Difference between revisions of "Plasmid backbones/Other standards"
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==Plasmids used in DNA synthesis of BioBrick&reg; parts==
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==Silver assembly standard plasmid backbones==
  
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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.
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Please see [[Plasmid_backbones/Assembly_of_protein_fusions|plasmid backbones for protein fusions]]
  
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<parttable>synthesis_plasmid</parttable>
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==Freiburg assembly standard plasmid backbones==
  
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<!-- 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. -->
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Please see [[Plasmid_backbones/Assembly_of_protein_fusions|plasmid backbones for protein fusions]]
  
 
==Berkeley assembly standard plasmid backbones==
 
==Berkeley assembly standard plasmid backbones==
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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.
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{{:Assembly_standard_21/Overview}}
  
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<parttable>berkeley_plasmid</parttable>
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<parttable>berkeley_plasmid_backbone</parttable>
  
 
<!-- To include a plasmid in this table, make the part type "Plasmid" and include the categories "//plasmid //standard/berkeley" 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/berkeley" under the Hard Information tab of the part. -->
  
 
==Lim assembly standard plasmid backbones==
 
==Lim assembly standard plasmid backbones==
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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.
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{{:Assembly standard 28/Overview}}
  
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<parttable>lim_plasmid</parttable>  
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While any vector can be adapted to adhere to the Lim standard, most of the available vectors from the Registry that adhere to the Lim standard are derived from the yeast pRS__ series of vectors.  The Registry has several types of acceptor vectors built in the pRS315 or 305 backbone. When necessary, markers can be exchanged by one-piece subclones of the completed cassettes into alternative pRS vectors, using the Kpn1/PspOMI and SacI sites.
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<parttable>lim_plasmid_backbone</parttable>  
  
 
<!-- 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. -->
  
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==SynBERC Tumor killing bacteria testbed==
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{{:Plasmid backbones/Yeast/Credit}}
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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.
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<parttable>tumor_killing_bacteria_plasmid</parttable>
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<!-- 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. -->
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{|
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|[[Image:JCA Photo.png|60px|center]]
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|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.
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===References===
 
<biblio>
 
<biblio>
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#Anderson pmid=16330045
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#Sikorski pmid=2659436
 
</biblio>
 
</biblio>
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==Other miscellaneous vectors==
 
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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.
 

Latest revision as of 21:29, 28 June 2017

< 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.

Silver assembly standard plasmid backbones

Please see plasmid backbones for protein fusions

Freiburg assembly standard plasmid backbones

Please see plasmid backbones for protein fusions

Berkeley assembly standard plasmid backbones

Researchers at UC Berkeley have developed the BglBrick assembly standard, or Assembly standard 21, based on idempotent assembly with BamHI and BglII restriction enzymes. In a nutshell, most parts look like this: 

        Prefix                        Suffix
5' GAATTC atg AGATCT ...part... GGATCC taa CTCGAG 3'
   EcoRI      BglII             BamHI   *   XhoI

Fusing two parts leaves the following scar: 

5' [part A] GGATCT [part B] 3'
             G  S

Note, however, that Assembly standard 20 is intended as a minimal physical assembly standard, and only those features needed for interconversion of BglBrick assembly standard plasmids are formally defined. Therefore, atg and taa spacers are not core definitions of the standard.

See [http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats The BioBricks Foundation wiki] for a discussion and comparison of different technical standards.


There are no parts for this table


Lim assembly standard plasmid backbones

The Lim standard is based on a multi-part/combinatorial cloning technique that is particularly well suited to shuffling protein domains. The key to this approach is the Type IIS restriction enzyme, AarI, a rare (7-cutter) that cuts 4bp offset from its binding site. Thus, AarI can generate four base overhangs of any sequence. LimStandardFigure1.png
LimStandardFigure2.png Since the user can specify the overhangs, this method can be used to "stitch-together" fragments without a scar, which is sometimes necessary to preserve protein function. More importantly, these overhangs can be non-palindromic thereby avoiding a key problem of trying to do multipart ligations using standard restriction enzymes: the self ligation of a part (which blocks proper assembly of parts).
The Lim standard enables high efficiency ligations of up to 4 parts simultaneously (vector plus 3 inserts). While parts can be made with any 4 base overhangs, we chose a standard set, termed A, B, C, and D to facilitate exchange of parts between researchers.

Note that most parts that adhere to the Lim standard are primarily intended for use when working with yeast.

LimStandardFigure3.png

While any vector can be adapted to adhere to the Lim standard, most of the available vectors from the Registry that adhere to the Lim standard are derived from the yeast pRS__ series of vectors. The Registry has several types of acceptor vectors built in the pRS315 or 305 backbone. When necessary, markers can be exchanged by one-piece subclones of the completed cassettes into alternative pRS vectors, using the Kpn1/PspOMI and SacI sites.


There are no parts for this table


SergioPeisajovichPhoto.jpg AndrewHorowitzPhoto.jpg Sergio Peisajovich and Andrew Horowitz, from Wendell Lim's lab, developed several of the yeast plasmid backbones as an instructor of the 2008 UCSF iGEM team.

References

<biblio>

  1. Sikorski pmid=2659436

</biblio>