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Happy Valentine's day from oxDNA!
The 'heart' is a 114 base-pair DNA minicircle with a nick at the top. The system was constrained via two mutual traps, between the top/bottom and sides of the heart. These constraints induce strain in the system, which is relaxed by kinking at the nick. DNA kinks preferentially at nicks since only base-base coaxial stacking must be disrupted. In contrast, kinks in duplex DNA require both disruption of stacking and base pairing. Kinking, vis-à-vis strain, is a property that depends on the DNA length. In this example, longer DNA segments would not kink at the nick, yielding an ellipse. Shorter DNA segments, being more strained, would kink at both the nick and the duplex region opposite, yielding a figure 8.
oxDNA
oxDNA is a simulation code that implements the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. The code implements Monte Carlo and Brownian Dynamics and can be used as a basis to numerically study DNA systems. The developers are F. Romano, P. Šulc and T. E. Ouldridge in the Doye and Louis groups at the University of Oxford and L. Rovigatti in the Sciortino group in Rome.
The model is intended to provide a physical representation of the thermodynamic and mechanical properties of single- and double-stranded DNA, as well as the transition between the two. At the same time, the representation of DNA is sufficiently simple to allow access to assembly processes which occur on long timescales, beyond the reach of atomistic simulations. Basic examples include duplex formation from single strands, and the folding of a self-complementary single strand into a hairpin. These are the underlying processes of the fast-growing field of DNA nanotechnology, as well as many biophysical uses of DNA, allowing the model to be used to understand these fascinating systems.
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Acknowledgments
We thank our co-workers C. Matek, B. Snodin and W. Smith for having contributed bits of code and/or material for the examples and to our webmaster Russell Jones for maintaining the website.