Anomalous Dynamics of DNA Hairpin Folding

By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous; i.e., the characteristic time tau scales nonlinearly with N, the hairpin length, tau similar to N-alpha with alpha > 1. This is in sharp contrast to the prediction of the zipper model for which tau similar to N. We show that the anomalous dynamics originates from an increase in the friction during zippering due to the tension built in the closing strands. From a simple polymer model we get alpha = 1 + v approximate to 1.59 with being the Flory exponent, a result which is in agreement with the simulations. We discuss transition path times data where such effects should be detected.