Chiral effects in dual-DNA braiding

• Published in: Soft matter 2013-01, Vol.9 (41), p.9833-9848
• Main Authors: Lee, D. J, Cortini, R, Korte, A. P, Starostin, E. L, van der Heijden, G. H. M, Kornyshev, A. A
• Format: Article
• Language: English
• ISSN: 1744-683X; 1744-6848
• DOI: 10.1039/c3sm51573g

The biologically important problem of DNA braiding was studied in the past by means of dual-DNA magnetic tweezer experiments. In such experiments, two DNA molecules are braided about each other using an externally imposed force and torque. Here we develop a theoretical model of molecular braiding that includes interactions between molecules, thermal fluctuations, and the elastic response of molecules, all in a consistent manner. This is useful to study the chiral effects of helix-dependent electrostatic interactions on the braid's equilibrium geometrical and mechanical properties. When helix-dependent forces are weak, our model yields a reasonably accurate reproduction of previously measured extension-rotation curves, where only very slight chirality has been observed. On the other hand, when helix-specific electrostatic forces are strong, the model predicts several new features of the extension-rotation curves. These are: (a) a distinct asymmetry between left-handed and right-handed DNA braiding; (b) the emergence, under a critical pulling force, of coexistence regions of tightly and loosely wound DNA; (c) spontaneous formation of left-handed DNA braids at zero external torque (zero bead rotations). Strong chiral forces are expected for braiding experiments conducted in solutions in which there are counter-ions that bind specifically in the DNA grooves. We develop a model to describe dual-DNA braiding experiments and use this model to study the effect of helix-specific interactions in such experiments.