The issue of how a protein or a drug molecule can recognize a particular DNA sequence predates the era of single-crystal DNA structure analysis. From this came the concept of sequence-dependent local helix deformability of the DNA duplex. The duplex is not a Venus di Milo, frozen in marble immobility, but neither is it a plate of formless sphagetti. A better analogy is with the human arm, which contains a forearm and upper arm that can be rotated but not bent, an elbow that can bend but not rotate, and a wrist that is capable of both deformations.
Ergonomic design depends upon knowing the motions available to different regions of the human body.
Only sequence-specific complexes were used since the intent was to invesigate the role of DNA bending in recognition. Accordingly, proteins such as DNase I, polymerases, reverse transcriptases, and the nucleosome itself were omitted. The present analysis, in contrast, deletes the protein and looks only at local structure deformations in the DNA duplex. Three local helix rotations and three local translations were examined, as depicted in Figure 1. Roll of adjacent base pairs about their long axes.