<td>RBS template</td>
 +
 
 +
</tr>
 +
<tr>
 +
<td></html>[[Part:BBa_K3425019|<partinfo>BBa_K3425019</partinfo>]]<html></td>
 +
<td>CDS template</td>
 +
 
 +
</tr>
 +
<tr>
 +
<td></html>[[Part:BBa_K3425020|<partinfo>BBa_K3425020</partinfo>]]<html></td>
 +
<td>Terminator template</td>
 +
 
 +
</tr>
 +
</table>
 +
</center>
 +
 
 +
</html>
 +
 
 +
<html><span class='h3bb'><b>Sequence and Features</b></span></html>
 
<partinfo>BBa_K3425017 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K3425017 SequenceAndFeatures</partinfo>
  
 +
'''Note:''' The part contains restriction sites for its cloning into Level 0 universal Type IIS acceptor pSB1C00, therefore it is marked as not compatible with RFC1000 standard, even though it is.
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
Line 16: Line 96:
 
<partinfo>BBa_K3425017 parameters</partinfo>
 
<partinfo>BBa_K3425017 parameters</partinfo>
 
<!-- -->
 
<!-- -->
 +
 +
===References===
 +
[1] https://parts.igem.org/Help:Promoters/Construction#Constructing_a_part_from_synthetic_oligos

Latest revision as of 21:04, 25 October 2020


iGEM Type IIS standard promoter template

This series of iGEM Type IIS templates present easy to use blueprints to design parts for this assembly standard. These parts provide ready-made sequences which contain the different fusion sites for a promoter, RBS, CDS and terminator part according to the following image*.

PCR_for_pSB1C00.png

By adding the fusion and restriction sites by DNA synthesis or PCR, the part is ready to be cloned into the Type IIS universal acceptor pSB1C00. More information about this backbone can be found in its page. It can also be found, together with all our experience in this cloning method, in Team Uppsala 2020's iGEM Type IIS standard guidebook.

*Note: This image was taken from the pSB1C00 page to provide visual aid for the explanation without redirecting to another page.

This part is part of iGEM Uppsala 2020's iGEM Type IIS standard collection.

Usage and biology

This part is a promoter template, and it is used to clone promoter-type parts (such as BBa_J23119) into pSB1C00, the first step towards assembling transcriptional units with iGEM Type IIS assembly. The template is flanked by fusion sites FS_a (GGAG) and FS_b (TACT), which will allow it to take the first position when using it for assembly to a Level 1 or pOdd plasmid (such as pSB1K01).

Follow these steps to use this template:

  1. Obtain the template sequence from "Sequence and features"
  2. Substitute the A homopolymer (annotated as Promoter template) by the desired promoter part
  3. Order the corresponding primers to anneal and extend*.

For ease of use, we provide a .dna file which also contains example primers. This file can be found in Team Uppsala 2020's Parts page

*Note: These parts are short so they should be ordered as oligos and extended by PCR [1]. The Fw and Rv oligos should overlap by at least 20bp. If the entire part (including fusion sites and SapI sites) is less than 60bp long, each strand can be ordered as an oligo and then annealed directly.

The following table details the part numbers and names of the design templates.

Registry Number Name
BBa_K3425017 Promoter template
BBa_K3425018 RBS template
BBa_K3425019 CDS template
BBa_K3425020 Terminator template

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 32
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI site found at 5
    Illegal SapI.rc site found at 39

Note: The part contains restriction sites for its cloning into Level 0 universal Type IIS acceptor pSB1C00, therefore it is marked as not compatible with RFC1000 standard, even though it is.


References

[1] https://parts.igem.org/Help:Promoters/Construction#Constructing_a_part_from_synthetic_oligos