Difference between revisions of "Plasmid backbones/Other standards"

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[[Plasmids|< Back to Plasmids]]
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[[Plasmid backbones|< Back to Plasmid backbones]]
  
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==BioBrick plasmid==
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{{:Template:Plasmid backbone types}}
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*[[Part:BBa_J52017]] - BioBrick eukaryotic terminator plasmid; needs to be split into plasmid and ccdB? part
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*[[Part:BBa_J63009]] - Silver lab BioBrick fusion vector with shortened prefix and suffix; missing feature annotations
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*[[Part:BBa_J63010]] - Silver lab BioBrick fusion vector with shortened prefix and suffix; missing feature annotations
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==Partial BioBrick cloning site==
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<html>
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*[[Part:BBa_J61031]] - partial BioBrick cloning site, amplifiable BAC plasmid
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<style>
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*[[Part:BBa_I714945]] - partial BioBrick cloning site
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#assembly_plasmid_table {margin-left:auto;margin-right:auto; border: 3px solid #444444;}
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*[[Part:BBa_I713002]] - no features entered
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#assembly_plasmid_table td {background-color:#eeeeee; padding: 5px; font-size: 12px;}
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#assembly_plasmid_table th {background-color: #aaaaaa;padding: 5px; font-size:14px;}
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</style>
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</html>
  
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==BioBrick-compatible plasmid==
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==Silver assembly standard plasmid backbones==
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*[[Part:BBa_J23006]] - BioBrick-compatible plasmid for cloning parts downstream of R0040 promoter, needs to be reentered SpeI->EcoRI?
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*[[Part:BBa_J61002]] - BioBrick-compatible plasmid for cloning protein generators downstream of R0040
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*[[Part:BBa_J61003]] - BioBrick-compatible plasmid for cloning ORFs downstream of R0040.B0034 or assembling promoter/RBS's in front of GFP.B0015
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*[[Part:BBa_J23018]] - BioBrick-compatible plasmid for cloning ORFs downstream of R0040.B0034 or assembling promoter/RBS's in front of RFP.B0015
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*[[Part:BBa_J23019]] - BioBrick-compatible plasmid for cloning ORFs downstream of R0040.B0034 or assembling promoter/RBS's in front of RFP.B0015
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*[[Part:BBa_J61035]] - BioBrick-compatible plasmid with GenR between E and X
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==Different assembly standard==
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Please see [[Plasmid_backbones/Assembly_of_protein_fusions|plasmid backbones for protein fusions]]
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*[[Part:BBa_I716101]] - not a BioBrick plasmid ... BB2.0 standard, no features entered
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==Too many BioBrick sites==
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==Freiburg assembly standard plasmid backbones==
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*[[Part:BBa_I713001]] - no features entered
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*[[Part:BBa_I714945]] - multiple BioBrick enzyme sites
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==Not a BioBrick plasmid at all==
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Please see [[Plasmid_backbones/Assembly_of_protein_fusions|plasmid backbones for protein fusions]]
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*[[Part:BBa_J61007]]
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*[[Part:BBa_J61009]]
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*[[Part:BBa_I713003]]
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==Actually a part in a plasmid==
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==Berkeley assembly standard plasmid backbones==
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*[[Part:BBa_I732950]] - no features entered, missing a NotI site
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{{:Assembly_standard_21/Overview}}
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*[[Part:BBa_I732951]] - no features entered, missing a NotI site
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<parttable>berkeley_plasmid_backbone</parttable>
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<!-- 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. -->
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==Lim assembly standard plasmid backbones==
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{{:Assembly standard 28/Overview}}
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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>
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<!-- 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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{{:Plasmid backbones/Yeast/Credit}}
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===References===
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<biblio>
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#Sikorski pmid=2659436
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</biblio>

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>