Difference between revisions of "Loop Assembly"

Revision as of 19:02, 29 November 2018

As we prepare for iGEM 2019, I have been trying to decide how to support Type IIS assembly methods for the Registry and the 2019 iGEM Competition. Since [http://2016.igem.org/Resources/Plant_Synthetic_Biology/PhytoBricks 2016], iGEM has allowed teams to submit parts in the PhytoBricks (Type IIS Golden Gate) standard , but have not fully supported any Type IIS standard.

Our current proposal is as follows:

iGEM fully adopts the Loop Assembly standard with Level 0 (basic) parts adhering to the MoClo and/or PhytoBricks Golden Gate assembly standards.
Adoption of Loop would include:

giving teams full credit for submitting samples in this standard

updating the Registry software to support the standard

creating documentation for our users

distributing a collection of basic parts and cloning vectors in the 2019 Distribution Kit.

iGEM would, of course, continue to support and send out BioBrick parts for the foreseeable future. 

Before we finalize the plans for adopting Loop, I would like to collect input from our community. If you have any comments or thoughts on iGEM adopting and supporting Loop (including the MoClo and/or PhytoBricks assembly standards), please send an email to:

Type IIS assembly methods used Type IIS restriction enzymes, which cleave DNA outside their recognition site. First introduced in Golden Gate cloning (Engler et al. 2008), these assembly methods standardize the cleavage sites of the Type IIS enzymes to allow for multiple parts to be assembled in one reaction. Two or more part samples cut with a Type IIS enzyme will produce compatible overhangs which can be ligated in the desired orientation. These standardized overhangs are often referred to as fusion sites.

The MoClo assembly standard (Weber et al. 2011) built on Golden Gate and defined a standard by which

Why Loop Assembly

Adoption

We know several groups, including academic/research labs and industry, that are already using Loop Assembly. We want to ensure that the assembly method we support is widely used, tested, and has flexibility for different applications and groups.

Loop Assembly is compatible with a variety of Golden Gate standards for Level 0 parts, most importantly MoClo and PhytoBricks. Both of these standards are widely used, and MoClo's fusion sites completely overlap with PhytoBricks.

Complexity and Flexibility

OpenMTA

Developed by OpenPlant and The BioBricks Foundation, the OpenMTA

Loop Assembly

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 ===Background===
+Type IIS assembly methods used Type IIS restriction enzymes, which cleave DNA outside their recognition site. First introduced in Golden Gate cloning ([https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003647 Engler et al. 2008]), these assembly methods standardize the cleavage sites of the Type IIS enzymes to allow for multiple parts to be assembled in one reaction. Two or more part samples cut with a Type IIS enzyme will produce compatible overhangs which can be ligated in the desired orientation. These standardized overhangs are often referred to as fusion sites.
+The MoClo assembly standard ([https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016765 Weber et al. 2011]) built on Golden Gate and defined a standard by which