Dynamics and mechanics of knotted DNA and RNAs: insights from molecular dynamics simulations

Abstract: I will report on a series of studies where we used molecular dynamics simulations and various models to study how the properties of DNA and RNAs are affected by the presence of knots and other forms of structural entanglement[1]. I will first consider model DNA plasmids that are both knotted and supercoiled, and discuss how the simultaneous presence of knots and supercoiling creates long-lived multi-strand interlockings that might may be relevant for the simplifying action of topoisomerases. I next consider how entangled nucleic acids behave when driven through narrow pores[2-4], a setting that models translocation through the lumen of enzymes, and discuss the biological implication for a certain class of viral RNAs[4].

[1] L. Coronel, A. Suma and C. Micheletti, "Dynamics of supercoiled DNA with complex knots", Nucleic Acids Res. (2018) 46 , 7533

[2] A. Suma, V. Carnevale and C. Micheletti, Nonequilibrium thermodynamics of DNA nanopore unzipping, Phys. Rev. Lett., (2023), 130 048101

[3] A. Suma, A. Rosa and C. Micheletti, Pore translocation of knotted polymer chains: how friction depends on knot complexity, ACS Macro Letters, (2015), 4 , 1420-1424

[4] A. Suma, L. Coronel, G. Bussi and C. Micheletti, "Directional translocation resistance of Zika xrRNA” Nature Communications (2020), 11 , art no. 3749

geometric topology

Audience: researchers in the topic

( video )

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GEOTOP-A seminar

Series comments: Web-seminar series on Applications of Geometry and Topology

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