The rise of single-molecule DNA biochemistry

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Abstract
We have known about conformational changes in DNA far longer than we have known its three-dimensional structure. Early experiments showing the irreversibility of acid-base titration of DNA and of changes in the ultraviolet absorption associated with heating suggested that changes in conformation were occurring. Experiments with DNA fibers that facilitated the derivation of the double helix by Watson and Crick started with the observation of a conformational change, visualized in fiber x-ray diffraction patterns. The first fibers drawn by M. F. Wilkins, R. Franklin, and their collaborators were usually allowed to dry in air. The air-dried fibers produced a characteristic helical diffraction pattern, which was called the A type. On the other hand, drawing a fiber and maintaining it in the hydrated-state produced a different diffraction pattern, which was called the B type. We speak of B-DNA as the usual form of the double helix in biological systems. When the three-dimensional structures of both the A and B forms were worked out, it turned out that the differences between them are related to a change in the extension of the sugar-phosphate backbone. Thus, the backbone of DNA can be regarded as elastic. The basis of this elasticity is associated with changes in the conformation of the ribose ring. In the A form, the ring has a C3′ endo conformation, which has a phosphate-to-phosphate distance close to 5.9 Å. However, in the B form, the ring is in the C2′ endo pucker in which there is ≈7 Å between adjacent phosphate groups. The shorter distance in the A form resulted in a wider double helix in which there is actually a hole running down the axis of the helix, with the double-stranded molecule wrapped around it. In the B form, the hole disappears, and the bases form an axial stack in …