Hi, I read through your message and I'm wondering whether this is a general question about gel electrophoresis or whether you are having trouble with your electrophoresis equipment. Are you using our IO Rodeo gel box and electrophoresis power supply ? It doesn't seem from your message to be an equipment problem, but more a problem with a new loading dye that you are using ? If that is the case, you might be better off asking the manufacturer of the loading dye whether you should expect to see you DNA sample behave differently in their buffer. I'm sorry I haven't used the GoTaq loading dye.
I hope that helps. Good luck with your PCR experiments and let us know if you have any specific questions about our electrophoresis equipment.
Electrophoresis and Gel Imaging