Help:Standards

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Parts | Plasmid Backbones | BioBrick Prefix and Suffix | Standards | Assembly Standards | Assembly Methods | Shipping

Why are standards important?

When we talk about standards, we are not just referring to assembly standards (RFCs): the Registry supports and requires a variety of standards to allow for better organization, documentation and efficiency of all material and resources.

  • The shipping standard ensures that the Registry is able to properly maintain and test user submitted samples.
  • Measurement standards, like PoPS, can be used to easily evaluate and compare part function and characterization.
  • The assembly standards (RFCs) set requirements so parts can be compatible, and assembled together without issue.

The goal of most engineers is to create; standardizing elements simplifies the process allowing the engineer to focus on building a system, without spending time on researching each individual component or worrying about how to assemble them.


Assembly Standards (RFCs)

What are assembly standards

An assembly standard defines how part samples will be assembled together by the engineer. An assembly standard, like the BioBrick RFC[10], ensures compatibility between parts, allowing part samples to be assembled together creating new longer and more complex parts, while still maintaining the structural elements of the assembly standard. This idempotent assembly means that any newly composed part will adhere to its assembly standard without need for manipulation, and can be used in future assemblies without issue.

How does an assembly standard work

An assembly standard defines assembly through the use of a prefix and suffix (found on plasmid backbones), which flank the beginning and end of a part sample, respectively. The prefix and suffix contain restriction sites, which when used with specific restriction enzymes (cutting) and DNA ligase (connecting), allow part samples to be assembled together forming a new part. This new part sample will maintain the same prefix and suffix as its "parents" and contain a scar, where the cut and re-ligated restriction sites were stitched together. Note: There are also scarless assembly methods, which allow for the assembly of parts without the traditional use of the prefix and suffix restriction sites.

A part is compatible with an assembly standard as long as it meets the requirements defined by said standard. This means that the part will not have any restriction sites that also appear in the prefix and suffix. If there are "illegal" restriction sites in a part this would interfere in its assembly.

Assembly standards in relation too...

  • Part - A part is compatible with an assembly standard, as long as its sequence meets the requirements of said standard; this means that the part does not have any restriction sites that would interfere with the assembly. It is important to remember that a part does not include the prefix and suffix as defined by the assembly standard.
  • Assembly Method is combining two part samples together in series to form a new composite part. Traditional assembly is done through the use of restriction sites (cutting and ligating) as defined by the assembly standard. Assembly methods are facilitated through assembly standards.
  • Plasmid Backbones - A plasmid backbone propagates a sample of a part, located inbetween the prefix and suffix of the plasmid backbone. Therefore the plasmid backbone will define the assembly standard for the part it maintains.

Example

  • You'll notice that many parts on the Registry are BioBrick RFC[10] compatible: BBa_R0051 is a part that is compatible with all five Registry supported assembly standards.
  • If you were to find a physical location for this part (using the Get This Part page) you'll see that all available samples are in the pSB1A2 plasmid backbone.
  • The pSB1A2 plasmid backbone has a prefix and suffix as defined by the BioBrick RFC[10] assembly standard. The available samples of BBa_R0051 are flanked by this prefix and suffix.
  • In order to assemble an available sample of BBa_R0051 to a different part you will need to make sure that a sample of that additional part is on a plasmid backbone that also belongs to the BioBrick RFC[10] assembly standard.

See the Registry Supported Assembly Standards (RFCs)

The Shipping Standard

The Registry uses pSB1C3 as its shipping standard. When submitting parts to the Registry, part samples must be packaged in pSB1C3.

At the Registry, submission in pSB1C3 allows us to analyze and maintain part samples properly and efficiently:

  • pSB1C3 has VF2 and VR primer sites, which means all samples can be sequenced using the VF2 and VR primers
  • For restriction digests, plasmid backbone length remains the same, allowing for easier analysis of part length
  • pSB1C3 is a BioBrick RFC[10] backbone, so it will flank the part sample with the BioBrick prefix and suffix
    • This means that all submitted parts will be BioBrick RFC[10] compatible, and will work with any current assembly method

Since all new parts submitted to the Registry will be in pSB1C3 (and as we transfer the older parts over), these same benefits are passed on to users: when you get part samples in pSB1C3 you can sequence them and run quality control tests using the same methods. It's expected that you'll be using your part sample outside of pSB1C3, and since pSB1C3 is a BioBrick RFC[10] backbone, you can easily transfer it to another plasmid backbone for operational, measurement, assembly, or other purposes.