First, the DNA nanostructure, "Cylinder in barrel" , was used for pilot study.
To know the optimum condition of the structure assembly, we did experiments in three conditions as follows.
- At different concentration of MgCl2
- At different incubate temperature
- At different length of incubate time
Fast-migrating species upon agarose-gel electrophoresis was yielded at 20mM MgCl2 condition. Correctly folded structures were yielded at 20mM of MgCl2, because they were more compact than misfolded versions. Also, the structures at high concentration (30 and 40mM) of MgCl2 tend to aggregate because of positive charge.
Fast-migrating species upon agarose-gel electrophoresis was yielded at 47.7 or 51.6 degree C. The band at 47.7 degree C is more clear than that of at 51.6 degree C. The band of 47.7 degree C is fast migrated and strong.
The structure assembled for 4h or longer are compact. The band for 4h is fast migrated and strong.