The knotted strands of life
published: April 15, 2013, recorded: April 2013, views: 3672
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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 analysed 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 modelling 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.
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