IGEM:IMPERIAL/2009/Encapsulation/Biobricks: Difference between revisions

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==Module 3==
==Module 3==
[[Media:BB_new M3.docx | Module 3 (provisional) biobricks]]
[[Media:BB_new M3 table.docx | Module 3 biobricks]]


==Module Timer==
==Module Timer==
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<i>Table 1. Biobricks we need from the registry</i>
<i>Table 1. Biobricks we need from the registry</i>
===Promoters===


<table border=1>
<table border=1>
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<tr>
<tr>
<td>1,2,3</td>
<td>M1</td>
<td>RBS</td>
<td>Inducible (IPTG)</td>
<td>BBa_B0034</td>
<td>BBa_R0011</td>
<td>KP1 2009</td>
<td>KP1 2009</td>
<td>2M</td>
<td>6G</td>
<td>pSB1A2</td>
<td>pSB1A2</td>
<td>A</td>
<td>A</td>
<td>100-300</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_B0034 RBS]</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_R0011 Inducible (IPTG)]</td>
</tr>
</tr>


<tr>
<tr>
<td>1,2,3</td>
<td>M2</td>
<td>Double terminator</td>
<td>Inducible (cAMP)</td>
<td>BBa_B0015</td>
<td>BBa_K118011</td>
<td>KP1 2009</td>
<td>KP2 2009</td>
<td>23L</td>
<td>18D</td>
<td>pSB1AK3</td>
<td>AK</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_B0015 Double terminator]</td>
</tr>
 
 
<tr>
<td>M1,M2,M3 (Testing)</td>
<td>COMPOSITE PART = GFP generator</td>
<td>BBa_E0240</td>
<td>KP1 2009</td>
<td>12M</td>
<td>pSB1A2</td>
<td>pSB1A2</td>
<td>A</td>
<td>A</td>
<td>100-300</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_E0240 GFP generator]</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_K118011 Inducible (cAMP)]</td>
</tr>
</tr>


<tr>
<tr>
<td>M1,M2,M3 (Testing)</td>
<td>M3</td>
<td>COMPOSITE PART = Variable input (testing)</td>
<td>Constitutive</td>
<td>BBa_F2620</td>
<td>KP2 2009 BB_Barry Box 1</td>
<td>6E</td>
<td>pSB1A2</td>
<td>A</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_F2620 Variable input]</td>
</tr>
 
<tr>
<td>M3, Timer</td>
<td>PROMOTER = Constitutive</td>
<td>BBa_J23114</td>
<td>BBa_J23114</td>
<td>KP1 2009</td>
<td>KP1 2009</td>
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<tr>
<tr>
<td>M3</td>
<td>M3</td>
<td>PROMOTER = Constitutive</td>
<td>Constitutive</td>
<td>BBa_J23103</td>
<td>BBa_J23103</td>
<td>KP1 2009</td>
<td>KP1 2009</td>
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<tr>
<tr>
<td>M3</td>
<td>M3</td>
<td>PROMOTER = REPRESSIBLE (lambda cI)</td>
<td>Repressible (lambda cI)</td>
<td>BBa_R0051</td>
<td>BBa_R0051</td>
<td>KP1 2009</td>
<td>KP1 2009</td>
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<tr>
<tr>
<td>M3</td>
<td>M3-Testing</td>
<td>COMPOSITE PART = HARVARD - cI QPI with high promoter (heat sensitive)</td>
<td>Inducible(Arabinose)</td>
<td>BBa K098995</td>
<td>BBa_I0500</td>
<td>KP3 2009</td>
<td>KP1 2009</td>
<td>1E</td>
<td>14N</td>
<td>pSB2K3</td>
<td>K</td>
<td>Variable – IPTG results in high copy # (++100 per cell)</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_I0500 pBAD Promoter]</td>
</tr>
 
