Hi All
At the moment most of the Reclone Open DNA collection parts (not expression cassettes) are stored in the FreeGenes pOpen_v3 (aka pOpenBuild) vector or pOpen_v4 (aka pInducible).
This doesn’t need to be the default going forward and indeed we know some people are already thinking about recloning (!) some parts into different standard backbones for various reasons.
@osn_scott has been thinking a lot about this and we were just geeking out on a Zoom call about it so I would kindly invite him to share his thoughts!
It would be great to also get feedback from the rest of the community on plans going forward, to what extent they are back-compatible with the current vectors and/or any compelling reasons to change direction now while the collections are relatively small.
The refactoring job will only get bigger the more we expand the collections, so it is good to have this discussion now.
Let the battle of the plasmids commence 
Jenny
Thanks @jenny_molloy for starting this thread.
We are trying to get a discussion going on what makes a good storage plasmid for Golden Gate parts. Some of you might have experience with other parts collections and their storage plasmids.
pOpen_v3 is the standard storage plasmid for all parts in FreeGene’s DNA collections including my Open Yeast. I have worked with many parts from the various FreeGenes collections and have talked with various people who have also been having problems with, in particular, plasmid yields of specific parts.
In addition, last summer I set about cloning into pOpen_v3, in addition to a bunch of other DNA fragments, the three CDSs for the BsaI restriction system - the restriction enzyme and it’s two methyltransferases as separate CDSs. Their synthesis was done at IDT via the iGEM Engineering committee. All parts (16 in total) appeared to clone okay except the M1 methyltransferase. They all were perfect by Whole Plasmid Sequencing (WPS) except: The first clone of the BsaI restriction enzyme came back with a single bp deletion resulting in a dead enzyme! I then sent the remaining 5 clones and each of them had different mutations! All but one were single bp deletions leading to reading frame errors. The missense residue put a proline near what appears to be the catalytic site in the alphafold model. There should be no promoter & RBS in pOpen_v3 that causes expression any of these parts. Of course, a restriction enzyme expressed in a cell, even at low levels, without it’s methyltransfrases is not a good thing. The genes ATG is proximal to the beta lactamase promoter in pOpen_v3 and there is a tonB terminator between the promoter and cargo area. This terminators is not particularly strong. My hypothesis is that there is a cryptic promoter driving low level transcription and E. coli is inducing/selecting for dead genes.
I am building a ccdB dropout construct that has pOpen_v3’s AarI sites to permit migration of parts away from pOpen_v3 but also to be used for new parts. I’ve added PacI & SpeI sites to allow cloning into any SEVA (has oriT) /BASIC_SEVA (no oriT) vector. These vectors have no MTA attached and have strong terminators flanking the cargo area. I’ve been using BASIC_SEVA as destination/receiving vectors that I developed for GGA with Open Yeast.
My question is what characteristics are needed for the best storage plasmids? I have not yet seen a publication just focusing on storage plasmids. Obviously, no transcription of the cargo area where the parts are located. High plasmid yields when extracting plasmid DNA is important. Anything else? Any incites from other (non-FreeGenes) storage plasmids that could be useful?