Topologically Active Polymers

DNA is much more than the "molecule of life", it arguably is nature’s smartest polymer. It is used to make complex 3D shapes at nanoscale (DNA origami) or hydrogels for organoids and tissue regeneration and even biocompatible batteries. In this project, we use special proteins that change DNA topology to design non-equilibrium viscoelastic fluids which can change properties in time. We approach this via both simulations (molecular dynamics) and experiments (microrheology).
This project is funded by the European Reearch Council via a Starting Grant.

[1] Michieletto et al., Topological digestion drives time-varying rheology of entangled DNA fluids, Nature Communications 2022
[2] Bonato et al., Topological gelation of reconnecting polymers, PNAS, 2022
[3] Panoukidou et al., Runaway Transition in Irreversible Polymer Condensation with Cyclisation, arXiv,, 2022

Microrheology of DNA and DNA origami

DNA can now be used to make complex structures such as hydrogels, scaffolds, origami, etc. In this project I aim to harness the topological complexity of DNA to design entangled solutions of DNA with interesting rheological properties. For example, I intend to design DNA origami which can, when in concentrated conditions, give rise to emergent collective behaviours that are not present in dilute regimes [1]. Another example is to harness DNA supercoiling to tune the microrheology of entangled plasmids [2].
This project is funded by Leverhulme and the Royal Society.

[1] Rosa, Smrek, Turner, Michieletto, Threading-Induced Dynamical Transition in Chimeric Polymers ACS Macro Letters, 2020
[2] Smrek, et al, Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids Science Advances, 2022

DNA Recombination and Retroviral Integration

Recombination of DNA molecules and DNA integration are ubiquitous processes that are essential for meiosis, horizontal gene transfer, retroviral infection, genome expansion and diversity in plants, immunological response, etc. Intriguingly, the some DNA integration events are more frequently found in specific regions of genomes and do not display a random distribution. For HIV retroviral integration, the process underlying this non-random integration site selection has been subject of decades of intense research and debate. Most of this phenomenology is reported as empirical observations and attributed to the action of proteins, such as chaperones. We are working on understanding the physical principles underlying DNA integration site selection. In this context, we have discovered the existence of "geometric catalysts" that accelerate the integration of foreign DNA into a host [1,4].

[1] Michieletto et al, Nature Communications, 2019
[2] Bousios et al, Mobile DNA, 2020
[3] Bonato et al., Topological gelation of reconnecting polymers, PNAS, 2022
[3] Fosado et al., Fluidification of entanglements by a DNA bending protein to appear, 2022

DNA and Chromatin Organisation

Understanding DNA and chromatin organisation inside the cellular nucleus is one of the current big challenges in biology and biophysics. The 3D folding of DNA and chromatin affects the behaviour of genes, while gene activity often determines the compactness and location of genomic regions. We are working on "bottom-up" models to understand this mututal relationship by starting from 1D "epigenetic" information that can be obtained, for instance, via chip-seq experiments. From the 1D pattern of histone modification, our polymer models can reproduce very closely and without fitting the typical 3D folding as captured via "Hi-C" contact maps [o0-o6].

[o6] Michieletto et al, NAR, 2018
[o5] Brackley et al, Biophys J., 2017
[o4] Brackley et al, NAR, 2016
[o3] Brackley et al, Nucleus, 2016
[o2] Michieletto, Orlandini and Marenduzzo, Phys Rev X, 2016
[o1] Brackley et al, Genome Biol., 2016
[o0] Brackley et al, PNAS, 2013

Recolourable Polymer Models for Chromatin with Dynamic Epigenome

All cells in your body have the exact same DNA sequence, and yet a cell in your heart is very different from a cell in your brain! This specialisation (or differentiation) is made possible by "epigenetic" marks which are positioned along DNA in a different way in your heart cells than in your brain. How are epigenetic marks established in the first place on "blank" chromatin and how are these marks remembered by the cells after division are outstanding question in Biology. In this project we aim to understand the interplay between 1D epignetic information and 3D chromatin organisation in order to shed light into epigenetic memory and cellular fate. [e1-e3].
See also the Physics Focus on "How cells remember who they are"

[e3] Michieletto et al, NAR, 2017
[e2] Michieletto, Orlandini and Marenduzzo, Sci. Rep., 2017
[e1] Michieletto, Orlandini and Marenduzzo, Phys Rev X, 6, 2016

Ring Polymers

Unknotted and unlinked ring polymers in the melt behave very differently than their linear counterparts. The reason behind this difference lies in the closed topology of the rings and on the global topological invariance of the system. As a consequence, ring polymers offer a rich variety of behaviours that I am studying through large scale MD simulations. One important aspect that we have discovered is that melts of ring polymers can become glassy when subject to random pinning pertubrations, and this can be explained by threading of ring polymers as forming a spanning network of topological constraints[r1-r4].

[r1] Michieletto et al, MacroLetters, 2014
[r2] Michieletto and Turner, PNAS, 2016
[r3] Michieletto, Soft Matter, 2016
[r4] Michieletto et al, Polymers, 2017

Knots and Links in Complex Environments

Knots and links are ubiquitous when dealing with long fibers such as polymers or even headphones strings. Nature has found ingenious ways to get rid of knots in the genome of most organisms, through "topological enzymes". On the other hand, there are biological examples in which knots and links are still abundant. One such example is the DNA inside viral capsids: it is so highly knotted that one requires fine techniques such as 2D gel electrophoresis to identify all the possible knots. An example of abundatly linked structures can be found in the mitochondrion of flagellated protists of the class Kinetoplastida, which displays an arrangement aking to that of a "medieval chainmail" [k1]. In this project we aim to understand the behaviour of knots and links when moving through complex environments such as agarose gels [k2-k3] and, at the same time, we also try to shed light into topologically complex systems such as that of the Kinetoplast DNA.

[k4] Orlandini, Marenduzzo, Michieletto, Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology, PNAS 2019
[k3] Michieletto, Marenduzzo, Orlandini, PNAS , 2015
[k2] Michieletto et al,Soft Matter, 2015
[k1] Michieletto Orlandini Marenduzzo, Phys. Biol., 2015