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Revision as of 20:52, 26 March 2009

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Bioscaffold sites are BioBrick parts that contain restriction enzyme recognition sites that enable full or partial removal of the Bioscaffold site from a composite BioBrick part. Bioscaffold parts address some of the limitations of BioBrick standard assembly by enabling protein fusions, cloning of part libraries within a composite BioBrick part, and removal of BioBrick scars.

BioScaffold parts

The enzymes that facilitate the removal of BioScaffold parts are defined by what region of the part that they excise:

  • External Enzymes: Do not cut solely inside the BioBrick Part (extend to Prefix, Suffix, and/or Scar regions)
  • Internal Enzymes: Cut inside the BioBrick Part (between the Prefix, Suffix, and/or Scar regions)

The classes of α, β, and γ BioScaffold parts are defined for assemblies of the form:

<Prefix> part1 <Scar> BioScaffold part <Scar> part2 <Suffix>

  • Class α parts: specific enzymes cut outside of scars surrounding the BioScaffold part
  • Class β parts: specific enzymes cut within scars surrounding BioScaffold part
  • Class γ parts: no specific enzymes, internal enzymes cut within the BioScaffold part
  • Mixed parts: contain properties of several classes, name classes involved

Compatibility of plasmid backbones with BioScaffold sites

For a plasmid backbone to be compatible with BioScaffold sites, remove the following restriction enzymes.

  • PpiI
  • PsrI
  • AarI
  • MabI.

Also note that

  • XmaI is being considered as an additional site for inclusion in BioScaffold sites.
  • AscI and PacI are sometimes used instead of MabI because their restriction site sequences make them orthogonal to many parts based on GC content.

Contributing to the BioScaffold part collection

To join the BioScaffold community, you can construct and test existing BioScaffold part designs, design new BioScaffold parts, design new uses for BioScaffold parts, or convert high use plasmids to a BioScaffold compatible format.

If you are interested joining the community or have already done so, please contact Julie Norville at (julie dot norville at gmail dot com and norville at mit dot edu) with the subject heading "BioScaffold parts" so that your work and insights can be described in future BioScaffold parts BBF RFCs or publications and/or you can be solicited as a co-author on these documents.

You may also wish to describe your intent to test already designed BioScaffold parts or convert BioBrick vectors to the BioScaffold format on the BioScaffold Part User Group wiki [http://openwetware.org/wiki/BioScaffold_Parts_Users_Group BioScaffold Parts User Group wiki] (especially if you wish to convert plasmids or other important parts to a BioScaffold part compatible format, since this is a task that a number of users may contemplate) so that others in the community do not duplicate your efforts. As the community grows, we will create a mailing list.

References

  1. [http://openwetware.org/wiki/The_BioBricks_Foundation:BBFRFC15 BioBricks Foundation RFC 15] by Julie Norville, Angie Belcher and Tom Knight