Difference between revisions of "Help:Assembly Compatibility"

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==Assembly Compatibility==
 
==Assembly Compatibility==
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'''Choose your method, support the standard.'''
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===Choose your method, support the standard===
  
 
'''Choose your method''' and assemble your parts the way you want. You can use 3A Assembly, synthesis, Gibson, and more.  
 
'''Choose your method''' and assemble your parts the way you want. You can use 3A Assembly, synthesis, Gibson, and more.  

Revision as of 17:31, 19 June 2014

Add a Part to the Registry: Related Registry Help Pages
  • Add a Basic Part - A tutorial on how to add a basic part
  • Add a Composite Part - A tutorial on how to add a composite part
  • Scars - Information on assembly scars, and how to specify them for a composite part
  • Synthesis - Things to keep in mind if you're adding and documenting a part you've synthesized
  • Assembly Compatibility - Make sure your part is compatible with an assembly standard
  • Twins - Parts are twins if they have the same sequence
  • Document Parts - Recommendations on how to document your parts
  • Make a Contribution - Improve existing parts
Ready to add your part? Go to the Add a Part page.
Have questions on adding a part to the Registry? Send an email to hq (at) igem . org.

Assembly Compatibility

Choose your method, support the standard

Choose your method and assemble your parts the way you want. You can use 3A Assembly, synthesis, Gibson, and more.

Support the standard. BioBrick RFC[10] is the Registry's current standard; all part samples submitted to the Registry must be BioBrick compatible and in the shipping plasmid backbone, pSB1C3.

Standard parts ensure that the Registry can maintain and test all new parts in the same way. Registry members can easily and reliably use and assemble these parts in the future. Standard parts can be moved from one plasmid backbone to another for operation, assembly, measurement, and shipping.


How is a part compatible?

The part's sequence must not contain illegal restriction sites (or other specified sequences) as defined by the assembly standard.

BioBrick compatible parts must not have the following restriction sites:

Sequence Type Enzyme Note
gaattc Illegal EcoRI
tctaga Illegal XbaI
actagt Illegal SpeI
ctgcag Illegal PstI
gcggccgc Avoid NotI

All of these restriction sites belong to the prefix and suffix of the BioBrick assembly standard.


Supported Standards

By supporting an assembly standard, the Registry software can detect and understand the assembly process for parts. This includes:

  • Detection of illegal restriction sites in a part's sequence
  • Recognizing assembly scars in composite parts
  • Identification of a sample's assembly standard, through sequence verification of the sample's prefix and suffix
    • Remember, a part can have many samples in the Registry's Repository. Those samples can be in plasmid backbones of different assembly standards.


View the Assembly Systems Page to see exactly what the Registry software looks for in these supported assembly standards

Click below to view the supported assembly standards as specified by their original RFC

  • 10 - BioBrick - [http://dspace.mit.edu/handle/1721.1/45138 RFC Documentation]
  • 12 - BioBrick 2 - [http://dspace.mit.edu/handle/1721.1/45139 RFC Documentation]
  • 21 - Berkeley/BglBricks - [http://dspace.mit.edu/handle/1721.1/46747 RFC Documentation]
  • 23 - Silver Standard - [http://dspace.mit.edu/handle/1721.1/32535 RFC Documentation]
  • 25 - Freiburg Standard - [http://dspace.mit.edu/handle/1721.1/45140 RFC Documentation]
  • 1000 - MoClo


Help Pages: Assembly Standards || Assembly Compatibility || Supported Assembly Systems || Scars

Accepted Standards: BioBrick RFC[10] | iGEM Type IIS RFC[1000]

Depracated Standards: BioBrick BB-2 RFC[12] | Berkeley RFC[21] | Silver RFC[23] | Freiburg RFC[25]


FAQ

Why is compatibility important?

The iGEM Registry is built on Standard Biological Parts.

  • Assembly Standards are one of the facets of the standardization of biology
    • All users can easily and reliably assemble and use these parts. They are not conducting an experiment when putting them together.
  • BioBrick and Type IIS compatibility allows the Registry to test and maintain all received parts in the same way.


My part is not BioBrick or Type IIS compatible

Before working with your part in the lab (characterizing/measuring), make sure it is BioBrick compatible or Type IIS compatible. If not...

  • Synthesize your part to remove any illegal restriction sites, through synonymous substitutions (silent mutations).
  • Use site-specific mutagenesis to remove any illegal restriction sites, through synonymous substitutions (silent mutations).