Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs

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 5-50 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 similar to 6 bps at each helix end. Correspondingly, the apparent persistence length l(p) of short DNAs increases gradually from similar to 29 nm to similar to 45 nm 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 similar to 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 l(p) similar to 50 nm. (C) 2015 AIP Publishing LLC.