Modelling DNA stretching for physics and biology

We have used internal coordinate molecular mechanics calculations to study how the DNA double helix deforms upon stretching. Results obtained for poly meric DNA under helical symmetry constraints suggest that two distinct form s, an unwound ribbon and a narrow fibre, can be formed as a function of whi ch ends of the duplex are pulled. Similar results are also obtained with DN A oligomers. These experiments lead to force curves which exhibit a plateau as the conformational transition occurs. This behaviour is confirmed by ap plying an increasing force to DNA and observing a sudden length increase at a critical force value. It is finally shown some DNA binding proteins can also stretch DNA locally, to conformations related to those created by nano manipulation.