Difference between revisions of "Help:Plasmid backbones/Nomenclature"

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[[Help:Plasmids|Plasmids]] in the Registry of Standard Biological parts adhere to a particular naming convention.  This page describes the details of this naming scheme.   
 
[[Help:Plasmids|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 [[Help:Plasmids|Plasmids]] and are submitting it to the Registry, please follow this naming convention.  Questions or comments can be directed to [[User:Rshetty|Reshma Shetty]].
+
If you are interested in designing and/or constructing a new BioBricks compatible [[Help:Plasmids|plasmid]] and are submitting it to the Registry, please follow this naming convention.  Questions or comments can be directed to [[User:Rshetty|Reshma Shetty]].
  
 
==pSBxyz-a==
 
==pSBxyz-a==

Revision as of 03:08, 23 June 2006

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 = nothing
  • 1 = complete Biobricks insertion site
  • 2 = 5’ terminator and complete Biobricks insertion site
  • 3 = 5’ terminator and complete Biobricks insertion site and 3’ terminator
  • 4 = misc restriction sites removed for the T7 project
  • 5 = Held for next generation of cloning plasmid. See [http://openwetware.org/wiki/Synthetic_Biology:Vectors/Parts].
  • 10 = Held for a version of Jason's measurement plasmid
  • 11 = Held for a version of Jason's measurement plasmid
  • 12 = Held for a version of Jason's measurement plasmid

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.