Difference between revisions of "BioScaffold Parts"

(→‎Plasmid Compatibility with BioScaffold Part Internal and External Enzymes)
(→‎Plasmid Compatibility with BioScaffold Part Internal and External Enzymes)
Line 55: Line 55:
 
| pSB1A3, discontinued [https://parts.igem.org/Plasmid_backbones/Archive]  
 
| pSB1A3, discontinued [https://parts.igem.org/Plasmid_backbones/Archive]  
 
| PpiI(2)
 
| PpiI(2)
−
| AarI, AscI, MabI, PacI, PsrI, XmaI
+
| AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI
 
| No
 
| No
 
|-
 
|-
 
| pSB1AC3, high copy [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB1AC3, high copy [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| PpiI
+
| PpiI(2)
−
| 2
+
| AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI
 
| Yes
 
| Yes
 
|-
 
|-
 
| pSB1AK3, high copy [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB1AK3, high copy [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| PpiI  
+
| PpiI(2)
−
| 2
+
| AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI
 
| Yes
 
| Yes
 
|-
 
|-
 
| pSB1AT3, high copy [https://parts.igem.org/Plasmid_backbones/Assembly]  
 
| pSB1AT3, high copy [https://parts.igem.org/Plasmid_backbones/Assembly]  
−
| PpiI
+
| PpiI(2), BamHI(?)
−
| 2
+
| AarI, AscI, MabI, PacI, PsrI, XmaI
 
| Yes
 
| Yes
 
|-
 
|-
 
| pSB1A7, transcriptionally insulated high copy [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB1A7, transcriptionally insulated high copy [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| PsrI and PpiI
+
| PsrI(2) and PpiI(2)
−
| 2 each
+
| AarI, AscI, BamHI, MabI, PacI, XmaI
 
| Sometimes
 
| Sometimes
 
|-
 
|-
 
| pSB2K3, use pSB2K4 instead
 
| pSB2K3, use pSB2K4 instead
−
| AscI
+
| AscI(1)
−
| 1
+
| AarI, BamHI, MabI, PacI, PpiI, PsrI, XmaI
 
| No
 
| No
 
|-
 
|-
 
| pSB2K4, inducible copy [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB2K4, inducible copy [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| None
+
| BamHI(?)
−
| None
+
| AarI, AscI, MabI, PacI, PpiI, PsrI, XmaI
 
| Yes
 
| Yes
 
|-
 
|-
 
| pSB3C5, low to medium copy [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB3C5, low to medium copy [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| PpiI  
+
| PpiI(1)
−
| 1
+
| AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI
 
| Yes
 
| Yes
 
|-
 
|-
 
| pSB3K3, probably discontinued
 
| pSB3K3, probably discontinued
−
| PpiI  
+
| PpiI(1), XmaI(?)
−
| 1
+
| AarI, AscI, BamHI, MabI, PacI, PsrI
 
| No
 
| No
 
|-
 
|-
 
| pSB3T5, low to medium copy [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB3T5, low to medium copy [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| PpiI and PsrI
+
| PpiI(1) and PsrI(1)
−
| 1 each
+
| AarI, AscI, BamHI, MabI, PacI, XmaI
 
| Yes
 
| Yes
 
|-
 
|-
 
| pSB4A3, discontinued [https://parts.igem.org/Plasmid_backbones/Archive]
 
| pSB4A3, discontinued [https://parts.igem.org/Plasmid_backbones/Archive]
−
| PpiI  
+
| PpiI(1)
−
| 1
+
| AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI
 
| No
 
| No
 
|-
 
|-
 
| pSB3K5, low to medium copy standard vector [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB3K5, low to medium copy standard vector [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| PpiI
+
| PpiI(1)
−
| 1
+
| AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI
 
| Yes
 
| Yes
 
|-  
 
|-  
 
| pSB4C5, low copy standard vector [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB4C5, low copy standard vector [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| None
 
| None
−
| None
+
| AarI, AscI, BamHI, MabI, PacI, PpiI, PsrI, XmaI
 
| Yes
 
| Yes
 
|-
 
|-
Line 121: Line 121:
 
| None  
 
| None  
 
| None
 
| None
−
| Yes
+
| AarI, AscI, BamHI, MabI, PpiI, PsrI, XmaI
 
|-
 
|-
 
| pSB4A5, low copy standard vector [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB4A5, low copy standard vector [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| PpiI
+
| PpiI(1)
−
| 1
+
| AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI
 
| Yes
 
| Yes
 
|-
 
|-
 
| pSB4T5, low copy standard vector [https://parts.igem.org/Plasmid_backbones/Assembly]
 
| pSB4T5, low copy standard vector [https://parts.igem.org/Plasmid_backbones/Assembly]
−
| PsrI
+
| PsrI(1)
−
| 1
+
| AarI, AscI, BamHI, MabI, PacI, PpiI, XmaI
 
| Yes
 
| Yes
 
|}
 
|}

Revision as of 05:41, 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, BamHI, MabI, PacI, PsrI, XmaI No
pSB1AC3, high copy [2] PpiI(2) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB1AK3, high copy [3] PpiI(2) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB1AT3, high copy [4] PpiI(2), BamHI(?) AarI, AscI, MabI, PacI, PsrI, XmaI Yes
pSB1A7, transcriptionally insulated high copy [5] PsrI(2) and PpiI(2) AarI, AscI, BamHI, MabI, PacI, XmaI Sometimes
pSB2K3, use pSB2K4 instead AscI(1) AarI, BamHI, MabI, PacI, PpiI, PsrI, XmaI No
pSB2K4, inducible copy [6] BamHI(?) AarI, AscI, MabI, PacI, PpiI, PsrI, XmaI Yes
pSB3C5, low to medium copy [7] PpiI(1) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB3K3, probably discontinued PpiI(1), XmaI(?) AarI, AscI, BamHI, MabI, PacI, PsrI No
pSB3T5, low to medium copy [8] PpiI(1) and PsrI(1) AarI, AscI, BamHI, MabI, PacI, XmaI Yes
pSB4A3, discontinued [9] PpiI(1) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI No
pSB3K5, low to medium copy standard vector [10] PpiI(1) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB4C5, low copy standard vector [11] None AarI, AscI, BamHI, MabI, PacI, PpiI, PsrI, XmaI Yes
pSB4K5, low copy standard vector [12] None None AarI, AscI, BamHI, MabI, PpiI, PsrI, XmaI
pSB4A5, low copy standard vector [13] PpiI(1) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB4T5, low copy standard vector [14] PsrI(1) AarI, AscI, BamHI, MabI, PacI, PpiI, XmaI Yes