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Theoretical physicists working at a blackboard collaboration pod in the Beecroft building.
Credit: Jack Hobhouse

Eryk Ratajczyk

Graduate Student

Research theme

  • Biological physics

Sub department

  • Rudolf Peierls Centre for Theoretical Physics

Research groups

  • Nucleic acid nanotechnology
eryk.ratajczyk@physics.ox.ac.uk
Rudolf Peierls Centre for Theoretical Physics, room 70.31
  • About
  • Publications

Controlling DNA–RNA strand displacement kinetics with base distribution

Proceedings of the National Academy of Sciences Proceedings of the National Academy of Sciences 122:23 (2025)

Authors:

Eryk J Ratajczyk, Jonathan Bath, Petr Šulc, Jonathan PK Doye, Ard A Louis, Andrew J Turberfield

Abstract:

<jats:p>DNA–RNA hybrid strand displacement underpins the function of many natural and engineered systems. Understanding and controlling factors affecting DNA–RNA strand displacement reactions is necessary to enable control of processes such as CRISPR-Cas9 gene editing. By combining multiscale modeling with strand displacement experiments, we show that the distribution of bases within the displacement domain has a very strong effect on reaction kinetics, a feature unique to DNA–RNA hybrid strand displacement. Merely by redistributing bases within a displacement domain of fixed base composition, we are able to design sequences whose reaction rates span more than four orders of magnitude. We extensively characterize this effect in reactions involving the invasion of dsDNA by an RNA strand, as well as the invasion of a hybrid duplex by a DNA strand. In all-DNA strand displacement reactions, we find a predictable but relatively weak sequence dependence, confirming that DNA–RNA strand displacement permits far more thermodynamic and kinetic control than its all-DNA counterpart. We show that oxNA, a recently introduced coarse-grained model of DNA–RNA hybrids, can reproduce trends in experimentally observed reaction rates. We also develop a simple kinetic model for predicting strand displacement rates. On the basis of these results, we argue that base distribution effects may play an important role in natural R-loop formation and in the function of the guide RNAs that direct CRISPR-Cas systems.</jats:p>
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Non-equilibrium remodelling of collagen-IV networks in silico

(2024)

Authors:

Billie Meadowcroft, Valerio Sorichetti, Eryk Ratajczyk, Nargess Khalilgharibi, Yanlan Mao, Ivan Palaia, Andela Saric
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Coarse-grained modeling of DNA–RNA hybrids

Journal of Chemical Physics American Institute of Physics 160:11 (2024) 115101

Authors:

Eryk Ratajczyk, Petr Sulc, Andrew Turberfield, Jonathan Doye, Ard A Louis

Abstract:

We introduce oxNA, a new model for the simulation of DNA–RNA hybrids that is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA–RNA hydrogen bonding interaction, we fit the model’s thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model’s applicability, we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.
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Details from ORA

Controlling DNA-RNA strand displacement kinetics with base distribution

(2024)

Authors:

Eryk Ratajczyk, Jonathan Bath, Petr Šulc, Jonathan PK Doye, Ard Louis, Andrew Turberfield
More details from the publisher

Coarse-grained modelling of DNA-RNA hybrids

arXiv (2023) 1-15

Authors:

Eryk J Ratajczyk, Petr Šulc, Andrew J Turberfield, Jonathan PK Doye, Adriaan A Louis

Abstract:

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.
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