BasePairer (click the cap above for a teaser movie) is an interactive web app that allows students to assign 'feels' (H-bond donor/acceptor partial charges) to basepairing positions on 3D nucleotides and then to explore how bases interact by orienting them relative to one another. Tautomers and deaminations can also be investigated. Thoughts on key concepts re: DNA
Walk through of basic operations (apply to the older, working version; newer version is 'push buttons and see what happens' for now)
Link goes to a list of activities where students characterize bases and pairing.
BasePairer is now an HTML5 app in jsMOL. Icon above links to the current version with 'roll your own' menus; for pre-designed views and exercises, use the paper airplane icon