Dangling DNA pinpoints a protein’s chemical groups

X-ray crystallography and electron microscopy can each provide a wealth of structural information about proteins and other biomolecules. But neither can operate under physiologically relevant conditions, so they’re unable to observe the dynamic processes that are central to proteins’ biological function. Atomic force microscopy, on the other hand, can work in water. Now Duckhoe Kim and Ozgur Sahin (Columbia University) have used that capability to create a functionalized atomic force microscope (AFM) that can locate specific chemical groups in a protein under biological conditions. From their AFM tip they dangled two single-stranded DNA hexamers, shown in the figure in red and green. The like-colored complementary strands, attached to a protein’s chemical groups of interest, served as imaging labels. The researchers operated the AFM in tapping mode, with the cantilever vibrating up and down, so each hexamer had a chance to bind with its complement. When a binding event took place, the T-shaped cantilever was seen to twist—a signal that one of the labeled chemical groups had been found. Paradoxically, the key to the method’s success lies in the weakness of the interaction between the short strands. The stronger force between longer strands can induce a distortion in the protein that would muddy the signal, but shorter strands bind only when precisely aligned—and they spontaneously unbind as the cantilever is moved away. In their proof-of-principle experiment, Kim and Sahin used a protein with a known crystal structure and found that the measured locations of their target chemical groups agreed with the groups’ crystal-structure locations to within 0.2 nm. (D. Kim, O. Sahin, Nat. Nanotechnol., in press, doi:10.1038/nnano.2014.335 .)