The elegant selectivity of Watson-Crick base-pairing makes DNA an extremely useful tool for the construction of nanoscale objects and machines. Stable structures and mechanical cycles can be programmed into a system of single strands by careful choice of the sequences of bases.


Despite the experimental successes, there is no clear theoretical description of the processes involved. Our goal is to develop a coarse-grained model of DNA, detailed enough to capture the essential physics of assembly processes, yet simple enough to be applicable over long time scales. Code, user guides and examples for simulating the model can be downloaded from this site.


We are currently using the model to develop and understand walking DNA devices, in collaboration with the pioneering experimental group of Andrew Turberfield.


We are also interested in using and developing efficient algorithms to simulate our models - in particular Monte Carlo and Langevin algorithms for rigid bodies.

 

DNA Tweezers

A simple molecular motor in two stages of its cycle.

  1. 1.Closed configuration - the purple strand has started to bind to the green, which holds the tweezers (blue, red & yellow) in the closed configuration.

  2. 2.Open configuration - the purple strand has now almost completely removed the green, thereby opening the tweezers

Publications

2014


1. DNA hairpins primarily promote duplex melting rather than inhibiting hybridization

    Submitted.

    John S. Schreck, Thomas E. Ouldridge, Flavio Romano, Petr Sulc, Liam Shaw, Ard A. Louis and Jonathan P. K. Doye


2. Programmable Energy Landscapes for Kinetic Control

    In press at Nat. Commun.

    Robert R. F. Machinek, Thomas E. Ouldridge, Natalie E. C. Haley, Jonathan Bath and Andrew J. Turberfield


3. The robustness of proofreading to crowding-induced pseudo-processivity in the MAPK pathway

    Submitted to Biophys. J.

    Thomas E. Ouldridge and Pieter Rein ten Wolde


4. Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

    Submitted.

    Christian Matek, Thomas E. Ouldridge, Jonathan P. K. Doye and Ard A. Louis


5. A nucleotide-level coarse-grained model of RNA (arxiv)

    J. Chem. Phys. 140, 235102, 2014

    Petr Sulc, Flavio Romano, Thomas E. Ouldridge, Jonathan P. K. Doye and Ard A. Louis

2013


6. Coarse-graining DNA for simulations of DNA nanotechnology (arxiv)

    Phys. Chem. Chem. Phys. 15, 20395-20414, 2013

    Jonathan P. K. Doye, Thomas E. Ouldridge, Ard A. Louis, Flavio Romano, Petr Sulc, Christian Matek, Benedict E. K. Snodin,
    Lorenzo Rovigatti, John S. Schreck, Ryan M. Harrison and William P. Smith


7. On the biophysics and kinetics of toehold-mediated DNA strand displacement

    Nucl. Acids Res. 41, 10641-10658, 2013

    Niranjan Srinivas, Thomas E. Ouldridge, Petr Sulc, Joseph M. Schaeffer, B.Yurke, Ard A. Louis, Jonathan P. K. Doye and E. Winfree


8. DNA hybridization kinetics: zippering, internal displacement and sequence dependence (arxiv)

    Nucl. Acids Res. 41, 8886-8895, 2013

    Thomas E. Ouldridge, Petr Sulc, Flavio Romano, Jonathan P. K. Doye and Ard A. Louis


9. Optimizing DNA nanotechnology through coarse-grained modelling: A two-footed DNA walker

    ACS nano 7, 2479-2490, 2013. A link to a subscription-free copy is available on personal request. 

    Thomas E. Ouldridge, Rollo L. Hoare, Jonathan P. K. Doye, Ard A. Louis, Jonathan Bath and Andrew J. Turberfield


10. Simulating a burnt-bridges DNA motor with a coarse-grained DNA model (arxiv)

    Nat. Comput. 1-13, 2013

    Petr Sulc, Thomas E. Ouldridge, Flavio Romano, Jonathan P. K. Doye and Ard A. Louis


11. Coarse-grained simulations of DNA overstretching (arxiv)

    J. Chem. Phys. 138, 085101 (2013) 

    Flavio Romano, Debayan Chakraborty, Jonathan P. K. Doye, Thomas E. Ouldridge and Ard A. Louis

2012


12. Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)

    J. Chem. Phys. 137, 135101 (2012) - image from this paper selected for the journal cover 

    Petr Sulc, Flavio Romano, Thomas E. Ouldridge, Lorenzo Rovigatti, Jonathan P. K. Doye and Ard A. Louis


13. DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism (arxiv)

    J. Phys. Chem. B 116(38):11616-25 (2012) 

    Christian Matek, Thomas E. Ouldridge, Adam Levy, Jonathan P. K. Doye and Ard A. Louis


14. Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble (arxiv)

    J. Chem. Phys. 137, 144105 (2012). 

    Thomas E. Ouldridge


15. The effect of topology on the structure and free energy landscape of DNA kissing complexes (arxiv)

    J. Chem. Phys. 136, 215102 (2012) 

    Flavio Romano, Alex Hudson, Jonathan P. K. Doye, Thomas E. Ouldridge and Ard A. Louis

2011


16. Coarse-grained modelling of DNA and DNA self-assembly

    D.Phil. thesis completed at Oxford University (2011)

    Selected for publication as part of Springer Theses

    Awarded the IOP Computational Group Annual PhD Thesis Prize


17. Structural, mechanical and thermodynamic properties of a coarse-grained model of DNA (arxiv)

    J. Chem. Phys. 134, 085101 (2011) - image from this paper selected for the journal cover 

    Thomas E. Ouldridge, Ard A. Louis and Jonathan P. K. Doye

2010


18. DNA nanotweezers studied with a coarse-grained model of DNA (arxiv)

    Phys. Rev. Lett. 104, 178101 (2010)

    Thomas E. Ouldridge, Ard A. Louis and Jonathan P. K. Doye


19. Extracting bulk properties of self-assembling systems from small simulations (arxiv)

    J. Phys.: Condens. Matter 22, 104102 (2010)

    Thomas E. Ouldridge, Ard A. Louis and Jonathan P. K. Doye

2009


20. The self-assembly of DNA Holliday junctions studied with a minimal model (arxiv)

    J. Chem. Phys. 130, 065101 (2009)

    Thomas E. Ouldridge, Iain G. Johnston, Ard A. Louis and Jonathan P. K. Doye