Coarse-grained modelling of DNA for biophysics and nanotechnology

Add to your list(s) Download to your calendar using vCal

• Dr Ard Louis, Rudolph Peierls Centre for Theoretical Physics, University of Oxford, UK
• Friday 19 October 2012, 14:00-15:00
• Small Lecture Theatre, Cavendish Laboratory.

If you have a question about this talk, please contact Tracy Inman.

The remarkable ability of biological matter to robustly self-assemble into well defined composite objects excites the imagination, suggesting that these processes could perhaps be emulated through the judicious design of synthetic building blocks. DNA is a particularly promising candidate for large-scale self-assembly because the specific binding of DNA bases can be accurately designed to build dynamic structures at the nanoscale.

We have developed a coarse-grained model of DNA [1,2,3] that is simple enough to be tractable, but complex enough to capture structural, thermodynamic and mechanical properties of DNA that are crucial to DNA nanotechnology. We have used it to study basic biophysical properties of DNA such as hybridization and the stacking transition in single-stranded DNA [3], the response of DNA to tension leading to overstretching of double-stranded DNA and unstacking in single-stranded DNA [4], the response of DNA to twist, leading to bubble, cruciform [5] and plectoneme formation, and (4) the effect of topology on self-assembly processes [6]. Applications to nanotechnology include DNA nanotweezers [1], DNA displacement reactions, A two-footed DNA walker, and DNA origami. Our code is publicly accessible at: http://dna.physics.ox.ac.uk/

References

[1] DNA nanotweezers studied with a coarse-grained model of DNA , T.E. Ouldridge, A.A. Louis and J.P.K. Doye, Phys. Rev. Lett. 104, 178101 (2010)

[2] Structural, mechanical and thermodynamic properties of a coarse-grained DNA model, T.E. Ouldridge, A.A. Louis and J.P.K. Doye, J. Chem. Phys, 134, 085101 (2011)

[3] Sequence-dependent thermodynamics of a coarse-grained DNA model, P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye and A.A. Louis, arXiv:1207.3391.

[4] Coarse-grained simulations of DNA overstretching Flavio Romano, Debayan Chakraborty, Jonathan P. K. Doye, Thomas E. Ouldridge, Ard. A. Louis, arXiv:1209.5892

[5] DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism, C. Matek, T.E. Ouldridge, A. Levy, J.P.K. Doye, and A.A. Louis, arXiv:1206.2636.

[6] The effect of topology on the structure and free energy landscapes of DNA kissing complexes, F. Romano, A. Hudson, J.P.K. Doye, T.E. Ouldridge and A.A. Louis, J. Chem. Phys. 136, 215102 (2012)

This talk is part of the BSS Formal Seminars series.

This talk is included in these lists:

• All Cavendish Laboratory Seminars
• All Talks (aka the CURE list)
• BSS Formal Seminars
• Biology
• CamBridgeSens
• Cambridge talks
• Centre for Health Leadership and Enterprise
• Dobson Group - General Interest
• Featured lists
• Life Science Interface Seminars
• Life Sciences
• Life Sciences
• ME Seminar
• Neurons, Fake News, DNA and your iPhone: The Mathematics of Information
• School of Physical Sciences
• Small Lecture Theatre, Cavendish Laboratory
• Thin Film Magnetic Talks
• Trust & Technology Initiative - interesting events
• my_list
• other talks

Note that ex-directory lists are not shown.