Periodic Reporting for period 3 - TAP (Topologically Active Polymers)
Período documentado: 2024-01-01 hasta 2025-06-30
The physical properties of soft and polymeric materials underpin a myriad of healthcare and industrial applications, from drug delivery and cosmetics to plastics, recycling and even batteries.
The study of how polymers behave in solution is a well-established research field.
In spite of this, most of the polymers used in everyday applications have a fixed structure and cannot be changed in time.
This assumption lies at the heart of classic polymer physics but it spectacularly fails for arguably one of the most important natural polymer, i.e. DNA.
Our genomes are constantly mechanically and topologically reshaped over time, and this plasticity and constant change underlies life itself.
For instance, certain proteins that allow DNA to cross through itself by creating transient breaks, i.e. Topoisomerases, are essential for cell division and DNA replication.
The issue I want to address in this project is that current polymer physics is not equipped to tackle problems where polymers are allowed to change structure and topology in time.
Developing theory and simulations for "topologically active polymers" and apply them to real situations via experiments using DNA and proteins is the grand goal of the project.
Achieving this goal will allow us to (i) design materials with novel properties in which polymers are made to change structure and topology over time and (ii) better understand the organisation and topology of the DNA in living cells. Both these outcomes will benefit society by enabling novel materials and novel and better healthcare therapies of drugs.
In the original proposal I had envisioned the following objectives:
O1. Develop algorithms for modelling polymers undergoing topological operations [OC1-3, WP1]
O2. Characterise the topological and rheological phases of solutions of generic TAPs subject to different classes of topological operations [OC1-2, WP2&4]
O3. Experimentally realise TAP solutions with DNA and selected classes of proteins [OC2-3, WP4]
O4. Understand the impact of physical, geometrical and topological constraints on the workings of DNA-topology-regulating proteins [OC2-3, WP1-3]
O5. Understand the behaviour of entangled solutions of circular, supercoiled DNA and chimeric polymers with fixed topology [OC1, WP3]
The study of how polymers behave in solution is a well-established research field.
In spite of this, most of the polymers used in everyday applications have a fixed structure and cannot be changed in time.
This assumption lies at the heart of classic polymer physics but it spectacularly fails for arguably one of the most important natural polymer, i.e. DNA.
Our genomes are constantly mechanically and topologically reshaped over time, and this plasticity and constant change underlies life itself.
For instance, certain proteins that allow DNA to cross through itself by creating transient breaks, i.e. Topoisomerases, are essential for cell division and DNA replication.
The issue I want to address in this project is that current polymer physics is not equipped to tackle problems where polymers are allowed to change structure and topology in time.
Developing theory and simulations for "topologically active polymers" and apply them to real situations via experiments using DNA and proteins is the grand goal of the project.
Achieving this goal will allow us to (i) design materials with novel properties in which polymers are made to change structure and topology over time and (ii) better understand the organisation and topology of the DNA in living cells. Both these outcomes will benefit society by enabling novel materials and novel and better healthcare therapies of drugs.
In the original proposal I had envisioned the following objectives:
O1. Develop algorithms for modelling polymers undergoing topological operations [OC1-3, WP1]
O2. Characterise the topological and rheological phases of solutions of generic TAPs subject to different classes of topological operations [OC1-2, WP2&4]
O3. Experimentally realise TAP solutions with DNA and selected classes of proteins [OC2-3, WP4]
O4. Understand the impact of physical, geometrical and topological constraints on the workings of DNA-topology-regulating proteins [OC2-3, WP1-3]
O5. Understand the behaviour of entangled solutions of circular, supercoiled DNA and chimeric polymers with fixed topology [OC1, WP3]
The project is structured so that the objectives are cross-cutting work packages, which can then be developed in parallel.
1. (O1-O3) We developed codes, theory and designed experiments to understand how DNA digestion by restriction enzymes affects the rheology of dense solutions of DNA.
-Michieletto, Davide, et al. "Topological digestion drives time-varying rheology of entangled DNA fluids." Nature Communications 13.1 (2022): 4389.
