Help:Plasmid backbones/Nomenclature

< Help:Plasmid backbones
Revision as of 20:25, 24 January 2008 by Rshetty (Talk | contribs) (→‎Selection marker)

Plasmids in the Registry of Standard Biological parts adhere to a particular naming convention. This page describes the details of this naming scheme.

If you are interested in designing and/or constructing a new BioBricks compatible plasmid and are submitting it to the Registry, please follow this naming convention. Questions or comments can be directed to Reshma Shetty.

pSBxyz-a

pSB = plasmid Synthetic Biology
x = origin of replication
y = selection marker
z = version number
-a = insert

Origin of replication

  • 1= pUC19-derived pMB1 (in pSB series)
  • 2 = pSCANS-derived
  • 3 = p15A pMR101-derived
  • 4 = rep101, repA pSC101-derived
  • 5 = F plasmid
  • 6 = pBR322

Selection marker

BioBrick vector names take the form pSB#X#. The letter X indicates the antibiotic to which the vector confers resistance. The letter code and corresponding antibiotic resistance marker are listed. The absence of a letter indicates that no antibiotic 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

(used to indicate miscellaneous interesting changes to backbone)

  • 0 = absent or incomplete BioBricks™ cloning site
  • 1 = complete BioBricks™ cloning site (BCS)
  • 2 = 5’ terminator and BCS
  • 3 = 5’ terminator and BCS and 3’ terminator
  • 4 = pSB2K3-derived plasmid free of many restriction site (designed for T7.1 project)
  • 5 = Second generation of cloning plasmid. See [http://openwetware.org/wiki/Synthetic_Biology:Vectors/pSB%2A%2A5_design] for details.
  • 6 = Held for some vector versions that the Berkeley iGEM team has made. (Chris Anderson).
  • 7 = Held for some vector versions that the Davidson iGEM team has made.
  • 10 = Screening plasmid 1.0 by Josh Michener and Jason Kelly. See [http://openwetware.org/wiki/Endy:Screening_plasmid] for details.
  • 11 = Held for a version of Jason's measurement plasmid
  • 12 = Held for a version of Jason's measurement plasmid
  • 13 = Held for a measurement plasmid by Reshma Shetty.
  • 20-29 = Held for Berkeley iGEM plasmids

Insert

  • generally a BioBricks part number where multiple parts are separated by periods
  • no dash = no insert
  • -P1010 = ccd operon insert
    • -1 = ccdB <-- this has now become legacy nomenclature.

Contact

Questions or comments can be directed to Reshma Shetty.