Title: End-to-end distance and contour length distribution functions of DNA helices,
Abstract: We present a computational method to evaluate the end-to-end and the contour
length distribution functions of short DNA molecules described by a mesoscopic
Hamiltonian. The method generates a large statistical ensemble of possible
configurations for each dimer in the sequence, selects the global equilibrium
twist conformation for the molecule and determines the average base pair
distances along the molecule backbone. Integrating over the base pair radial
and angular fluctuations, we derive the room temperature distribution functions
as a function of the sequence length. The obtained values for the most probable
end-to-end distance and contour length distance, providing a measure of the
global molecule size, are used to examine the DNA flexibility at short length
scales. It is found that, also in molecules with less than $\sim 60$ base
pairs, coiled configurations maintain a large statistical weight and,
consistently, the persistence lengths may be much smaller than in kilo-base
DNA.