Difference between revisions of "Help:Assembly standard 21"
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Fusing two parts leaves the following scar:
 
Fusing two parts leaves the following scar:
  
−
<table>
+
5' [part A] GGATCT [part B] 3'
−
<tr>
+
              G  S
−
<td>5' ...part A...</td>
+
−
<td><pre>
+
−
GGATCT
+
−
G  S
+
−
</pre></td>
+
−
<td>...part B... 3'</td>
+
−
</tr>
+
−
</table>
+
  
 
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.
 
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.

Revision as of 00:12, 5 February 2009

< Back to Berkeley standard parts

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:

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

Fusing two parts leaves the following scar: 

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

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.

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