Does the PartsLibrary work for circular sequences?

[andrewshvv]

Context

I have a setup of:

• Golden gate parts library supplier with expression vectors.
• Gene synthesis supplier.
• Golden Gate assembly station.

I have uploaded the backbone sequence to the GoldenGatePartsLibrary, expecting DnaWeawer to find it.

I am giving the library a final sequence of expression vector with inserted gene as input.

Expected behavior:

• Gene being synthesized
• Backbone being taken from the parts library

Actual behaviour:

• Everything is synthesised and assembled with GoldenGate

Question:

Q: Does the PartsLibrary work for circular sequences?

[andrewshvv]

If I understand correctly, for PartsLibrary to support the circular sequences, the sequence decomposer has to work differently, or the sequence has to be re-indexed so that it started with insert. In this case, the sequence decomposer will find it.

[Zulko]

It is difficult to say for sure without a minimal runnable example but I believe you are right in your assumptions:

• DnaWeaver expects backbones to be represented like other parts: the linear sequence of the backbone that will end up in the final constructs, flanked by two restriction sites. If you loaded the complete backbone (as a circular construct) the parts library won't know what to do with it.
• DnaWeaver won't deal correctly with parts and backbones if they are appear cut in the final sequence you submit (e.g. one bit of the backbone of the left and another bit on the right).

Does that make sense?

[andrewshvv]

Yeah, it does! I will try to play with it. Thanks, @Zulko!