Difference between revisions of "Plasmid backbones/Other standards"
Line 11: Line 11:
 
</html>
 
</html>
  
−
==Plasmids used in DNA synthesis of BioBrick&reg; parts==
+
'''For plasmid backbones that adhere to the Silver or Freiburg standards, please see [[Plasmid_backbones/Assembly_of_protein_fusions|plasmid backbones for protein fusions]].'''
−
 
+
−
Most DNA synthesis companies do not currently use BioBrick&reg; plasmid backbones to clone synthesized BioBrick&reg; parts.  Therefore, some parts in the Registry are available in non-standard plasmid backbones because they were constructed via direct DNA synthesis.  Here is a list of plasmid backbones used by assorted DNA synthesis companies.
+
−
 
+
−
<parttable>synthesis_plasmid</parttable>
+
−
 
+
−
<!-- To include a plasmid in this table, make the part type "Plasmid" and include the categories "//plasmid/synthesis" under the Hard Information tab of the part. -->
+
  
 
==Berkeley assembly standard plasmid backbones==
 
==Berkeley assembly standard plasmid backbones==
Line 33: Line 27:
 
<!-- To include a plasmid in this table, make the part type "Plasmid" and include the categories "//plasmid //standard/lim" under the Hard Information tab of the part. -->
 
<!-- To include a plasmid in this table, make the part type "Plasmid" and include the categories "//plasmid //standard/lim" under the Hard Information tab of the part. -->
  
−
==SynBERC Tumor killing bacteria testbed==
+
==Plasmids used in DNA synthesis of BioBrick&reg; parts==
  
−
One of the testbeds for the NSF-funded [http://synberc.org Synthetic Biology Engineering Research Center (SynBERC)] is designing and engineering modules that will be integrated to construct a bacterium capable of moving to and attacking a chemical or biological entity; for example, a tumor or a chemical warfare agent. There are a number of environmental cues that bacteria could use to distinguish a tumor from healthy tissue.  The environment is hypoxic and more nutritious, and bacteria grow to significantly higher cell densities (Yu ''et al.'', 2003). Components that sense these differences can be linked to genetic circuits that integrate the information. The circuits will activate engineered pathways that control bacterial chemotaxis and the interaction between the bacterium and a mammalian cell. These systems will be engineered into a non-pathogenic ''E. coli'' chassis.
+
Most DNA synthesis companies do not currently use BioBrick&reg; plasmid backbones to clone synthesized BioBrick&reg; parts.  Therefore, some parts in the Registry are available in non-standard plasmid backbones because they were constructed via direct DNA synthesis. Here is a list of plasmid backbones used by assorted DNA synthesis companies.
  
−
<parttable>tumor_killing_bacteria_plasmid</parttable>
+
<parttable>synthesis_plasmid</parttable>
−
 
+
−
<!-- To include a plasmid in this table, make the part type "Plasmid" and include the categories "//plasmid //project/tumorkillingbacteria" under the Hard Information tab of the part. -->
+
−
 
+
−
{|
+
−
|[[Image:JCA Photo.png|60px|center]]
+
−
|Chris Anderson, an assistant professor of bioengineering at UC Berekeley and the SynBERC testbed leader, has submitted a set of plasmids associated with his paper on ''Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria''.  Please read the paper for details or contact Chris for details.
+
−
|}
+
−
 
+
−
<biblio>
+
−
#Anderson pmid=16330045
+
−
</biblio>
+
  
 +
<!-- To include a plasmid in this table, make the part type "Plasmid" and include the categories "//plasmid/synthesis" under the Hard Information tab of the part. -->
  
 
==Other miscellaneous vectors==
 
==Other miscellaneous vectors==
  
−
The Registry also have miscellaneous other plasmids and plasmids backbones.  These plasmids and plasmid backbones have not undergone Registry curation, but we include them here for completeness.
+
The Registry also have miscellaneous other plasmid backbones.  These plasmid backbones have not undergone Registry curation, but we include them here for completeness.

Revision as of 23:02, 11 December 2008

< Back to Plasmid backbones


   
Plasmid backbones/Other standards
Part assembly System operation Protein expression Assembly of protein fusions Part measurement Screening of part libraries Building BioBrick vectors DNA synthesis Other standards Archive
Or get some help on plasmid backbones.

For plasmid backbones that adhere to the Silver or Freiburg standards, please see plasmid backbones for protein fusions.

Berkeley assembly standard plasmid backbones

Researchers at UC Berkeley have developed a new assembly standard. See [http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats#The_Berkeley_.28BBb.29_Format the BioBricks Foundation wiki] for more details.


There are no parts for this table


Lim assembly standard plasmid backbones

Students in Wendell Lim's lab have developed a new assembly standard. See [http://2008.igem.org/Everything_you_ever_wanted_to_know_about_AarI the 2008 UCSF iGEM team wiki] for more details.


There are no parts for this table


Plasmids used in DNA synthesis of BioBrick® parts

Most DNA synthesis companies do not currently use BioBrick® plasmid backbones to clone synthesized BioBrick® parts. Therefore, some parts in the Registry are available in non-standard plasmid backbones because they were constructed via direct DNA synthesis. Here is a list of plasmid backbones used by assorted DNA synthesis companies.


More...
NameDescriptionResistanceRepliconCopy
number		ChassisLength
BBa_J70003Geneart Cloning Plasmid pGA4A   2961
BBa_J70004BioBasic Cloning Plasmid pUC57A   2710
BBa_J70022GENEART pGA4 plasmid    2978
BBa_K2812001Coding sequence for trunctated Lysostaphin     738
BBa_K2812003Coding sequence for trunctated Lysostaphin regulated by T7-promoter    776
BBa_K2812004Coding sequence for trunctated Lysostaphin fused to His-tagged HlyA    1458
BBa_K2812005Coding sequence for trunctated Lysostaphin with HlyA and His6-tag regulated by T7-promoter    1496
BBa_K2812006Coding sequence for Pyocin S5 with HlyA and His6-tag    2217
BBa_K2812007Coding sequence for Pyocin S5 with HlyA and His6-tag regulated by pBAD-ara promoter    2288
BBa_K5293014pHREAC_eGFP_ER    10477
pSB1A1pUC19 with a BioBrick cloning site (Replaced by pSB1A3)ApMB1500-700 2708


Other miscellaneous vectors

The Registry also have miscellaneous other plasmid backbones. These plasmid backbones have not undergone Registry curation, but we include them here for completeness.