BioScaffold Parts
Revision as of 08:43, 28 December 2008 by Norville (Talk | contribs) (→Plasmid Compatibility with BioScaffold Part Internal and External Enzymes)
| BioScaffold parts are BioBrick parts that contain restriction enzyme recognition sites that enable their full or partial removal from a BioBrick assembly. |
| 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) |
| 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 |
| -?- | 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 | Digestion temperature | Heat killable (for automated assembly) | Buffers | Efficiency |
|---|---|---|---|---|---|---|---|---|
| AarI | External | Library Vector or Insert Creation, Rapid prototyping | Good for cutting into BioBrick scars | High | 37 | 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 | 37 | 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 | 37 | Yes, 80 | BamHI, G, Tango1X | >95% ligated and recut |
| EcoRI | BioBrick | BioBrick | BioBrick | High | 37 | Yes, 65 | > 90% ligated and recut | G, O, W, Y(75%); EcoRI, O, R*, Tango2X |
| 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 | 37 | Yes, 65 | >90% ligated and recut | B(50%), G(75%), O, W, Y(75%) |
| PacI | Internal | Cutting BioScaffold part into small pieces for removal with spin column | Good to use in combination with low GC content parts | Low | 37 | 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 | 30 | Yes, 65 | > 90% ligated and recut | R(100%) or Tango1X,2X(50-100%) |
| PsrI | External | Cutting outside BioBrick scars | Good for making protein fusions | High for vectors and protein parts | 30 | Yes, 65 | 70% ligated, 80% recut (peg improves) | Y |
| PstI | BioBrick | BioBrick | BioBrick | High | 37 | Yes, 80 | >90% ligated and recut | O, Y(50%); B,G,O,T, Tango1X,2X (50-100% |
| SpeI | BioBrick | BioBrick | BioBrick | High | 37 | No (AhlI), No (BcuI) | >90% ligated and recut (AhlI); >80% ligated, 90% recut (BcuI) | B, G, Y for AhlI; B, G, Tango1X for BcuI |
| XbaI | BioBrick | BioBrick | BioBrick | High | 37 | 65 | >90% ligated and recut; >95% | B,G,O,Y; (B,G,Tango2X all 50-100%), Tango2X |
| XmaI | Internal | Cutting BioScaffold part into small pieces for removal with spin column | Typically used with AarI parts for historical reasons | Low | 30 | 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 |