The BioBricks Foundation:Standards/Technical/Formats

Biobrick Formats: This working group aims to specify Biobrick DNA formats.

Aim / Application scenarios for this standard

[ add ]

Overview over proposed Biobrick formats

All biobrick formats proposed so far follow the same basic scheme where restriction and ligation of two biobricks forms a new biobrick.

1.0 classic Format

This is the de-facto standard used by most iGem teams and most biobricks in the MIT registry.

Note, for coding parts, the prefix is shortened so that the ATG is fully part of the biobrick sequence.

Pros:

• de-facto standard

Cons

• no protein fusions (frame shift, stop codon)

"2.0" Biofusion (Silver lab)

The Silver lab modified the classic format to allow for protein fusions:

Pros:

• in-frame fusion of protein parts
• compatible to 1.0 non-coding parts

Cons:

• not compatible to 1.0 protein parts (frame shift)
• Arg in scar can be problematic
• Thr-Arg at the N-term. is a destabilization signal (N-end rule)
• methylation site blocks cloning when prefix is followed by "TC"

"3.0" (Freiburg iGem team)

The Freiburg 2007iGem team proposed a more radical modification or rather extension of 1.0, which would enable protein fusions but alleviate the disadvantages of the Biofusion format:

Pros:

• in-frame fusion of protein parts
• less intrusive protein scar
• N-end rule safe (longer protein half-life)
• stand-alone protein expression (start + stop in prefix / suffix)
• compatible to 1.0 and 2.0 non-coding parts

Cons:

• stand-alone protein expression (start + stop in prefix / suffix)
• not compatible to 1.0 protein parts (stop codon)
• not compatible to 2.0 protein parts (frame shift + stop codon)

"2.0-3.0" (CRG proposal)

Biobrick users at the CRG propose a modification to the Freiburg format which would make 3.0 and 2.0 biobricks compatible with each other and allow 3.0 biobricks to be fused N-terminally to 1.0 protein coding parts. The modification sacrifices the possibility to have a single coding biobrick ready for expression (start and stop in the prefix and suffix are deleted). This may also be considered am advantage though, as it somewhat reduces the risk of uncontrolled expression leading to toxicity.

Pros:

• in-frame fusion of protein parts
• less intrusive protein scar
• N-end rule safe (longer protein half-life)
• full backwards-compatibility (coding and non-coding 1.0 and 2.0 parts)

Cons

• no stand-alone protein expression