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iGEM-Engineering / iGEM-distribution

Repository for collective design of an iGEM DNA distribution
https://igem-distribution.readthedocs.io
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Padding for short sequences #100

Closed jakebeal closed 2 years ago

jakebeal commented 3 years ago

Twist has a minimum synthesis length that is longer than many promoters and terminators (150 bp, iirc). How should we approach padding for short sequences?

Sonjabillerbeck commented 3 years ago

One could add standard stretches 5' and 3' that are cleaved during the type II assembly.

vinoo-igem commented 3 years ago

I'll reach out to Marc about what Freegenes normally does, we don't have to follow them though. But as an example, they have B0034 here https://freegenes.github.io/genes/BBF10K_003410.html where they have a 43 bp insert with 400bp additionally synthesized (60 of which is for their barcode)

I made some quick additions and deletions to their annotations, to show the extra bases that they added. Not great, just to be quick https://benchling.com/s/seq-b8FOT2bE7kCrp4z7pCeY. Couldn't attach a .gb file.

GC-repeat commented 2 years ago

Should the padding sequences adjusted the minimum length requirement so we're not paying for extra unused bases what could represent a substantial price on the volume ? I would probably not go to an adjustment by the base but rather with couple sets of padding sequences with intermediate length that we know get synthesized nicely.

vinoo-igem commented 2 years ago

Closing this as #213 and #231 exist