In early 90’s it became possible to perform experiments on single molecules like proteins and DNA. These experiments are normally carried out by fixing the position of one end of the molecule and attaching the other end for example by a tip of an atomic force microscope or with a optical or magnetic tweezers. The molecule can be pulled and rotated and the force to do it can be measured accurately. We have reproduced the pioneering DNA stretching experiment from 1992 using non-equilibrium MD simulations. Like in the experiment we overstretched double strand DNA (a 22mer) to 2.3-fold of its original length. Imagine stretching a telephone cord until it is straight. After we started to pull DNA it went soon to another conformation after changing two backbone torsion angles about 100 degrees corresponding to so called B-S transition proposed previously. Upon continued stretching the base pairs were broken in a co-operative manner and the bases became stacked on top of each other like in a zipper while the two strands moved closer to each other. The new conformation was thermally stable and stacked structure was maintained due to H-bonds to surrounding water and due to hydrophobic interactions. This new conformation has not been reported previously.

References
Lohikoski, Timonen & Laaksonen,
Molecular dynamics simulation of single DNA stretching reveals a novel structure.
Chem. Phys. Lett. 407, 23-29 (2005).

Raimo Lohikoski, Martin Dahlberg and Aatto Laaksonen,
Computer Simulations of DNA Stretching, In Modern methods for
theoretical physical chemistry of biopolymers.
(Eds. S. Tanaka, J.Lewis, and E. Starikow). Elsevier (2006)

Juraj Bunta, Martin Dahlberg, Leif A. Eriksson, Nikolai Korolev, Aatto
Laaksonen, Raimo Lohikoski, Alexander Lyubartsev, Miroslav Pinak
and Patric Schyman, Solvating, manipulating, damaging and repairing DNA in a computer,
International Journal of Quantum Chemistry, 107, 279291 (2006).