Difference between revisions of "BioScaffold Parts"

Revision as of 05:08, 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 (# of Sites)	Commonly Used Plasmid
pSB1A3, discontinued [1]	PpiI	2	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

@@ Line 49: / Line 49: @@
 |-
 ! Plasmid
-! Enzyme
+! Incompatible Enzymes (# of Sites)
-! Number of Recognition Sites
+! Compatible Enzymes (# of Sites)
 ! Commonly Used Plasmid
 |-