2. (O1, O4) We developed code and studied how the geometry and topology of DNA substrates affect DNA integration:
- Forte, G., et al. "Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids." Journal of the Royal Society Interface 18.181 (2021): 20210229.
- Battaglia, Cleis, and Davide Michieletto. "Loops are Geometric Catalysts for DNA Integration." bioRxiv (2023): 2023-06.
the action of SMC proteins and loop extrusion:
- Bonato, Andrea, Davide Marenduzzo, and Davide Michieletto. "Simplifying topological entanglements by entropic competition of slip-links." Physical Review Research 3.4 (2021): 043070.
- Ryu, Je-Kyung, et al. "Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events." Nucleic acids research 50.2 (2022): 820-832.
the action of Topoisomerases:
- Michieletto, Davide, et al. "Dynamic and facilitated binding of topoisomerase accelerates topological relaxation." Nucleic Acids Research 50.8 (2022): 4659-4668.
- Bonato, Andrea, and Davide Michieletto. "Three-dimensional loop extrusion." Biophysical Journal 120.24 (2021): 5544-5552.
3. (O5) We computationally and experimentally studied the behaviour of entangled supercoiled plasmids and topologically linked DNA rings in kinetoplast DNA.
- Smrek, Jan, et al. "Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids." Science Advances 7.20 (2021): eabf9260.
- He, Pinyao, et al. "Single-molecule structure and topology of kinetoplast DNA networks." Physical Review X 13.2 (2023): 021010.
1. (O1-O3) We developed codes, theory and designed experiments to understand how DNA digestion by restriction enzymes affects the rheology of dense solutions of DNA.
-Michieletto, Davide, et al. "Topological digestion drives time-varying rheology of entangled DNA fluids." Nature Communications 13.1 (2022): 4389.
2. (O1, O4) We developed code and studied how the geometry and topology of DNA substrates affect DNA integration:
- Forte, G., et al. "Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids." Journal of the Royal Society Interface 18.181 (2021): 20210229.
- Battaglia, Cleis, and Davide Michieletto. "Loops are Geometric Catalysts for DNA Integration." bioRxiv (2023): 2023-06.
the action of SMC proteins and loop extrusion:
- Bonato, Andrea, Davide Marenduzzo, and Davide Michieletto. "Simplifying topological entanglements by entropic competition of slip-links." Physical Review Research 3.4 (2021): 043070.
- Ryu, Je-Kyung, et al. "Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events." Nucleic acids research 50.2 (2022): 820-832.
the action of Topoisomerases:
- Michieletto, Davide, et al. "Dynamic and facilitated binding of topoisomerase accelerates topological relaxation." Nucleic Acids Research 50.8 (2022): 4659-4668.
- Bonato, Andrea, and Davide Michieletto. "Three-dimensional loop extrusion." Biophysical Journal 120.24 (2021): 5544-5552.
3. (O5) We computationally and experimentally studied the behaviour of entangled supercoiled plasmids and topologically linked DNA rings in kinetoplast DNA.
- Smrek, Jan, et al. "Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids." Science Advances 7.20 (2021): eabf9260.
- He, Pinyao, et al. "Single-molecule structure and topology of kinetoplast DNA networks." Physical Review X 13.2 (2023): 021010.
Currently, we among the few groups (if not the only one) in the world that is developing both computer codes and designing experiments to understand topologically complex polymers.
All the codes we write are deposited open access at the "TAPLab" page https://git.ecdf.ed.ac.uk/taplab(se abrirá en una nueva ventana)
Some of these codes are being integrated into popular molecular dynamics engines such as LAMMPS in the form of user-friendly "fixes".
Creating this library is pushing the field beyond the state-of-the-art as the codes we are developing are enhancing the capabilities and possibilities of the polymer physics community.
For instance, thanks to these new codes we can study the biophysical processes of DNA integration (Battaglia and Michieletto. "Loops are Geometric Catalysts for DNA Integration." bioRxiv (2023)).
My goal is that by the end of the project the TAPLab will generate a library of fixes that the polymer physics community can use out-of-the-box to simulate polymers that undergo various topological changes in time and inform the design of novel materials.
In parallel to developing new codes, we are developing new ways of integrating simulations and experiments. For instance we have recently performed high-resolution AFM on Kinetoplast DNA (kDNA) networks and developed "AFM-steered MD simulations" to allow us to resolve the 3D structure and topology of the kDNA from a 2D image (see He et al. Physical Review X 13.2 (2023)).
This type of reconstruction was never done before in the literature, mainly because of the separation between modelling and experimental efforts in this field.
One of the successes in my group is that we are fully integrating the modelling and experimental aspects and each paper aims to contain both modelling and experiments whenever possible and needed.
The work we carried out until now has been well received by the community.
As a testimony of this I have started to be invited at major conferences on polymer rheology and topology as invited speaker:
British Society of Rheology MidWinter Meeting, January 2021 (https://www.bsr.org.uk/events/3-2021-mid-winter-meeting(se abrirá en una nueva ventana))
British Society of Rheology Midwinter Meeting, December 2022 (https://www.bsr.org.uk/events/copy-of-rheology-of-active-evolving-and-responsive-systems(se abrirá en una nueva ventana))
Complex rheology in biological systems, Leeds, October 2023 (https://royalsociety.org/science-events-and-lectures/2023/10/complex-rheology/(se abrirá en una nueva ventana))
GEOTOP-A, Merida, Mexico, January 2024 (https://seminargeotop-a.com/merida24/list-of-participants(se abrirá en una nueva ventana))
Organization and dynamics of active polymers and filaments: from single chain to collectives, Leiden, February 2024 (no website yet)
All the codes we write are deposited open access at the "TAPLab" page https://git.ecdf.ed.ac.uk/taplab(se abrirá en una nueva ventana)
Some of these codes are being integrated into popular molecular dynamics engines such as LAMMPS in the form of user-friendly "fixes".
Creating this library is pushing the field beyond the state-of-the-art as the codes we are developing are enhancing the capabilities and possibilities of the polymer physics community.
For instance, thanks to these new codes we can study the biophysical processes of DNA integration (Battaglia and Michieletto. "Loops are Geometric Catalysts for DNA Integration." bioRxiv (2023)).
My goal is that by the end of the project the TAPLab will generate a library of fixes that the polymer physics community can use out-of-the-box to simulate polymers that undergo various topological changes in time and inform the design of novel materials.
In parallel to developing new codes, we are developing new ways of integrating simulations and experiments. For instance we have recently performed high-resolution AFM on Kinetoplast DNA (kDNA) networks and developed "AFM-steered MD simulations" to allow us to resolve the 3D structure and topology of the kDNA from a 2D image (see He et al. Physical Review X 13.2 (2023)).
This type of reconstruction was never done before in the literature, mainly because of the separation between modelling and experimental efforts in this field.
One of the successes in my group is that we are fully integrating the modelling and experimental aspects and each paper aims to contain both modelling and experiments whenever possible and needed.
The work we carried out until now has been well received by the community.
As a testimony of this I have started to be invited at major conferences on polymer rheology and topology as invited speaker:
British Society of Rheology MidWinter Meeting, January 2021 (https://www.bsr.org.uk/events/3-2021-mid-winter-meeting(se abrirá en una nueva ventana))
British Society of Rheology Midwinter Meeting, December 2022 (https://www.bsr.org.uk/events/copy-of-rheology-of-active-evolving-and-responsive-systems(se abrirá en una nueva ventana))
Complex rheology in biological systems, Leeds, October 2023 (https://royalsociety.org/science-events-and-lectures/2023/10/complex-rheology/(se abrirá en una nueva ventana))
GEOTOP-A, Merida, Mexico, January 2024 (https://seminargeotop-a.com/merida24/list-of-participants(se abrirá en una nueva ventana))
Organization and dynamics of active polymers and filaments: from single chain to collectives, Leiden, February 2024 (no website yet)