The effect of undulations on Spontaneous Braid formation

This paper extends on a recent work where it was shown that forces dependent on the helical structure may cause two DNA molecules to spontaneously braid [R. Cortini et Al, Biophys. J. 101, 875 (2011)]. Here, bending fluctuations of DNA centre lines about the braid axis are incorporated into the braiding theory. The free energy of the pair of molecules is recalculated and compared to its value without incorporating undulations. We find that the loss of configurational entropy due to confinement of the molecules in the braid is rather high. This contribution to the Free Energy pushes up the amount of attraction needed for spontaneous braiding due to helix dependant forces. The theory will be further developed for plectonemes and braids under mechanical forces, in later work.