<tr>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
</table><br>
<br>
 
 
===Ribosome Binding Sites===
 
 
<table border=1>
<tr>
<td><b>Module</b></td>
<td><b>Part</b></td>
<td><b>BB #</b></td>
<td><b>Kit</b></td>
<td><b>Well #</b></td>
<td><b>Plasmid</b></td>
<td><b>Resistance</b></td>
<td><b>Copy #</b></td>
<td><b>Link</b></td>
</tr>
 
<tr>
<td>M1,M2,M3</td>
<td>RBS</td>
<td>BBa_B0034</td>
<td>KP1 2009</td>
<td>2M</td>
<td>pSB1A2</td>
<td>pSB1A2</td>
<td>A</td>
<td>A</td>
<td>100-300</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_K098995 cI QPI with high promoter ]</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_B0034 RBS]</td>
</tr>
 
<tr>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
</table><br>
<br>
 
 
===Terminators===
 
 
<table border=1>
<tr>
<td><b>Module</b></td>
<td><b>Part</b></td>
<td><b>BB #</b></td>
<td><b>Kit</b></td>
<td><b>Well #</b></td>
<td><b>Plasmid</b></td>
<td><b>Resistance</b></td>
<td><b>Copy #</b></td>
<td><b>Link</b></td>
</tr>
 
<tr>
<td>1,2,3</td>
<td>Double terminator</td>
<td>BBa_B0015</td>
<td>KP1 2009</td>
<td>23L</td>
<td>pSB1AK3</td>
<td>AK</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_B0015 Double terminator]</td>
</tr>
 
<tr>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
</table><br>
<br>
 
 
===Composite Parts===
 
 
<table border=1>
<tr>
<td><b>Module</b></td>
<td><b>Part</b></td>
<td><b>BB #</b></td>
<td><b>Kit</b></td>
<td><b>Well #</b></td>
<td><b>Plasmid</b></td>
<td><b>Resistance</b></td>
<td><b>Copy #</b></td>
<td><b>Link</b></td>
</tr>
</tr>


<tr>
<tr>
<td>M1(M3-Testing)</td>
<td>M1,M2,M3 (Testing)</td>
<td>PROMOTER = INDUCIBLE (pBAD)</td>
<td>GFP generator</td>
<td>BBa_I0500</td>
<td>BBa_E0240</td>
<td>KP1 2009</td>
<td>KP1 2009</td>
<td>14N</td>
<td>12M</td>
<td>pSB2K3</td>
<td>pSB1A2</td>
<td>K</td>
<td>A</td>
<td>Variable – IPTG results in high copy # (++100 per cell)</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_I0500 pBAD Promoter]</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_E0240 GFP generator]</td>
</tr>
</tr>


<tr>
<tr>
<td>Timer</td>
<td>M1,M2,M3 (Testing)</td>
<td>PROMOTER = INDUCIBLE (LuxR + HSL)</td>
<td>GFP generator</td>
<td>BBa_R0062</td>
<td>BBa_I13504</td>
<td>KP1 2009</td>
<td>KP1 2009</td>
<td>6O</td>
<td>22I</td>
<td>pSB1A2</td>
<td>pSB1A2</td>
<td>A</td>
<td>A</td>
<td>100-300</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_R0062 lux pR]</td>
<td>[http://partsregistry.org/Part:BBa_I13504 GFP generator]</td>
</tr>
</tr>


<tr>
<tr>
<td>Timer</td>
<td>M1,M2,M3 (Testing)</td>
<td>PROTEIN GENERATOR = LuxI+RBS</td>
<td>RFP generator</td>
<td>BBa_C0261</td>
<td>BBa_I13507</td>
<td>KP1 2009</td>
<td>KP1 2009</td>
<td>14C</td>
<td>22O</td>
<td>pSB1A2</td>
<td>pSB1A2</td>
<td>A</td>
<td>A</td>
<td>100-300</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_C0261 LuxI Coding + RBS]</td>
<td>[http://partsregistry.org/Part:BBa_I13507 RFP generator]</td>
</tr>
</tr>


<tr>
<tr>
<td>Timer</td>
<td>M1,M2,M3 (Testing)</td>
<td>PROTEIN GENERATOR = LuxR+RBS</td>
<td>Variable input (testing)</td>
<td>BBa_J37033</td>
<td>BBa_F2620</td>
<td>KP2 2009</td>
<td>KP2 2009 BB_Barry Box 1</td>
<td>4O</td>
<td>6E</td>
<td>pSB1A2</td>
<td>pSB1A2</td>
<td>A</td>
<td>A</td>
<td>100-300</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_J37033 LuxR Coding + RBS]</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_F2620 Variable input]</td>
</tr>
</tr>


<tr>
<td>M3</td>
<td>HARVARD - cI QPI with high promoter (heat sensitive)</td>
<td>BBa K098995</td>
<td>KP3 2009</td>
<td>1E</td>
<td>pSB1A2</td>
<td>A</td>
<td>100-300</td>
<td>[http://partsregistry.org/partsdb/get_part.cgi?part=BBa_K098995 cI QPI with high promoter ]</td>
</tr>


<tr>
<tr>
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==Biobricks from MrGene==
==Biobricks from MrGene==


Under construction
 
<i>Table 1. Biobricks we need to synthesise</i>
<i>Table 1. Biobricks we need to synthesise.</i>
<br>
 
[[Image:BBsynthDpnII.jpg]]
<br>
<br>


[[Image:BBSynthesis.jpg]]
[[Image:BBsynthTaqI.jpg]]
<br>


[[Image:BBsynthcI.jpg]]
<br>
<br>


==Biobricks==
==Biobricks==


''Under construction''


<table width="550" border=1>
<table width="550" border=1>
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<td width="45" align="center"><b>Stop?</b></td>
<td width="45" align="center"><b>Stop?</b></td>
<td width="45" align="center"><b>ORF</b></td>
<td width="45" align="center"><b>ORF</b></td>
<td width="45" align="center"><b>Sequence</b></td>
<td width="45" align="center"><b>References</b></td>
<td width="45" align="center"><b>References</b></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">1359bp (+1)</font></td>
<td align="center"><font color="green">1359bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">[[IGEM:IMPERIAL/2009/Encapsulation/PKU | PAH]]</font></td>
<td align="center"><font color="green">[[IGEM:IMPERIAL/2009/Encapsulation/PKU | PAH]]</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">2445bp (+1)</font></td>
<td align="center"><font color="green">2445bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">651bp (+1)</font></td>
<td align="center"><font color="green">651bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">483bp (+1)</font></td>
<td align="center"><font color="green">483bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">1260bp (+1)</font></td>
<td align="center"><font color="green">1260bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">1425bp (+1)</font></td>
<td align="center"><font color="green">1425bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">612bp (+1)</font></td>
<td align="center"><font color="green">612bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">837bp (+1)</font></td>
<td align="center"><font color="green">837bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">777bp (+1)</font></td>
<td align="center"><font color="green">777bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>
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<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">Yes</font></td>
<td align="center"><font color="green">867bp (+1)</font></td>
<td align="center"><font color="green">867bp (+1)</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
<td align="center"><font color="green">Add</font></td>
</tr>
</tr>

