Difference between revisions of "Help:Plasmid backbones/Nomenclature"
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===Version number===
 
===Version number===
−
(used to indicate miscellaneous interesting changes to backbone)
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BioBrick vector names take the form pSB#X#. The second number indicates the BioBrick vector 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.
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*0 = absent or incomplete BioBricks™ cloning site
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*1 = complete BioBricks™ cloning site (BCS)
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−
*2 = 5’ terminator and BCS
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*3 = 5’ terminator and BCS and 3’ terminator
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−
*4 = pSB2K3-derived plasmid free of many restriction site (designed for T7.1 project)
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−
*5 = Second generation of cloning plasmid.  See [http://openwetware.org/wiki/Synthetic_Biology:Vectors/pSB%2A%2A5_design] for details.
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*6 = Held for some vector versions that the Berkeley iGEM team has made.  (Chris Anderson).
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*7 = Held for some vector versions that the Davidson iGEM team has made.
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*10 = Screening plasmid 1.0 by Josh Michener and Jason Kelly. See [http://openwetware.org/wiki/Endy:Screening_plasmid] for details.
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*11 = Held for a version of Jason's measurement plasmid
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*12 = Held for a version of Jason's measurement plasmid
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*13 = Held for a measurement plasmid by Reshma Shetty.
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*20-29 = Held for Berkeley iGEM plasmids
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===Insert===
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{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" <!-- This line here formats your table for you.  Change the code to change the formatting of your table.-->
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*generally a BioBricks part number where multiple parts are separated by periods
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! align="left" style="background:#f0f0f0;"| Number
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*no dash = no insert
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! align="left" style="background:#f0f0f0;"| Key features
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*-P1010 = ccd operon insert
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! align="left" style="background:#f0f0f0;"| Purpose
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**-1 = ccdB  <-- this has now become legacy nomenclature.
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! align="left" style="background:#f0f0f0;"| Example
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! align="left" style="background:#f0f0f0;"| Designer
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|-
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| 0
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| absent or incomplete BioBrick cloning site
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|                         
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| [[Part:pSB2K0|pSB2K0]]
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| Brookhaven National Lab
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|-
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| 1
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| complete BioBrick cloning site (BCS) 
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| assembly of BioBrick parts
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| [[Part:pSB4A1|pSB4A1]]
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| Reshma Shetty
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|-
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| 2
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| 5' terminator and BCS
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| transcriptional insulation of vector upstream of cloned BioBrick part
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| [[Part:pSB1A2|pSB1A2]]
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| Tom Knight
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|-
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| 3
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| 5' terminator and BCS and 3' terminator
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| transcriptional insulation of vector downstream of cloned BioBrick part
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| [[Part:pSB1AC3|pSB1AC3]]
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| Reshma Shetty & Tom Knight
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|-
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| 4
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| pSB2K3-derived vector free of many restriction sites
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| Genome refactoring<cite>Chan-Mol-Syst-Biol-2005</cite>
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| [[Part:pSB2K4|pSB2K4]]
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| Leon Chan
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|-
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| 5
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| constructed from BioBrick base vector
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|  standardized BioBrick vector design
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| [[Part:pSB4K5|pSB4K5]]
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| Reshma Shetty
 +
|-
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| 6
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| Reserved for some vector versions that the Berkeley iGEM team has made
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|
 +
|
 +
|
 +
|-
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| 7
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| BCS flanked by terminator [[Part:BBa_B0015|BBa_B0015]]         
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| transcriptional insulation of cloned BioBrick part
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| [[Part:pSB1A7|pSB1A7]]
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| Karmella Haynes
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|-
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| 8
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| Unassigned
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|
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|
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|
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|-
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| 9
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| Unassigned
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|
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|
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| 
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|-
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| 10
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| [http://openwetware.org/index.php?title=Endy:Screening_plasmid/v1.0 Screening plasmid v1.0]
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| characterization of single input, single output transcriptional devices
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| [[Part:pSB1A10|pSB1A10]]
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| Josh Michener  & Jason Kelly
 +
|-
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| 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
 +
|
 +
|
 +
|
 +
|-
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| 20-29
 +
| Reserved for a version of Berkeley iGEM team's plasmids
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|
 +
|
 +
|
 +
|}
  
 
==Contact==
 
==Contact==
  
 
Questions or comments can be directed to [[User:Rshetty|Reshma Shetty]].
 
Questions or comments can be directed to [[User:Rshetty|Reshma Shetty]].
 +
 +
==References==
 +
<biblio>
 +
#Chan-Mol-Syst-Biol-2005 pmid=16729053
 +
</biblio>

Revision as of 20:52, 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.

Origin of replication

BioBrick vector 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

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

BioBrick vector names take the form pSB#X#. The second number indicates the BioBrick vector 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 vector upstream of cloned BioBrick part pSB1A2 Tom Knight
3 5' terminator and BCS and 3' terminator transcriptional insulation of vector downstream of cloned BioBrick part pSB1AC3 Reshma Shetty & Tom Knight
4 pSB2K3-derived vector 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 vector 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 Unassigned
9 Unassigned
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
20-29 Reserved for a version of Berkeley iGEM team's plasmids

Contact

Questions or comments can be directed to Reshma Shetty.

References

<biblio>

  1. Chan-Mol-Syst-Biol-2005 pmid=16729053

</biblio>