What is it?
Originally developed for plant genetic engineering, Loop assembly is a DNA assembly system that uses standardised DNA modules for composition of genetic constructs. It is integrated in pGreenII-derivatives, for ease of handling and Agrobacterium-mediated plant transformation.
Loop assembly is simple, intuitive and efficient as it is flexible and powerful.
Loop assembly, explained
DNA elements are domesticated into standardised DNA components such as promoters, coding sequences and terminators. Standardised DNA components are used to build transcriptional units, which are then composed into multi-gene constructs.
We have shown that constructs up to 16 transcriptional units (composed of a total of 60 basic genetic components) can be easily assembled in under a week.
What can I use it for?
Loop assembly is both robust as it is flexible. We have previously demonstrated that you can apply it to many DNA assembly problems succesfully.
Build DNA constructs composed of several genetic elements. Up to 16 transcription units can be assembled in under a week.
Rearrange DNA modules into specific configurations to generate synthetic promoters elements.
Build and handle complex DNA such as repetitive sequences. Flanking UNSs enable sequence verification of these sequences.
Use Loop assembly to build large DNA constructs up to 50 kb without worrying about plasmid loss in E. coli DH5-beta strains.
Efficient and effective
Loop assembly is both efficient and effective. We've demonstrated over 80 % efectivity of assembly in any level, meaning that at least 4 out of 5 colonies are bound to be correct irrespective of assembly. Assemblies are highly productive, yielding hundreds of colonies using chemically competent cells (even homemade).
Due to standardisation of basic DNA components and the simplicity of the assembly protocol, working at the sequence level is not required unless you are creating new L0 parts. Assembly of DNA is no longer an issue and you can dedicate your time to more engaging problems. An increase in productivity is to be expected.
Loop assembly is truly standardised. All assemblies encompass four components being joined in the reaction. As genetic constructs grow by a factor of four in each level, hierarchical designs enable the use and reuse of genes and devices built previously, ensuring reliability and performance.
As levels increase, technical details from composing parts becomes less relevant than their joint function, establishing abstraction layers between levels. Level 0 parts contain basic subgene elements. Level 1 parts contain transcriptional units (i.e. genes, reporters, transcriptional activators, repressors). Level 2 parts contain several genes that can be designed as a genetic device. Level 3 constructs contain several genetic devices that can be tethered to work as a system.
Loop assembly plasmids are distributed through the OpenMTA, a novel material transfer agreement that simplifies and streamlines the process of colaborating and sharing material.
In the OpenMTA, plasmids can be shared without further permission from the original distributors. Also, they can be shared from Academia to Industry and viceversa for research or comercial purposes. For more information, see the Nature Biotechnology article.
As such, all components developed for other Type IIS assembly systems are compatible with Loop assembly given that no SapI sites are present. A plethora of standardised DNA components are readily available.
Can I get Loop assembly?
Yes you can! Just shoot us an e-mail!.
Plants are lame, can I do Loop assembly for my really cool non-plant organism?
We've also developed a new version of Loop assembly in bare backbones. It's called Universal Loop (uLoop) and we will submit early (March-April) 2019. If you want to try them out before just let us know!
Where can I obtain parts to use with Loop assembly?
There are a number of DNA parts compliant with the Loop assembly schema. You will find that the GoldenBraid library and the MoClo library can be used with Loop assembly, given that there is abscence of SapI sites. PhytoBricks from IGEM are also compliant with the common syntax and thus compatible with Loop assembly.