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

Revision as of 07:39, 31 May 2012

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Overview

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

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

Origin of replication

BioBrick plasmid backbone 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.

Selection marker

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

Version number

BioBrick vector names take the form pSB#X#. The second number indicates the BioBrick plasmid backbone 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.

Contact

Questions or comments can be directed to Reshma Shetty.

References

<biblio>

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

</biblio>

Engineering BioBrick vectors from BioBrick parts
Journal of Biological Engineering, 2008 Apr 14;2:5
Reshma Shetty, Drew Endy, Tom Knight
[http://www.jbioleng.org/content/2/1/5 URL]