  Flexibility of short DNA helices is important for the biological functions
such as nucleosome formation and DNA-protein recognition. Recent experiments
suggest that short DNAs of tens of base pairs (bps) may have apparently higher
flexibility than those of kilo bps, while there is still the debate on such
high flexibility. In the present work, we have studied the flexibility of short
DNAs with finite-length of 5 to 50 bps by the all-atomistic molecular dynamics
simulations and Monte Carlo simulations with the worm-like chain model. Our
microscopic analyses reveal that short DNAs have apparently high flexibility
which is attributed to the significantly strong bending and stretching
flexibilities of ~6 bps at each helix end. Correspondingly, the apparent
persistence length lp of short DNAs increases gradually from ~29nm to ~45nm as
DNA length increases from 10 to 50 bps, in accordance with the available
experimental data. Our further analyses show that the short DNAs with excluding
~6 bps at each helix end have the similar flexibility with those of kilo bps
and can be described by the worm-like chain model with lp~50nm.
