gel electrophoresis - What is the DNA/protein charge ratio?

This is really sounds like a guideline, a starting place, not necessarily your best protocol.

In practice its hard to be more specific as MS says. The pH of the buffer will affect the charge of the protein, and to a lesser extent the DNA.

Also the protein may have an ideal pH for binding which you could guess is in the range of 7.0-7.4, but might find that the strongest binding depends on unexpected pH and salt concentrations, or the addition of a small molecule.

The affinity of araC for instance is greatly increased by the presence of arabinose in sufficient concentration.

lac Repressor, in contrast releases itself from DNA in the presence of IPTG or lactose.