An 8.5kb plasmid prepared using QIAgen's Endo-toxin free MAXIprep and eluted at high concentration in the provided TE buffer.
In this gel electrophoresis, the plasmid was either diluted in 1X PBS or in destilled de-ionized H2O and gave different bands (0.8% TBE; 80V; 30min; please see image, top: H2O, bottom: PBS).
What's the explanation you can think of?
My guess is that plasmids form many different conformations and the stability of these will depend on the salt concentration and temperature of the solution so I assume that the salt in the buffer stabilises different conformations than does water.These conformations run at different speeds through the gel due to their shape and not their size
Distilled water can denature DNA. This can result in multiple bands in your gel that are different from the bands obtained from the plasmid isolation. I expect the isolation to primarily give you circular, supercoiled, and linear plasmid in varying ratios depending on handling. Denaturing the plasmids will disturb these ratios and may also produce linear and circular single strand (generally with a lower intensity signal, but this is dependent on your detection method).
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