Difference between revisions of "BioScaffold Parts"

(→‎Plasmid Compatibility with BioScaffold Part Internal and External Enzymes)
(→‎Plasmid Compatibility with BioScaffold Part Internal and External Enzymes)
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Revision as of 05:20, 28 December 2008

BioScaffold parts are BioBrick parts that contain restriction enzyme recognition sites that enable their full or partial removal from a BioBrick assembly.


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


Currently, BioScaffold parts and their status must be manually added to the following table.
-?- Class Name Description External Enzymes Internal Enzymes
A α Part:BBa_J70010 A BioScaffold Part (for offset see Part Design page) PpiI MabI, PacI
A α Part:BBa_J70012 A BioScaffold Part (Protein Head Remover) PsrI MabI, AscI
α Part:BBa_J70030 A BioScaffold Part (Protein Tail Remover/Protein Fusions) PpiI MabI, PacI
α Part:BBa_J70032 A Composite BioScaffold Part (Protein Fusions) PpiI, PsrI MabI, (AscI and PacI)
β Part:BBa_J70034 A BioScaffold Part (for Library Vector Preparation) AarI XmaI
β Part:BBa_J70036 A BioScaffold Part (for Library Insert Preparation) AarI XmaI


Plasmid Compatibility with BioScaffold Part Internal and External Enzymes

Plasmid Incompatible Enzymes (# of Sites) Compatible Enzymes Commonly Used Plasmid
pSB1A3, discontinued [1] PpiI(2) AarI, AscI, MabI, PacI, PsrI, XmaI No
pSB1AC3, high copy [2] PpiI 2 Yes
pSB1AK3, high copy [3] PpiI 2 Yes
pSB1AT3, high copy [4] PpiI 2 Yes
pSB1A7, transcriptionally insulated high copy [5] PsrI and PpiI 2 each Sometimes
pSB2K3, use pSB2K4 instead AscI 1 No
pSB2K4, inducible copy [6] None None Yes
pSB3C5, low to medium copy [7] PpiI 1 Yes
pSB3K3, probably discontinued PpiI 1 No
pSB3T5, low to medium copy [8] PpiI and PsrI 1 each Yes
pSB4A3, discontinued [9] PpiI 1 No
pSB3K5, low to medium copy standard vector [10] PpiI 1 Yes
pSB4C5, low copy standard vector [11] None None Yes
pSB4K5, low copy standard vector [12] None None Yes
pSB4A5, low copy standard vector [13] PpiI 1 Yes
pSB4T5, low copy standard vector [14] PsrI 1 Yes