The loading buffer can be the same, but without DTT or any reducing agent. No boiling of the samples either. Not sure about the buffer though, but I am sure there is a rich literature on native gel electrophoresis to have a look at! Just look for those terms on PubMed.

I am fully agreed with Daniel.there shouldn't be any DTT and SDS in the loading buffer, Prepare TGE buffer, Resolving gel and stacking gel without adding SDS..and after running the gel you can compare it with SDS-PAGE as well,so it may give you comparative analysis.with the Native one..

Gud Luck..

Good call on the SDS, Gaurav, forgot about that!

Thanks everyone. I will try to implements these important points and see what work best.