The nonlinear stretching model of hydrogen bonds and local self-fluctuation of base rotation in DNA Original Research Article

A new model in which the stretching of hydrogen bonds causes the rotation of bases around an axis being parallel to the helical axis in DNA has been proposed. When the angular displacement tends to zero, it is shown that a plane wave may be excited. When the angular displacement is in the range of several degrees, a cubic nonlinear term in the hydrogen bonds potential has been taken into account. Thus the following new results have been derived. (1) A solitary wave with narrow width (about obe base pair), small amplitude (5°), low energy (0.38 kcal/mol) and short life-time (about 10−13 s) may be excited by the collision of water molecules. (2) The nonlinearity of hydrogen bonds would ensure the rotation of bases toward the major groove. Accordingly, a local and quick self-fluctuation of bases rotation toward the major groove with small amplititude seems to occur in a DNA chain. This new prediction has been compared with the relevant experimental results available.