Have you looked at JMOL modeling? It's very cool and would be a good way to visualize the structure. This would be especially cool with a digital projector, a computer lab, or interactive whiteboard. Click here for a good JMOL resource collection from NYU. Hope you like it.
I like to use gel electrophoresis. With my freshmen I usually do a dye separation, and then I use bacteria with my AP students. The kids really get into making a "DNA fingerprint," especially because it is so CSI. Kits are relatively inexpensive and you can by gel boxes that run on 9 volt batteries. I think that Wards carries them.
Teach students to create an excel spreadsheet that automatically fills in nucleotides for complementary DNA, mRNA, tRNA, and/or amino acid. Allows student to see effect of mutation quickly and dramatically.
I did this in a workshop several years ago, so i honestly have no idea how to do it now. But it was well received then.
Good Luck. :-)
I find animations helpful in the teaching of all DNA topics. A good replication animation can be found at http://www.johnkyrk.com/DNAreplication.html and very good transcription and translation animations are at http://www-class.unl.edu/biochem/gp2/m_biology/animation/m_bio_ga.html#
I collect helpful and interesting resources in my biology wiki. I have a section devoted to genetics that you might find useful. One of my absolute favorite activities is the "Click and Clone" virtual lab created by the University of Utah. My students have a blast doing this activity.