Difference between revisions of "Part:BBa K3228005"

 
 
(One intermediate revision by one other user not shown)
Line 1: Line 1:
 +
 +
<html>
 +
<div class="titleWrapper"><div class="titleBackground" style="background-image:none"></div><div class="title"></div></div>
 +
<article>
 +
<style>
 +
.imageContainer1x2 {
 +
display: flex;
 +
flex-wrap: wrap;
 +
justify-content: space-around;
 +
align-items: center;
 +
}
 +
.imageContainer1x2 div {
 +
width: 50%;
 +
margin-bottom: 2%;
 +
text-align:center;
 +
}
 +
.imageContainer1x2 div img {
 +
width: 100%;
 +
}
 +
.imageContainer1x4 {
 +
display: flex;
 +
flex-wrap: wrap;
 +
justify-content: space-around;
 +
align-items: center;
 +
}
 +
.imageContainer1x4 div {
 +
width: 23%;
 +
margin-bottom: 2%;
 +
text-align:center;
 +
}
 +
.imageContainer1x4 div img {
 +
width: 100%;
 +
}
 +
<i>
 +
</style>
 +
</html>
  
 
__NOTOC__
 
__NOTOC__
−
{|width='80%'
 
−
|-
 
−
|width=35% valign='top'|
 
−
[[Image:Terminator.png]]
 
−
<partinfo>BBa_K3228005 parameters</partinfo>
 
−
| width=50% valign='top' style='border: 1px solid black'|
 
 
<partinfo>BBa_K3228005 short</partinfo>
 
<partinfo>BBa_K3228005 short</partinfo>
−
* A version of the terminator TB1003 that only covers the position 5-5a in the Marburg Collection Syntax. This terminator can be used to put another part into the position 5b (in the Marburg Collection Syntax from 5a to the end of 5). This can be used for example to insert an antibiotic resistance inbetween position 1-6 (the connector/homology parts of the Marburg Collection) when designing a construct for genome integration.
 
  
−
|}
+
===Sequence and Features===
 +
<partinfo>BBa_K3228005 SequenceAndFeatures</partinfo>
 +
 
 +
===Description===
 +
 
 +
<html>
 +
<p align="justify">
 +
 
 +
A version of the terminator B0015 that only covers the position 5-5a in the Marburg Collection syntax. This terminator can be used to put another part into the position 5b (in the Marburg Collection syntax from 5a to the end of 5). This can be used for example to insert an antibiotic resistance in between position 1-6 (the connector/homology parts of the Marburg Collection) when designing a construct for genome integration.
 +
 
 +
<br>
 +
<br>
 +
This part is contained in the Green Expansion, a range of parts from <a href="https://2019.igem.org/Team:Marburg">iGEM Marburg 2019</a>that enables users of the Marburg Collection 2.0 to design MoClo compatible vectors for cyanobacteria as well as to engineer the genome of several cyanobacterial species.
 +
 +
</p>
 +
</html>
 +
 
 +
===The Green Expansion===
 +
 
 +
<html>
 +
<p align="justify">
 +
 
 +
The Green Expansion is an addition of parts to the Marburg Collection 2.0 <a href="http://2018.igem.org/Team:Marburg/Design">(See: Design of the Marburg Collection)</a> that features the world's first MoClo compatible shuttle vector for cyanobacteria. <a href="https://parts.igem.org/Part:BBa_K3228069">BBa_K3228069</a>
 +
</html>
 +
 
 +
<div style="width:100%;display:flex;flex-direction:row;flex-wrap: wrap; justify-content:space-evenly; align-items:center;">
 +
 
 +
[[File:GE LVL1 ori.png|500px|thumb|left|'''Figure 1''':  Design of the first MoClo compatible shuttle vector for cyanobacteria for LVL 1 constructs. This can be used for the integration of simple genetic modules. ]]
 +
 
 +
</div style>
 +
 
 +
 
 +
<div style="width:100%;display:flex;flex-direction:row;flex-wrap: wrap; justify-content:space-evenly; align-items:center;">
 +
 
 +
[[File:GE LVL2 ori.png|500px|thumb|left|'''Figure 2''':  Design of the first MoClo compatible shuttle vector for cyanobacteria for LVL 2 constructs. This can be used for the integration of complex genetic devices.  ]]
 +
 
