Help:Standards/Assembly/RFC21

Motivation & Discussion

The Berkeley RFC[21] is optimized to enable in-frame assembly of proteins: it is based on idempotent assembly with BamHI and BglII restriction enzymes, which creates a benign 6bp scar between assembled parts.

The Berkeley RFC[21] is incompatible with BioBrick RFC[10]. Additionally the BglII enzyme cannot be heat inactivated, which prevents the RFC[21] from being used with the 3A assembly method.

Advantages

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

Disadvantages

  • BglII cannot be heat-inactivated therefore the current 3A Assembly procedures won't work
  • incompatible to BioBrick RFC[10] format
  • incompatible to Silver RFC[23] format


Technical Specifications

Prefix and Suffix

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


Scar

Assembling two parts leaves the following scar:

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


Compatibility/Illegal Sites

In order for a part to be compatible with Berkeley RFC[21] it must not contain the following restriction sites, as these will need to be unique to the prefix and suffix:

  • EcoRI site: GAATTC
  • BglII site: AGATCT
  • BamHI site: GGATCC
  • XhoI site: CTCGAG


Notes

Sources

  • [http://dspace.mit.edu/handle/1721.1/46747 BBF RFC 21: BglBricks Assembly Standard]
  • [http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats#BBF_RFC_21:_The_Berkeley_.28BBb.29_Format_.28now_called_BglBricks.29 The BioBricks Foundation - Format Discussion]
  • Old Registry RFC[21] Page


Help Pages: Assembly Standards || Assembly Compatibility || Supported Assembly Systems || Scars

Accepted Standards: BioBrick RFC[10] | iGEM Type IIS RFC[1000]

Depracated Standards: BioBrick BB-2 RFC[12] | Berkeley RFC[21] | Silver RFC[23] | Freiburg RFC[25]