Difference between revisions of "Help:Assembly Compatibility"

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[[Category:BioBrick RFC 10]][[Category:Adding Parts]][[Category:Synthesis]]
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{{HelpPage/MainLinks}}
 
{{HelpPage/AddingParts}}
 
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{{HelpPage/AssemblyStandards}}
 
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==Assembly Compatibility==
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{{HelpPage/AssemblyPhilosophy}}
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==How to view compatiblity==
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{{HelpPage/ViewCompatibility}}
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===How is a part compatible?===
 
===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.
 
The part's sequence must not contain illegal restriction sites (or other specified sequences) as defined by the assembly standard.
  
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'''BioBrick compatible parts must not have the following restriction sites:'''  
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For example, to be RFC 10 compatible, '''compatible parts must not have the following restriction sites:'''  
 
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All of these restriction sites belong to the prefix and suffix of the BioBrick assembly standard.
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All of these restriction sites belong to the '''[https://parts.igem.org/Help:Prefix-Suffix prefix and suffix]''' of the BioBrick assembly standard.
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{{HelpPage/SupportedStandards}}
 
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===Why is compatibility important?===
 
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iGEM and the Registry is built on Standard Biological Parts.
 
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*Compatibility ensures that a user can use the part with said assembly standard.
 
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*BioBrick compatible parts ensure that all teams can assemble parts with 3A Assembly, in addition to other assembly techniques
 
  
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===My part is not BioBrick compatible===
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Before working with your part in the lab (characterizing/measuring), make sure it is BioBrick compatible. If not...
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*'''[https://parts.igem.org/DNA_Synthesis Synthesize your part]''' to remove any illegal restriction sites, through synonymous substitutions (silent mutations).
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**Synthesis is also useful, since you can synthesize your part with the [https://parts.igem.org/Help:Prefix-Suffix BioBrick prefix and suffix], so it is ready for shipping to the Registry. [https://parts.igem.org/DNA_Synthesis See our synthesis offer with IDT]
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===FAQ===
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*Use site-specific mutagenesis to remove any illegal restriction sites, through synonymous substitutions (silent mutations).
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{{HelpPage/FAQ/Compatibility}}

Latest revision as of 09:49, 25 September 2024

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.

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]

Assembly Compatibility

Choose your assembly method, support the standard

Choose your assembly method and assemble your parts with a variety of assembly techniques. You can use 3A Assembly, Type IIS, synthesis, Gibson, and more.


Support the standard. Although users can add parts to the Registry that adhere to other assembly standards, BioBrick RFC[10] and Type IIS are the Registry's current de facto standards; all parts on the Registry that will be considered for the iGEM competition (medals, awards, etc.) must be assembly compatible for BioBrick or Type IIS.


In 2019, sample submission is no longer required. However, ensuring your parts are assembly compatible allows the Registry to synthesize your parts in BioBrick and/or Type IIS format. Registry members can easily and reliably use and assemble these parts in the future.


How to view compatiblity

The Sequence & Features box will show you assembly compatibility.

The Assembly Compatibility checks that a part will meet the requirements for the Registry's supported assembly standards. It will show if there are any illegal restriction sites for a part. The above image shows a basic part the is compatible with RFC 10 and 1000, amongst others.


Note: All parts submitted to the Registry for competition evaluation (medal criteria, awards) must be BioBrick (RFC[10] compatible or Type IIS RFC[1000], unless an exemption has been given.

See the competition delivearbles page for part requirements

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.

For example, to be RFC 10 compatible, 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



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).