Team:Edinburgh/Experiments

BioSandwich tests

The BioSandwich system is outlined on its own page. BioSandwich creates parts with homologous ends, but there are a number of ways in which the final assembly could be carried out.

For our tests, we attempted to make a construct containing a Plac-LacZ part, as well as EYFP. BioSandwich inserts short spacers between each part to be assembled. Note that after spacer2 we expect to see some extra bases before we reach the RFC10 suffix. We can call these extra bases the "stuffing". So, the expected sequence is:

Vector -- spacerT7 -- Plac,LacZ -- spacer1 -- EYFP -- spacer2 -- stuffing

Successful assemblies are expected to generate blue colonies that fluoresce yellow under a blue light. We tried several assembly methods, all of which generated many colonies with the correct phenotype, but also many colonies with an incorrect phenotype...

From each plate we sequenced a colony with the correct phenotype (if there were any) and some colonies with incorrect phenotypes, in an attempt to understand what the failure modes were.

BioSandwich with Gibson Assembly

• Colony gby [blue, yellow] - expected scar is missing at approx base 680 of the forward chromatogram. Also, the spacer ends with ATG and the part starts with ATG, but only one ATG is seen. In total 9 bases are missing. There is homology of "tatgg" at both ends of the deleted fragment. There is a point mutation at approx base 500 of the forward chromatogram.
• Colony gb [blue] - there is a deletion of about 80 bases at approx base 700 of the chromatogram. This has been caused by homology of a "gggcgagg" found at both ends of the deleted sequence. The 9 bases mentioned for gby are also missing.
• Colony gwy [yellow] - seem correct except for a point mutation in the reverse chromatogram. The mutation is synonymous (ctg -> ttg).

BioSandwich with Overlap Extension PCR

[Update 18 August] Chris informs us that the primers used for the OEPCR were not the normal ones, and in fact the expected product lacks spacer2 and has an RFC54 suffix.

• bby [blue, yellow] - mostly correct but the EYFP is followed not by spacer2 but by an RFC54 suffix, after which come a few mystery bases and the stuffing. [See update, below]
• bb [blue] - has a massive deletion (several hundred bases) in the EYFP gene after about 60 bases. There is partial homology between the start and end of the deletion: "tggtcgagctggac" vs "tggacgagctgtac". In addition to this, EYFP is not followed by spacer2 but instead by an RFC54 suffix (i.e. minus NotI). After this comes a few mystery bases, then the stuffing.
• bw [plain] - has start1 joined to spacer1, then ~60 bases of the start of EYFP, the same massive deletion as bb, ~20 bases of the end of EYFP, an RFC54 suffix (i.e. minus NotI), then the stuffing.

BioSandwich with Ligation Independent Cloning

We got very few colonies with this method; indeed in several attempts we have seen one correct colony.

• Colony b1 [blue, yellow] - sequence read is of low quality but things seem correct.
• Colony y2 [yellow] - appears to simply be <partinfo>BBa_K216011</partinfo>.
• Colony n4 [plain] - sequence is unreadable.

BioSandwich with Blunt-End Ligation Independent Cloning

This is expected to fail as Ligation Independent Cloning requires long overhangs at the end of each part, not blunt ends.

• bb1 [blue] - seems to be BBa_J33207 followed by part of E. coli ferrous iron transport gene A.
• bw2 [plain] - has start1 followed by the stuffing.
• bw3 [plain] - has RFC10 prefix followed by RFC10 suffix, as if XbaI and SpeI sites have joined in a normal vector.

BioSandwich with CPEC: Circular Polymerase Extension Cloning

• cby [blue, yellow] - there is a single-base deletion near the start of the PlacLacZ part, with no obvious cause. It is too early to affect expression. The last few bases of spacer1 are missing, as well as the first few bases of the EYFP part (9 bases total). This is explained by homology of "tatgg". Otherwise seems correct.
• cb [blue] - Normal until the end of spacer1, which is followed immediately by spacer2 and the stuffing.
• cw [plain] - start1 is followed immediately by a second copy of start1, after which comes spacer2 and a second copy of spacer2. Then the stuffing.