 +
</div style>
 +
 
 +
<html>
 +
The Green Expansion also offers all the parts needed for the genomic integration of one or multiple genes in cyanobacteria. This M.E.G.A. (Modularized Engineering of Genome Areas) kit convinces with a striking flexibility and a very intuitive workflow for the de novo assembly of your plasmid of choice. It encompasses five different neutral integration sites to choose from: three conventional sites frequently used in the cyanobacterial community (NSI to NSIII) as well as our own rationally designed artificial Neutral integration Site options a.N.S.o. 1 and 2 <a href="https://2019.igem.org/Team:Marburg/Design">(See: Finding new artificial Neutral integration Site options).</a>These sites show no transcriptional activity from neighboring regions according to RNA-seq data and are therefore completely orthogonal. Additionally we offer four different antibiotic markers to use (chloramphenicol, gentamicin, spectinomycin and kanamycin). With the Green Expansion up to 20 genes can be introduced into a cyanobacterial strain.
 +
</html>
 +
 
 +
<div style="width:100%;display:flex;flex-direction:row;flex-wrap: wrap; justify-content:space-evenly; align-items:center;">
 +
 
 +
[[File:GE genomic integration.png|500px|thumb|left|'''Figure 3''':  Overview over the modularized editing of genome area kit (M.E.G.A. kit)  ]]
 +
 
 +
</div style>
 +
<html>
 +
<br>
 +
<br>
 +
Thanks to the flexible design this expansion can also be used for the genomic modification of any chassis after the introduction of a new species specific LVL 0 integration sites to our Marburg Collection 2.0. As the workflow to build new homologies is a bit more intricate compared to the one pot on step assembly of our other parts due to the internal BsmBI cutting site, we described the workflow for that in our design section <a href="https://2019.igem.org/Team:Marburg/Design">(See: Design of neutral integration sites).</a>
 +
<br>
 +
<br>
 +
The Green Expansion proves a valuable addition to our Marburg Collection 2.0 and to the iGEM Registry of Standard Biological Parts. It services users of our chassis and other cyanobacterial strains with a useful tool for genomic modifications but it also contributes a shell that can be used to modify any other model organism as well.
 +
</p>
 +
</html>
 +
 
 +
===Compability===
 +
<html>
 +
<p align="justify">
 +
 
 +
These parts are compatible with the RCF [1000] standard and can be  used in any part collection that uses the PhytoBrick standard of overhangs. For more information we recommend to head over to <a href="http://2018.igem.org/Team:Marburg/Design">Design of the Marburg Collection iGEM Marburg 2018</a>.
 +
 
 +
</p>
 +
</html>
 +
 
 +
===Parts of the Green Expansion===
 +
 
 +
<div class="PCListIcon" style="display:flex;flex-direction:row; flex-wrap: nowrap; justify-content:space-evenly; align-items:flex-start;font-size:82%;">
 +
 
 +
[[File:Icon hConnector5.png|90px|thumb|none|
 +
 
 +
<html>
 +
<ul>
 +
<b>
 +
 
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228000">K3228000 </a> (aNSo1 integration up) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228001">K3228001 </a> (aNSo2 integration up) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228020">K3228020 </a> <br> (NS1 up) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228021">K3228021 </a> <br> (NS2 up) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228022">K3228022 </a> <br> (NS3 up) </li>
 +
 
 +
</b>
 +
</ul>
 +
</html>]]
 +
 
 +
[[File:T--Marburg--Terminator.png|90px|thumb|none|
 +
 
 +
<html>
 +
<ul>
 +
<b>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228004">K3228004 </a> (shortTB0010) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228005">K3228005 </a> (shortTB0015) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228006">K3228006 </a> (shortTB1002) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228007">K3228007 </a> (shortTB1003) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228008">K3228008 </a> (shortTB1004) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228009">K3228009 </a> (shortTB1005) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228010">K3228010 </a> (shortTB1006) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228011">K3228011 </a> (shortTB1007) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228012">K3228012 </a> (shortTB1008) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228013">K3228013 </a> (shortTB1009) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228014">K3228014 </a> (shortTB1010) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228015">K3228015 </a> (shortDummy) </li>
 +
 
 +
</b>
 +
</ul>
 +
</html>]]
 +
 
 +
[[File:T--Marburg--Antibiotic_Resistance.png|90px|thumb|none|
 +
<html>
 +
<ul>
 +
<b>
 +
 
 +
 
 +
    <li><a href="https://parts.igem.org/Part:BBa_K3228016">K3228016 </a> (SpecRes_short) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K3228017">K3228017 </a> <br> (CmlRes_short) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K3228018">K3228018 </a> <br> (TetRes_short) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K3228019">K3228019 </a> <br> (KanRes_short) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K3228027">K3228027 </a> <br> (GenRes_short) </li>
 +
 
