Researchers at the London Centre for Nanotechnology have determined the structure of DNA from measurements on a single molecule, and found that this structure is not as regular as one might think, reports the journal Small.

Our life depends on molecular machinery that is continuously at work in our bodies. The structure of these nanometre-scale machines is thus at the heart of our understanding of health and disease. This is very apparent in the case of the Watson-Crick DNA double-helix structure, which has been the key to understanding how genetic information is stored and passed on.

Watson and Crick’s discovery was based on diffraction of X-rays by millions of ordered and aligned DNA molecules. This method is extremely powerful and still used today—in a more evolved form—to determine the structure of biological molecules. It has the important drawbacks, however, that it only provides static, averaged pictures of molecular structures and that it relies on the accurate ordering and alignment of many molecules. This process, called crystallisation, can prove very challenging.

Building on previous work in Dr. Bart Hoogenboom’s research group at the London Centre for Nanotechnology, and in collaboration with the National Physical Laboratory, first author Alice Pyne has applied “soft-touch” atomic force microscopy to large, irregularly arranged and individual DNA molecules. In this form of microscopy, a miniature probe is used to feel the surface of the molecules one by one, rather than seeing them.

To demonstrate the power of their method, Pyne, Hoogenboom and collaborators have measured the structure of a single DNA molecule, finding on average good agreement with the structure as it has been known since Watson and Crick. Strikingly, however, the single-molecule images also reveal significant variations in the depths of grooves in the double helix structure.

While the origin of the observed variations is not yet fully understood, it is known that these grooves act as keyways for proteins (molecular keys) that determine to which extent a gene is expressed in a living cell. The observation of variations in these keyways may thus help us to determine the mechanisms by which living cells promote and suppress the use of genetic information stored in their DNA.

Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy