Help:Plasmid backbones/Nomenclature

< Help:Plasmid backbones
Revision as of 16:38, 23 July 2007 by Rshetty (Talk | contribs) (→‎Version number)

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

  • X = none
  • 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
  • AK = kanamycin and ampicillin
  • KT = kanamycin and tetracycline
  • AKT = ampicillin and kanamycin and tetracycline
  • AC = ampicillin and chloramphenicol

… etc

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.