On the Structure and Stretching of Microhydrated DNA

The structure of short double-stranded DNA oligomers in complex with varied amounts of water is investigated with classical molecular dynamics. Free simulations are performed first and mechanical stress is switched on afterward, resembling the conditions of single-molecule conductivity experiments. Water as well as counterions are seen to contribute to the stabilization of double-stranded DNA structure, and a collapse of the native DNA structure is observed upon the removal of a certain amount of water. Pulling with a moderate external force provides additional support to the double-stranded DNA structure, whereas larger forces lead to the overstretching transition followed by the separation of DNA strands, in a manner similar to that observed in fully hydrated DNA.