I'm still looking into this. I've seen a few of the same articles you have.
Lonza wasn't that helpful. I think he was saying not to bother. I've included the response below.
I couldn't find the paper discussing improved supercoiled yields from gyrase over-expression. I only found this one that said there were reduced overall yields: http://www.ncbi.nlm....les/PMC2735187/
The Life Technologies ChargeSwitch kit claims to give almost entirely supercoiled plasmid on this page:
However on this page they claim that their kit results in identical (not superior) transfection efficiency to their regular anion-exchange-based kit:
Thank you for your email. Indeed DNA quality plays a major role in transfection efficiency and also viability.
In principal nicked plasmid DNA (which is also called open circle; oc) seemed to be express less when transfected in a cell. This might be due to the fact that DNA is faster degraded when entering the cytoplasm and/ or nucleus. So it is best to have an endotoxin-free plasmid purification which showed most of the plasmid in its supercoiled form.
However due to the intracellular topoisomerases I and II the plasmid will be immediately relaxed when delivered to the cell . So, an incubation with Gyrase will change the supercoiling of the plasmid (visible on an agarose gel) but by transfecting it into the cell it will be relaxed by the intracellular topoisomerase enzymes.
Please find here some more information about the importance of supercoil for plasmid preparations and transfection into mammalian cells:
Cytotechnology. Jan 2011; 63(1): 7–12.
Published online Dec 1, 2010. doi: 10.1007/s10616-010-9322-9
Separation of supercoiled from open circular forms of plasmid DNA, and biological activity detection
Huangjin Li, Huaben Bo, Jinquan Wang, Hongwei Shao, and Shulin Huang
I hope my answers are of any help for you. Please let me know if you have further questions.