Latest revision as of 02:45, 20 August 2009

Biobricks

Module 1

Module 1 biobricks

Module 2

Module 2 biobricks

Module 3

Module 3 biobricks

Module Timer

Biobricks from the registry

Table 1. Biobricks we need from the registry


Promoters

Module Part BB # Kit Well # Plasmid Resistance Copy # Link
M1 Inducible (IPTG) BBa_R0011 KP1 2009 6G pSB1A2 A 100-300 Inducible (IPTG)
M2 Inducible (cAMP) BBa_K118011 KP2 2009 18D pSB1A2 A 100-300 Inducible (cAMP)
M3 Constitutive BBa_J23114 KP1 2009 20I BBa_J61002 A 15-20 (based on pBR322 ORI) Constitutive promoter
M3 Constitutive BBa_J23103 KP1 2009 18I BBa_J61002 A 15-20 (based on pBR322 ORI) Constitutive promoter
M3 Repressible (lambda cI) BBa_R0051 KP1 2009 6K pSB1A2 A 100-300 Promoter (lambda cI regulated)
M3-Testing Inducible(Arabinose) BBa_I0500 KP1 2009 14N pSB2K3 K Variable – IPTG results in high copy # (++100 per cell) pBAD Promoter




Ribosome Binding Sites

Module Part BB # Kit Well # Plasmid Resistance Copy # Link
M1,M2,M3 RBS BBa_B0034 KP1 2009 2M pSB1A2 A 100-300 RBS




Terminators

Module Part BB # Kit Well # Plasmid Resistance Copy # Link
1,2,3 Double terminator BBa_B0015 KP1 2009 23L pSB1AK3 AK 100-300 Double terminator




Composite Parts

Module Part BB # Kit Well # Plasmid Resistance Copy # Link
M1,M2,M3 (Testing) GFP generator BBa_E0240 KP1 2009 12M pSB1A2 A 100-300 GFP generator
M1,M2,M3 (Testing) GFP generator BBa_I13504 KP1 2009 22I pSB1A2 A 100-300 GFP generator
M1,M2,M3 (Testing) RFP generator BBa_I13507 KP1 2009 22O pSB1A2 A 100-300 RFP generator
M1,M2,M3 (Testing) Variable input (testing) BBa_F2620 KP2 2009 BB_Barry Box 1 6E pSB1A2 A 100-300 Variable input
M3 HARVARD - cI QPI with high promoter (heat sensitive) BBa K098995 KP3 2009 1E pSB1A2 A 100-300 cI QPI with high promoter



Biobricks from MrGene

Table 1. Biobricks we need to synthesise.




Biobricks

Gene NCBI Ref Nucleotide accession# Organism Xbal & SpeI sites Start? Stop? ORF References
PAH 5053 PAH # Homo Sapiens 1 and 0 Yes Yes 1359bp (+1) PAH
Cellulase 4810415 Cellulase # Clostridium thermocellum 0 and 0 Yes Yes 2445bp (+1) Add
RcsB 947441 RcsB # K12 MG1655 0 and 0 Yes Yes 651bp (+1) Add
B3023 945805 B3023 # K12 MG1655 0 and 0 Yes Yes 483bp (+1) Add
WaaL 948148 WaaL # K12 MG1655 0 and 0 Yes Yes 1260bp (+1) Add
OtsA 946405 OtsA # K12 MG1655 0 and 0 Yes Yes 1425bp (+1) Add
OtsB 946406 OtsB # K12 MG1655 0 and 0 Yes Yes 612bp (+1) Add
Dam 947893 Dam # K12 MG1655 0 and 0 Yes Yes 837bp (+1) Add
TaqI 6941926 TaqI # Thermodesulfovibrio yellowstonii DSM 11347 0 and 0 Yes Yes 777bp (+1) Add
DpnII 6029545 DpnII # Strepococcus pneumoniae Hungary19A-6 0 and 0 Yes Yes 867bp (+1) Add


Genes and biobrick compatibility

 

 PAH Cellulase rcsB B3023 waaL OtsA OtsB TaqI DpnII
EcoRI No No No No No No No No No
SpeI No No No No No No No No No
XbaI Yes No No No No No No No No
PstI Yes No Yes Yes No No No No No
NotI No No No Yes No No No No No
PvuII Yes (3) Yes No No No Yes No No No
XhoI Yes No No No No No No No No
AvrII No No No No Yes No No No No
NheI No No No No Yes No No No No
SapI No No No No No No No No No
Sequence modified?       Yes Yes        
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