Difference between revisions of "Help:Assembly standard 21"

(New page: Researchers at UC Berkeley have developed the Berkeley assembly standard based on idempotent assembly with BamHI and BglII restriction enzymes. In a nutshell, most plasmids look like this...)
 
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Researchers at UC Berkeley have developed the Berkeley assembly standard based on idempotent assembly with BamHI and BglII restriction enzymes.  In a nutshell, most plasmids look like this:
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[[Assembly standard 21|< Back to Assembly standard 21 parts]]
  
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<table>
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{{:Assembly standard 21/Overview}}
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<tr>
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  <td><center>Prefix</center></td><td></td><td><center>Suffix</center></td>
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<td><pre>
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5' GAATTC atg AGATCT
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  EcoRI      BglII
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</pre></td>
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<td>...part...</td>
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<td><pre>
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GGATCC taa CTCGAG 3'
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BamHI  *  XhoI </pre></td>
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Fusing two parts leaves the following scar:
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<table>
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<td>5' ...part A...</td>
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<td><pre>
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GGATCT
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G  S
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<td>...part B... 3'</td>
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</table>
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Note, however, that Berkeley standard is intended as a minimal physical assembly standard, and only those features needed for interconversion of Berkeley assembly standard plasmids are formally defined.  Therefore, "atg" and "taa" spacers are not core definitions of the standard.
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===Formal Definition:===
 
===Formal Definition:===
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*A Berkeley assembly standard part is a DNA sequence flanked on the 5' end by "GATCT" and on the 3' end by "G" lacking BglII, BamHI, EcoRI, and XhoI restriction sites
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*A Berkeley assembly standard part is a DNA sequence flanked on the 5' end by <code>GATCT</code> and on the 3' end by <code>G</code> lacking BglII, BamHI, EcoRI, and XhoI restriction sites
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*A Berkeley assembly standard vector is a DNA sequence flanked on its 5' end by "GATCC" and on its 3' end by "A"
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*A Berkeley assembly standard vector is a DNA sequence flanked on its 5' end by <code>GATCC</code> and on its 3' end by <code>A</code>
 
*A Berkeley assembly standard entry vector has a unique EcoRI site, no BamHI or BglII restriction sites, and at most one XhoI site 5' to the EcoRI site
 
*A Berkeley assembly standard entry vector has a unique EcoRI site, no BamHI or BglII restriction sites, and at most one XhoI site 5' to the EcoRI site
 
*A Berkeley assembly standard plasmid is represented as <vector_name>-<part_name> and has the sequence obtained by concatenating the vector and part sequences
 
*A Berkeley assembly standard plasmid is represented as <vector_name>-<part_name> and has the sequence obtained by concatenating the vector and part sequences
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* incompatible to original BioBrick assembly standard format
 
* incompatible to original BioBrick assembly standard format
 
* incompatible to BioFusion format
 
* incompatible to BioFusion format
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==References==
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# Anderson, J Christopher; Dueber, John E; Leguia, Mariana; Wu, Gabriel C; Goler, Jonathan A; Arkin, Adam P; Keasling, Jay D.  ''BBF RFC 21: BglBricks Assembly Standard''.  BBF <nowiki>RFC 21</nowiki>.  2009.

Latest revision as of 14:48, 18 September 2009

< Back to Assembly standard 21 parts

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.

Formal Definition:

  • A Berkeley assembly standard part is a DNA sequence flanked on the 5' end by GATCT and on the 3' end by G lacking BglII, BamHI, EcoRI, and XhoI restriction sites
  • A Berkeley assembly standard vector is a DNA sequence flanked on its 5' end by GATCC and on its 3' end by A
  • A Berkeley assembly standard entry vector has a unique EcoRI site, no BamHI or BglII restriction sites, and at most one XhoI site 5' to the EcoRI site
  • A Berkeley assembly standard plasmid is represented as <vector_name>-<part_name> and has the sequence obtained by concatenating the vector and part sequences
  • Further definition constraints are "sub-standards" of the Berkeley assembly standard format

Advantages

  • in-frame fusion of protein parts
  • benign protein scar
  • enzymes selected for efficient cutting

Disadvantages

  • BglII cannot be heat-inactivated therefore the current 3A standard assembly procedures won't work
  • incompatible to original BioBrick assembly standard format
  • incompatible to BioFusion format

References

  1. Anderson, J Christopher; Dueber, John E; Leguia, Mariana; Wu, Gabriel C; Goler, Jonathan A; Arkin, Adam P; Keasling, Jay D. BBF RFC 21: BglBricks Assembly Standard. BBF RFC 21. 2009.