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Frequently Asked Questions
From partsregistry.org
BioBrick Prefix
Q:I notice your guidelines for parts design say the following: For promoter parts, the transcriptional initiation site (in green) is placed 2 bp upstream of the SpeI site:
...CACtactagtagcggccgctgcag
This design makes for an exceedingly short leader sequence, which might be a bad idea. Studies have shown that very short leaders (i.e. 5' UTR) can result in very low expression levels and can increase the expression of our of frame peptides that initiate at subsequent ATGs.
A: The documentation not correct. You can put a promoter transcript initiation site wherever you feel is best. I have removed the incorrect information. (I think)
Nonstandard Parts
Q: The standardized cloning approach you're using has a lot of advantages. However, for those of us making larger more complex things it is somewhat constraining. If we make alterations to the suffix and prefix sequences are our parts disqualified? We want to make a series of variants an to that efficiently we'll need parts that are more "hot swappable" by including unique sites at strategic locations in the pre- or suffixes. I'm assuming as long as we describe what we've done it's OK. Please advise.
A: Here is the rub. If you make parts that have the standard cloning sites, then your parts can be used directly by others. That is the standardization idea. Standard parts fit together in the standard way. How you chose to make parts is up to you, but you need to deliver them in a standard format.
In fact, the set of parts you make will not fit together with any of the existing parts at all. Not even for you.
Now, some times, you could use just part of the assembly methods and your parts would fit together in some ways with some other parts. But you would not be so happy if the previous user had done this to you.
Just documenting what you did does not solve these problems.
