Difference between revisions of "Help:Plasmid backbones/Glossary"
 
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[[Help:Plasmid backbones|< Back to Plasmid backbone Help]]
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Here at the Registry, we use the term "plasmid" in three different ways:
 
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*"<b>[[Help:Plasmids/Construction Plasmids#Plasmid (backbone)|Plasmid (backbone)]]</b>" - the vector alone, WITHOUT BioBrick(s)
 
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*"<b>[[Help:Plasmids/Construction Plasmids#Construction Plasmid|Construction Plasmid]]</b>" - Plasmid backbones WITH specialized BioBricks to help you with [[Help:BioBrick Assembly| assembly]]
 
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*"<b>[[Help:Plasmids/Construction Plasmids#Plasmid (with any BioBrick)|Plasmid (with any BioBrick)]]</b>" - Plasmid backbone WITH some BioBrick(s). 
 
  
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Plasmids are circular, double-stranded DNA molecules typically containing a few thousand base pairs that replicate within the cell independently of the chromosomal DNA.  Plasmids are a convenient way to propagate pieces of DNA, such as BioBrick standard biological parts.
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The term "plasmid" can be a bit ambiguous.  Here at the Registry, we use the term "plasmid" in three different ways:
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*"'''[[Help:Plasmid backbones/Glossary#Plasmid with any BioBrick part(s)|Plasmid with some BioBrick part(s)]]'''" - the vector WITH some BioBrick part(s).
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*"'''[[Help:Plasmid backbones/Glossary#Construction plasmid|Construction plasmid]]'''" - the vector WITH a default BioBrick part(s) or insert
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*"'''[[Help:Plasmid backbones/Glossary#Plasmid backbone|Plasmid backbone]]'''" - the vector alone, WITHOUT any BioBrick part
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For more detailed descriptions of each term, read on...
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==Plasmid (backbone)==
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==Plasmid with some BioBrick part(s)==
 
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| [[Image:BioBrickvectorwithpart.png]]
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https://static.igem.org/mediawiki/parts/3/3d/Plasmid_nobb.png
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| Every BioBrick&reg; part available via the Registry is maintained on at least one BioBrick plasmid.  Sometimes, a part is maintained on multiple BioBrick plasmid backbones, which vary in antibiotic resistance and replication origin (the replication origin controls the plasmid copy number).  Thus, BioBrick parts are available from the Registry as plasmids.  The BioBrick part is usually cloned between the BioBrick prefix (denoted by E and X, for EcoRI and XbaI) and the BioBrick suffix (denoted by S and P, for SpeI and PstI). 
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BioBrick plasmids form the "backbone" of all BioBrick parts.  Every BioBrick part is maintained on at least one BioBrick plasmid.  Sometimes, a part is maintained on multiple BioBrick plasmid backbones, which vary in antibiotic resistance and copy number.
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To refer to both a BioBrick part and the plasmid backbone that contains the part, the Registry uses the terminology '''pSB1A2-R0040'''.  '''pSB1A2''' is the part number of the [[Help:Plasmids/Construction Plasmids#Plasmid backbone|plasmid backbone]] (see below) and '''R0040''' is the part number of BioBrick standard biological part [[Part:BBa_R0040|BBa_R0040]].
 
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*An example of a BioBrick plasmid without a part insert is '''[[Part:pSB1A3|pSB1A3]]'''.  You can find more on plasmid naming [[Help:Plasmids/Nomenclature|here]]
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==Construction plasmid==
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*To find a plasmid part using the "jump to part" sidebar function, erase the default "BBa_" prefix, and enter only the [[Help:Plasmids/Nomenclature|plasmid part name]] (''e.g.,'' pSBxyz).
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|[[Image:BioBrickconstructionplasmid.png]]
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| Plasmids are used not only to maintain existing BioBrick standard biological parts but also as tools to make and propagate new BioBrick&reg; standard biological parts as well as to assembly BioBrick parts together.  Thus, you'll often want to obtain available BioBrick plasmid backbones from the Registry for use when building new BioBrick parts, devices and systems.  For convenience, the Registry makes all BioBrick plasmid backbones available with one of a set of default parts.  The default parts each have a regular BioBrick part number and Registry entry documenting their sequence and function.  Plasmids that consist of a plasmid backbone and default part between the BioBrick&reg; prefix and suffix are called '''"construction plasmids"'''. 
  
