For the Contribution Part, we have decided to use the approach of replicating repetetive modules. In doing so, we have drawn on the preliminary work of the
Edinburgh team with the
Biobrick Part:BBa_K2940003 and want to use our laboratory experience to provide important guidelines for future iGEM teams.
Head-to-tail multimerization using
E. coli allows simple and controlled manipulations to be performed, with the particularity of incorporating additional variation from different gene modules.
However, the use of highly repetitive modules in
E. coli also has its difficulties. The main one is the individual sequence, which requires individual consideration in the following areas.
Not every
E.Coli strain is suitable for sufficient plasmid and protein synthesis.
Thus, at least three different strains should be chosen for optimal yield. You can try cheap and common
E. coli strains, but you should use more demanding variants.
In addition, different vectors offer different possibilities for plasmid propagation and restriction and should also be checked for optimal performance. It is recommended to amplify the gene sequence in a cloning plasmid (
pBluescript II KS (+)) and then later transfer it to an expression plasmid (
pET28a).
Finally, type II restriction enzymes offer a variety of different cutting options, with the main focus on single-cut compatible sticky ends.
Depending on availability and budget, care should be taken when planning.
A list for selection, depending on the vectors used, can be found in Table 1, whereby it is important to ensure that the cleavage site is only contained once in the plasmid. For better ligation, we restrict ourselves to CG-containing interfaces.
Table 1: Compatible single-cut restriction enzymes with a specific interface
Enzyme |
Ligated To |
ApaI (GGGCC/C)
|
BanII (GGGCC/C) |
AscI (GG/CGCGCC) |
AflIII (G/CGCGC) |
BssHII (G/CGCGC) |
MluI (A/CGCGT) |
EagI (C/GGCCG) |
EaeI (C/GGCCG) |
HpaII/MspI (C/CGG) |
AccI (GT/CGAC) |
KasI (G/GCGCC) |
BanI (G/GCGCC) |
NarI (GG/CGCC) |
AccI (GT/CGAC) |
NgoMIV (G/CCGGC) |
BsrFI (R/CCGGC) |
XmaI (C/CCGGG) |
BspEI (T/CCGGA) |