If the joint scares you
Consider this. Think of making a mitered or bevel sided box. Make your panels in the rectangular form, then bevel or miter all the edges like you would if the panels were solid hardwood or plywood. The joints will take care of themselves if the plexiglas panels are structurally sound. A bond of adhesive or silicone in the dado/groove will hold them together while the bevels are carefully cut on the edges. Your saw must be set dead on at 45 degrees. A sharp blade of 60 teeth or so should give a nice clean edge. I haven't done it this way so you are on your own with this suggestion, but I have made solid panel boxes this way.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)