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==Construction Plasmid==
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For an overview of construction plasmids and the default parts contained in construction plasmids, see [[Help:Plasmids/Construction plasmids]].
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[https://parts.igem.org/wiki/index.php/Part:BBa_P1010 https://static.igem.org/mediawiki/parts/8/8f/Plasmid_const.png]
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If you just want one of the BioBrick plasmids, it is probably available in the iGEM DNA distribution with the part
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[[Part:BBa_P1010| BBa_P1010]], [[Part:BBa_I52001| BBa_I52001]] or [[Part:BBa_I52002| BBa_I52002]] in the cloning site. You will need the cell strain [[Part:BBa_V1005|DB3.1]] since each of these three parts constitutively expresses the protein CcdB which is toxic to most strains.
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When making a brand new BioBrick part, you will need to choose an appropriate BioBrick plasmid (with the right antibiotic resistance marker, copy number etc.) for your construction purposes.  To make construction and assembly of BioBrick parts easier, most BioBrick plasmids include the ''ccdB'' positive selection marker (encoded in BioBrick parts [[Part:BBa_P1010| BBa_P1010]], [[Part:BBa_I52001| BBa_I52001]] and [[Part:BBa_I52002| BBa_I52002]]) by default.  The ''ccdB'' positive selection marker produces a toxic protein which kills most ''E. coli'' strains.  Successful insertion of a BioBrick part into a BioBrick vector replaces the ''ccdB'' gene and enables cells to grow and divide to form colonies.  A common problem during BioBrick part construction and assembly is that BioBrick vectors are not 100% digested when cut with restriction enzymes.  The ''ccdB'' toxic gene ensures that cells transformed with uncut or religated plasmids do not grow.  Thus, any colonies you obtain after a BioBrick part construction or assembly are more likely to be correct.
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==Plasmid backbone==
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*For a more in-depth walkthrough of how to use construction plasmids, check the [[Registry FAQ|FAQs]] or [[Featured Parts:Cell Death|"Cell Death" Featured Parts]] section
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|[[Image:BioBrickvectorbackbone.png]]
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|   Plasmids essentially serve as containers for BioBrick parts.  Thus, it is helpful to distinguish between the part itself and container of the part.  The term '''"plasmid backbone"''' refers to only the vector or "backbone" of the BioBrick part that it propagates.  The plasmid backbone includes the BioBrick prefix and suffix, but not any of the part sequence. 
  
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==Plasmid (with any BioBrick)==
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[[Part:pSB1A3|pSB1A3]], [[Part:pSB3K3|pSB3K3]], and [[Part:BBa_J52017|BBa_J52017]] are all examples of plasmid backbones.  These plasmid backbones each have an entry in the Registry, just as a normal BioBrick part does.  To find the Registry page of a particular plasmid backbone, enter the [[Help:Plasmids/Nomenclature|plasmid part name]] (e.g., pSB4K5 or pSB3K3 or pSB1AC3) in the text box at the top right corner of the page and click "Go".
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https://static.igem.org/mediawiki/parts/2/22/MultiPartsinplasmid.png
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This term refers to a plasmid backbone with singular or multiple BioBricks inserted.  An example of this can be seen to the left, where BioBrick parts [[Part:BBa_B0034|BBa_B0034]], [[Part:BBa_C0010|BBa_C0010]] & [[Part:BBa_B0015|BBa_B0015]] have been inserted into an ampicillin resistant plasmid.
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[[Help:Plasmids|'''Back to 'Plasmids' Overview''']] |[https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Plasmid '''Browse plasmid parts'''][[Image:Part icon plasmid.png]]
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Latest revision as of 18:48, 10 December 2008

< Back to Plasmid backbone Help


Plasmids are circular, double-stranded DNA molecules typically containing a few thousand base pairs that replicate within the cell independently of the chromosomal DNA. Plasmids are a convenient way to propagate pieces of DNA, such as BioBrick standard biological parts.

The term "plasmid" can be a bit ambiguous. Here at the Registry, we use the term "plasmid" in three different ways:

For more detailed descriptions of each term, read on...

Plasmid with some BioBrick part(s)

BioBrickvectorwithpart.png Every BioBrick® part available via the Registry is maintained on at least one BioBrick plasmid. Sometimes, a part is maintained on multiple BioBrick plasmid backbones, which vary in antibiotic resistance and replication origin (the replication origin controls the plasmid copy number). Thus, BioBrick parts are available from the Registry as plasmids. The BioBrick part is usually cloned between the BioBrick prefix (denoted by E and X, for EcoRI and XbaI) and the BioBrick suffix (denoted by S and P, for SpeI and PstI).

To refer to both a BioBrick part and the plasmid backbone that contains the part, the Registry uses the terminology pSB1A2-R0040. pSB1A2 is the part number of the plasmid backbone (see below) and R0040 is the part number of BioBrick standard biological part BBa_R0040.

Construction plasmid

BioBrickconstructionplasmid.png Plasmids are used not only to maintain existing BioBrick standard biological parts but also as tools to make and propagate new BioBrick® standard biological parts as well as to assembly BioBrick parts together. Thus, you'll often want to obtain available BioBrick plasmid backbones from the Registry for use when building new BioBrick parts, devices and systems. For convenience, the Registry makes all BioBrick plasmid backbones available with one of a set of default parts. The default parts each have a regular BioBrick part number and Registry entry documenting their sequence and function. Plasmids that consist of a plasmid backbone and default part between the BioBrick® prefix and suffix are called "construction plasmids".

For an overview of construction plasmids and the default parts contained in construction plasmids, see Help:Plasmids/Construction plasmids.

Plasmid backbone

BioBrickvectorbackbone.png Plasmids essentially serve as containers for BioBrick parts. Thus, it is helpful to distinguish between the part itself and container of the part. The term "plasmid backbone" refers to only the vector or "backbone" of the BioBrick part that it propagates. The plasmid backbone includes the BioBrick prefix and suffix, but not any of the part sequence.

pSB1A3, pSB3K3, and BBa_J52017 are all examples of plasmid backbones. These plasmid backbones each have an entry in the Registry, just as a normal BioBrick part does. To find the Registry page of a particular plasmid backbone, enter the plasmid part name (e.g., pSB4K5 or pSB3K3 or pSB1AC3) in the text box at the top right corner of the page and click "Go".