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.
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BioBrick vector names take the form pSB#X#.  The letters pSB are an acronym for '''p'''lasmid '''S'''ynthetic '''B'''iology. 
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*The first number denotes the origin of replication. 
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*The letter X identifies the antibiotic resistance marker(s) present in the vector.  Vectors with multiple resistance markers have multiple, successive letters. 
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*The last number in the vector name is a version number to differentiate between the various implementations of the pSB series of vectors. 
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When referring to both a BioBrick standard biological part and the vector in which it is cloned, the convention is to use the form [vector name]-[part number] like pSB4K5-T9003.  To refer to BioBrick standard vectors to be used for construction of BioBrick parts, use the full vector name and default cloned part.  For example, pSB4A3-P1010, pSB1A10-P1010, pSB4K5-I52002 and pSB3T5-I52001 are all available vectors from the Registry of Standard Biological Parts.  However, for convenience, these vector names are often abbreviated to pSB4A3, pSB1A10, pSB4K5 and pSB3T5, respectively. 
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New plasmid-based vectors constructed from [[Part:BBa_I51020|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 vector nomenclature beyond addition of new replication origins, antibiotic resistance markers and version numbers be needed.
  
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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 20:28, 24 January 2008

BioBrick vector 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. Vectors with multiple resistance markers have multiple, successive letters.
  • The last number in the vector name is a version number to differentiate between the various implementations of the pSB series of vectors.

When referring to both a BioBrick standard biological part and the vector in which it is cloned, the convention is to use the form [vector name]-[part number] like pSB4K5-T9003. To refer to BioBrick standard vectors to be used for construction of BioBrick parts, use the full vector name and default cloned part. For example, pSB4A3-P1010, pSB1A10-P1010, pSB4K5-I52002 and pSB3T5-I52001 are all available vectors from the Registry of Standard Biological Parts. However, for convenience, these vector 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 vector nomenclature beyond addition of new replication origins, antibiotic resistance markers and version numbers be needed.


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.