 +
</ul>
 +
</b>
 +
</html>]]
 +
 
 +
[[File:Icon hConnector3.png|90px|thumb|none|<html>
 +
<ul> <b>
 +
 
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228002">K3228002 </a> (aNSo1 integration down) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228003">K3228003 </a> (aNSo1 integration down) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228023">K3228023 </a> <br> (NS1 down) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228024">K3228024 </a> <br> (NS2 down) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K3228025">K3228025 </a> <br> (NS3 down) </li>
 +
 
 +
</ul>
 +
</b>
 +
</html>]]
 +
 
 +
[[File:Icon Shuttlevector.png|90px|thumb|none|<html>
 +
<ul> <b>
  
−
'''Secondary Structure'''
+
    <li> <a href="https://parts.igem.org/Part:BBa_K3228026">K3228026 </a> (oriT integration) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228069">K3228069 </a> (panS SpecRes LVL1) </li>
 +
    <li> <a href="https://parts.igem.org/Part:BBa_K3228089">K3228089 </a> (panS KanRes LVL2) </li>
  
−
[[Image:Mfold-K3228005-1.png]]
+
</ul>
 +
</b>
 +
</html>]]
 +
  
−
<hr>
+
</div>
−
'''Measurement'''
+
−
* [http://openwetware.org/wiki/Cconboy:Terminator_Characterization/Results How these parts were measured]
+

Latest revision as of 15:49, 20 October 2019


pMC_0_5a_11_shortTB0015

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]

Description

A version of the terminator B0015 that only covers the position 5-5a in the Marburg Collection syntax. This terminator can be used to put another part into the position 5b (in the Marburg Collection syntax from 5a to the end of 5). This can be used for example to insert an antibiotic resistance in between position 1-6 (the connector/homology parts of the Marburg Collection) when designing a construct for genome integration.

This part is contained in the Green Expansion, a range of parts from iGEM Marburg 2019that enables users of the Marburg Collection 2.0 to design MoClo compatible vectors for cyanobacteria as well as to engineer the genome of several cyanobacterial species.

The Green Expansion

The Green Expansion is an addition of parts to the Marburg Collection 2.0 (See: Design of the Marburg Collection) that features the world's first MoClo compatible shuttle vector for cyanobacteria. BBa_K3228069

Figure 1: Design of the first MoClo compatible shuttle vector for cyanobacteria for LVL 1 constructs. This can be used for the integration of simple genetic modules.


Figure 2: Design of the first MoClo compatible shuttle vector for cyanobacteria for LVL 2 constructs. This can be used for the integration of complex genetic devices.

The Green Expansion also offers all the parts needed for the genomic integration of one or multiple genes in cyanobacteria. This M.E.G.A. (Modularized Engineering of Genome Areas) kit convinces with a striking flexibility and a very intuitive workflow for the de novo assembly of your plasmid of choice. It encompasses five different neutral integration sites to choose from: three conventional sites frequently used in the cyanobacterial community (NSI to NSIII) as well as our own rationally designed artificial Neutral integration Site options a.N.S.o. 1 and 2 (See: Finding new artificial Neutral integration Site options).These sites show no transcriptional activity from neighboring regions according to RNA-seq data and are therefore completely orthogonal. Additionally we offer four different antibiotic markers to use (chloramphenicol, gentamicin, spectinomycin and kanamycin). With the Green Expansion up to 20 genes can be introduced into a cyanobacterial strain.

Figure 3: Overview over the modularized editing of genome area kit (M.E.G.A. kit)



Thanks to the flexible design this expansion can also be used for the genomic modification of any chassis after the introduction of a new species specific LVL 0 integration sites to our Marburg Collection 2.0. As the workflow to build new homologies is a bit more intricate compared to the one pot on step assembly of our other parts due to the internal BsmBI cutting site, we described the workflow for that in our design section (See: Design of neutral integration sites).

The Green Expansion proves a valuable addition to our Marburg Collection 2.0 and to the iGEM Registry of Standard Biological Parts. It services users of our chassis and other cyanobacterial strains with a useful tool for genomic modifications but it also contributes a shell that can be used to modify any other model organism as well.

Compability

These parts are compatible with the RCF [1000] standard and can be used in any part collection that uses the PhytoBrick standard of overhangs. For more information we recommend to head over to Design of the Marburg Collection iGEM Marburg 2018.

Parts of the Green Expansion