AAV Genome Topology Decides ITR Secondary Structure

Intra-strand base pairing is possible when double-stranded DNA contains inverted repeats, but vanishingly improbable without so-called negative superhelicity. This superhelicity itself is conditional upon whether the molecule can retain torsional stress-a question of "topology." This principle has been uncontroversial to biophysicists since the 1980s but has proven challenging for outsiders to grasp and retain. For those in AAV research, this constitutes a decades-long missed connection. AAV is one of a multitude of viruses bearing secondary-structure-forming elements on their termini. Its "inverted terminal repeats" (ITRs) can self-anneal into relatively large hammerhead structures on both ends of the dynamically structured genome and are central to numerous host interactions that drive the viral lifecycle. A standalone article such as this is therefore warranted to promote an understanding of these ideas in the AAV research community and highlight their significance in the basic biology of the virus and its vector gene delivery system.