Knots are part of our everyday life. In some cases they can serve useful purposes, think for instance of climbing or sailing. In other cases they can be a nuisance, as we know from the laborious procedures of disentangling extension cables or headphone wires. Like extension cables, long and densely packed biopolymers such as DNA can be knotted too. In several biological systems the detrimental effects of DNA knotting (which e.g. hinders the transcription and replication)  are kept at bay by enzymes that cut, disentangle and reseal DNA strands. However, within very small viruses, where there is space only for the DNA itself, knots inevitably accumulate because of the tight confinement. Yet these knots, which can be experimentally detected, do not prevent the translocation of the DNA from the virus to the infected cell. To gain insight into these important processes, we analyzed the powerful, albeit indirect clues on viral DNA packaging offered by experiments on viral DNA knotting. In particular, starting from the abundance of certain knot types (torus knots) we established that the aligning tendency of contacting DNA strands plays a major role in guiding the spatial organization and knotting of the packaged DNA. By explicitly modeling this aligning interaction, which is analogous to the one observed in cholesteric materials, we further investigated the DNA ejection process and observed that it is not affected by the degree of knotting. I will also report on more recent developments on the survey of knots in naturally occurring RNAs, and possible applicative avenues of topological profiling of biomolecules. 

Cristian Micheletti is a full professor at the International School for Advanced Studies (SISSA) in Trieste, Italy. After obtaining the PhD degree from Oxford University (1996) he joined the Statistical Mechanics group in SISSA, where he was part of the staff of the Molecular and Statistical and Biophysics unit. Prof. Micheletti’s group is focused on the application of tools and concepts typical of statistical mechanics to biological contexts. Their main interest is in the development of suitable coarse-grained models for describing the kinetics and thermodynamics of biomolecules such as nucleic acids, enzymes and protein assemblies.