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 49: Line 49:
 
|-
 
|-
 
! Enzyme
 
! Enzyme
−
! Internal or External Enzyme
+
! Internal, External, BioBrick Enzyme
 
! Typical Use
 
! Typical Use
 
! Special Property
 
! Special Property
 
! Priority for Removal from Vector or Part
 
! Priority for Removal from Vector or Part
 
! Heat killable (for automated assembly)
 
! Heat killable (for automated assembly)
 +
! Buffers
 +
! Efficiency
 
|-
 
|-
 
| AarI
 
| AarI
Line 60: Line 62:
 
| Good for cutting into BioBrick scars
 
| Good for cutting into BioBrick scars
 
| High
 
| High
 +
| Yes, 65 degrees
 +
| AarI+oligo, Tango2X
 +
| >95% ligated and recut
 
|-
 
|-
 
| AscI  
 
| AscI  
Line 66: Line 71:
 
| Good to use in combination with low GC content parts
 
| Good to use in combination with low GC content parts
 
| Low
 
| Low
 +
| Yes, 65 (SgsI)
 +
| Tango1X(SgsI), FastDigest(SgsI), Y(PalA I)
 +
| >95%(SgsI), >90%(PalA I) ligated and recut
 
|-
 
|-
 
| BamHI
 
| BamHI
Line 72: Line 80:
 
| DNA sequence translates into glycine-serine
 
| DNA sequence translates into glycine-serine
 
| Low
 
| Low
 +
| Yes, 80
 +
| BamHI, G, Tango1X
 +
| >95% ligated and recut
 
|-
 
|-
 
| MabI
 
| MabI
Line 78: Line 89:
 
| Due to recognition sequence, two sites can be used to create a recognition sequence that will not reanneal
 
| Due to recognition sequence, two sites can be used to create a recognition sequence that will not reanneal
 
| Medium
 
| Medium
 +
| Yes, 65
 +
| >90% ligated and recut
 +
| W
 
|-
 
|-
 
| PacI
 
| PacI
Line 84: Line 98:
 
| Good to use in combination with low GC content parts
 
| Good to use in combination with low GC content parts
 
| Low
 
| Low
 +
| Yes, 65
 +
| 70% ligated, >95% recut
 +
| NEB 1 and 4
 
|-
 
|-
 
| PpiI
 
| PpiI
Line 90: Line 107:
 
| Good for making protein fusions
 
| Good for making protein fusions
 
| High for vectors and protein parts
 
| High for vectors and protein parts
 +
| Yes, 65
 +
| > 90% ligated and recut
 +
| R(100%) or Tango1X or 2X(50-100%)
 
|-
 
|-
 
| PsrI
 
| PsrI
Line 96: Line 116:
 
| Good for making protein fusions
 
| Good for making protein fusions
 
| High for vectors and protein parts
 
| High for vectors and protein parts
 +
| Yes, 65
 +
| 70% ligated, 80% recut (peg improves)
 +
| Y
 
|-
 
|-
 
| XmaI
 
| XmaI
Line 102: Line 125:
 
| Typically used with AarI parts for historical reasons
 
| Typically used with AarI parts for historical reasons
 
| Low  
 
| Low  
 +
| Yes, 65
 +
| >95% ligated, 90% recut
 +
| Y
 
|}
 
|}
  

Revision as of 07:58, 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

Enzyme Internal, External, BioBrick Enzyme Typical Use Special Property Priority for Removal from Vector or Part Heat killable (for automated assembly) Buffers Efficiency
AarI External Library Vector or Insert Creation, Rapid prototyping Good for cutting into BioBrick scars High Yes, 65 degrees AarI+oligo, Tango2X >95% ligated and recut
AscI Internal Cutting BioScaffold part into small pieces for removal with spin column Good to use in combination with low GC content parts Low Yes, 65 (SgsI) Tango1X(SgsI), FastDigest(SgsI), Y(PalA I) >95%(SgsI), >90%(PalA I) ligated and recut
BamHI Other See BBFRFC15 for use in protein fusion strategies DNA sequence translates into glycine-serine Low Yes, 80 BamHI, G, Tango1X >95% ligated and recut
MabI Internal Cutting BioScaffold part into small pieces for removal with spin column Due to recognition sequence, two sites can be used to create a recognition sequence that will not reanneal Medium Yes, 65 >90% ligated and recut W
PacI Internal Cutting BioScaffold part into small pieces for removal with spin column Good to use in combination with low GC content parts Low Yes, 65 70% ligated, >95% recut NEB 1 and 4
PpiI External Cutting outside BioBrick scars Good for making protein fusions High for vectors and protein parts Yes, 65 > 90% ligated and recut R(100%) or Tango1X or 2X(50-100%)
PsrI External Cutting outside BioBrick scars Good for making protein fusions High for vectors and protein parts Yes, 65 70% ligated, 80% recut (peg improves) Y
XmaI Internal Cutting BioScaffold part into small pieces for removal with spin column Typically used with AarI parts for historical reasons Low Yes, 65 >95% ligated, 90% recut Y


Plasmid Incompatible Enzymes (# of Sites-priority for removal where H=high, M=medium, L=low, V=very low) Compatible Enzymes Commonly Used Plasmid
pSB1A3, discontinued [1] PpiI(2, V) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI No
pSB1AC3, high copy [2] PpiI(2, H) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB1AK3, high copy [3] PpiI(2, H) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB1AT3, high copy [4] PpiI(2, H), BamHI(?,M) AarI, AscI, MabI, PacI, PsrI, XmaI Yes
pSB1A7, transcriptionally insulated high copy [5] PsrI(2, L) and PpiI(2, L) AarI, AscI, BamHI, MabI, PacI, XmaI Sometimes
pSB2K3, use pSB2K4 instead AscI(1, V) AarI, BamHI, MabI, PacI, PpiI, PsrI, XmaI No
pSB2K4, inducible copy [6] BamHI(?, L) AarI, AscI, MabI, PacI, PpiI, PsrI, XmaI Yes
pSB3C5, low to medium copy [7] PpiI(1, L) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB3K3, probably discontinued PpiI(1, V), XmaI(?, V) AarI, AscI, BamHI, MabI, PacI, PsrI No
pSB3T5, low to medium copy [8] PpiI(1, M) and PsrI(1, M) AarI, AscI, BamHI, MabI, PacI, XmaI Yes
pSB4A3, discontinued [9] PpiI(1, V) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI No
pSB3K5, low to medium copy standard vector [10] PpiI(1, M) 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 AarI, AscI, BamHI, MabI, PpiI, PsrI, XmaI Yes
pSB4A5, low copy standard vector [13] PpiI(1, H) AarI, AscI, BamHI, MabI, PacI, PsrI, XmaI Yes
pSB4T5, low copy standard vector [14] PsrI(1, H) AarI, AscI, BamHI, MabI, PacI, PpiI, XmaI Yes