How does the helical structure of DNA affect its mechanical properties?
DNA is a semiflexible polymer; we typically characterize it by its “bending stiffness” (as for any bendable rod) or “persistence length” (the length scale on which it would bend under thermal fluctuations). But what aspects of its bending and thermal fluctuations are affected by the “handedness” of DNA? It turns out that DNA reveals its handedness in a tendency, once bent into an arc, to “coil” preferentially in one sense over the opposite sense, rather like a length of hemp rope “prefers” to be coiled in one sense rather than the opposite sense. This “tendency” can be expressed as a nonlinear elastic coefficient, and its magnitude determined by performing atomistic molecular dynamics simulations on a short length of DNA. (Basically, on a computer you take a piece of DNA, “grab hold” of it, bend it, and then try to twist it first one way, then the other. Or, you can sit back and watch as thermal fluctuations explore those motions for you, and note which occur more frequently.) As a con
