Help:Plasmid backbones/Nomenclature
Contents
Overview
BioBrick plasmid backbone names take the form pSB#X#. The letters pSB are an acronym for plasmid Synthetic Biology.
- The first number denotes the origin of replication.
- The letter X identifies the antibiotic resistance marker(s) present in the vector. Plasmid backbones with multiple resistance markers have multiple, successive letters.
- The last number in the plasmid backbone name is a version number to differentiate between the various implementations of the pSB series of plasmid backbones.
When referring to both a BioBrick standard biological part and the plasmid backbone in which it is cloned, the convention is to use the form [plasmid backbone name]-[part number] like pSB4K5-T9003. To refer to BioBrick standard plasmid backbones to be used for construction of BioBrick parts, use the full plasmid backbone name and default cloned part. For example, pSB4A3-P1010, pSB1A10-P1010, pSB4K5-I52002 and pSB3T5-I52001 are all available construction plasmids from the Registry of Standard Biological Parts. However, for convenience, these construction plasmid names are often abbreviated to pSB4A3, pSB1A10, pSB4K5 and pSB3T5, respectively.
New plasmid-based vectors constructed from BBa_I51020 should be named pSB#X5-I52002 where the # is determined by the identity of the replication origin and the letter X is determined by the antibiotic resistance marker(s) present. To expand the BioBrick vector nomenclature, submit new vectors or vector parts to the Registry of Standard Biological Parts and then document any new annotation needed here. [http://biobricks.org The BioBricks Foundation] will lead the standards setting process should any revisions to the BioBrick plasmid backbone nomenclature beyond addition of new replication origins, antibiotic resistance markers and version numbers be needed.
Origin of replication
BioBrick plasmid backbone names take the form pSB#X#. The first number indicates the identity of the origin of replication. The number, corresponding replication origin, expected plasmid copy number and typical purpose of that origin are listed. To expand this list to include additional replication origins, obtain an account with the Registry of Standard Biological Parts and edit this page.
| Number | Replication origin | [http://openwetware.org/wiki/Molecular_Cloning Copy number] | Purpose |
|---|---|---|---|
| 1 | modified pMB1 derived from pUC19 | 500-700 | Easy plasmid DNA purification |
| 2 | F and P1 lytic derived from [http://www.genome.bnl.gov/Vectors/pscans.php pSCANS-1-BNL] | 1-2 inducible to high copy | Inducible copy number |
| 3 | p15A derived from pMR101 | 10-12 | Multi-plasmid engineered systems |
| 4 | rep101, repA derived from pSC101 | ~5 | Small cell to cell copy number variation |
| 5 | derived from F plasmid | 1-2 | Improved plasmid stability |
| 6 | pMB1 derived from pBR322 | 15-20 | Multi-plasmid engineered systems |
| 7 | broad host range origin | by Ichiro et al. | |
| 8 | pSC101TS | temperature sensitive origin, only propagates at 30C | |
| 9 |
Selection marker
BioBrick plasmid backbone names take the form pSB#X#. The letter X indicates the antibiotic to which the plasmid backbone confers resistance. The letter code and corresponding antibiotic resistance marker are listed. The absence of a letter indicates that no antibiotic resistance marker is present. Multiple resistance markers in a vector are indicated by successive codes in alphabetical order e.g., AK, StT, AC and AKT. To expand this list to include additional antibiotic resistance markers, obtain an account with the Registry of Standard Biological Parts and edit this page.
| Code | Antibiotic |
|---|---|
| A | ampicillin |
| C | chloramphenicol |
| E | erythromycin |
| G | gentamycin |
| K | kanamycin |
| N | neomycin |
| Na | nalidixic acid |
| R | rifampicin |
| S | spectinomycin |
| St | streptomycin |
| T | tetracycline |
| Tm | trimethoprim |
| Z | zeocin |
Version number
BioBrick vector names take the form pSB#X#. The second number indicates the BioBrick plasmid backbone version number. The version number, key features, purpose for which that version was designed, example vector and vector designer(s) are listed. To expand this list to assign new vector version numbers, obtain an account with the Registry of Standard Biological Parts and edit this page.
| Number | Key features | Purpose | Example | Designer |
|---|---|---|---|---|
| 0 | absent or incomplete BioBrick cloning site | pSB2K0 | Brookhaven National Lab | |
| 1 | complete BioBrick cloning site (BCS) | assembly of BioBrick parts | pSB4A1 | Reshma Shetty |
| 2 | 5' terminator and BCS | transcriptional insulation of plasmid backbone upstream of cloned BioBrick part | pSB1A2 | Tom Knight |
| 3 | 5' terminator and BCS and 3' terminator | transcriptional insulation of plasmid backbone downstream of cloned BioBrick part | pSB1AC3 | Reshma Shetty & Tom Knight |
| 4 | pSB2K3-derived plasmid backbone free of many restriction sites | Genome refactoringChan-Mol-Syst-Biol-2005 | pSB2K4 | Leon Chan |
| 5 | constructed from BioBrick base vector | standardized BioBrick vector design | pSB4K5 | Reshma Shetty |
| 6 | Reserved for some plasmid backbone versions that the Berkeley iGEM team has made | |||
| 7 | BCS flanked by terminator BBa_B0015 | transcriptional insulation of cloned BioBrick part | pSB1A7 | Karmella Haynes |
| 8 | BCS followed by eukaryotic terminator | for cloning of eukaryotic composite parts | pSB1AK8 | Monika Ciglic and the 2007 Slovenian iGEM team |
| 9 | ||||
| 10 | [http://openwetware.org/index.php?title=Endy:Screening_plasmid/v1.0 Screening plasmid v1.0] | characterization of single input, single output transcriptional devices | pSB1A10 | Josh Michener & Jason Kelly |
| 11 | Reserved for a version of Jason's measurement plasmid | |||
| 12 | Reserved for a version of Jason's measurement plasmid | |||
| 13 | Reserved for a version of Reshma's measurement plasmid | |||
| 15-19 | Reserved for new lambda red compatible BioBrick backbones. | For chromosomal integration of single gene and operon of BioBricks. | Erik Lundin | |
| 20-29 | Reserved for a version of Berkeley iGEM team's plasmids | |||
| 30 | Expression Plasmid Backbone harbouring a LacI repressible T7 Promotor right in front of the BB prefix based on pSBXX3 backbones. | pSB1A30 | iGEM team Heidelberg 2014 | |
| 50 | Expression Plasmid Backbone harbouring a LacI repressible T7 Promotor right in front of the BB prefix based on pSBXX5 backbones. | pSB1A50 | iGEM team Heidelberg 2014 | |
| 51 | pBAD plasmid vector with an AraC operon with D family cameleon (D4) inserted in | pBAD was used as vector backbone for construct for the TPHS_San_Diego 2018 iGEM team | pSB4K5 | Allison Bien |
Contact
Questions or comments can be directed to Reshma Shetty.
References
<biblio>
- Chan-Mol-Syst-Biol-2005 pmid=16729053
</biblio>
Engineering BioBrick vectors from BioBrick parts
Journal of Biological Engineering, 2008 Apr 14;2:5
Reshma Shetty, Drew Endy, Tom Knight
[http://www.jbioleng.org/content/2/1/5 URL]