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Nature Nanotechnology 1, 137–141 (1 November 2006) | doi:10.1038/nnano.2006.63

High flexibility of DNA on short length scales probed by atomic force microscopy

Paul A. Wiggins , Thijn van der Heijden , Fernando Moreno-Herrero , Andrew Spakowitz , Rob Phillips , Jonathan Widom , Cees Dekker & Philip C. Nelson

The mechanics of DNA bending on intermediate length scales (5–100|[nbsp]|nm) plays a key role in many cellular processes, and is also important in the fabrication of artificial DNA structures, but previous experimental studies of DNA mechanics have focused on longer length scales than these. We use high-resolution atomic force microscopy on individual DNA molecules to obtain a direct measurement of the bending energy function appropriate for scales down to 5|[nbsp]|nm. Our measurements imply that the elastic energy of highly bent DNA conformations is lower than predicted by classical elasticity models such as the worm-like chain (WLC) model. For example, we found that on short length scales, spontaneous large-angle bends are many times more prevalent than predicted by the WLC model. We test our data and model with an interlocking set of consistency checks. Our analysis also shows how our model is compatible with previous experiments, which have sometimes been viewed as confirming the WLC.