National Institute of Genetics

A DNA-binding protein can slide along a helical groove of DNA

Proc. Nat. Acad. Sci. U.S.A. 101, 14731-35, 2004

Shimamoto Lab, Structural Biology Center

RNA polymerase can track a DNA groove during promoter search.
Kumiko Sakata-Sogawa, Nobuo Shimamoto,
Proc. Nat. Acad. Sci. U.S.A. 101, 14731-35, 2004

　　Many proteins bind to special DNA sequences to form functional complexes. How can DNA-binding proteins find their target sequences among a huge number of other sequences? Sogawa and Shimamoto constructed a device to detect nano-scale rotation that can detect rotational movements of DNA. They dragged a single DNA molecule attached the device and over a surface carrying fixed E. coli RNA polymerase holoenzyme, and detected its rotational movements (top movie). The movements were absent when DNA was omitted (bottom movie), when the protein-DNA interaction was disrupted, or when the dragging was stopped. The results show translational movement accompanies rotation, namely a helical movement, indicating that the protein can scan DNA sequences along a DNA groove. The results also confirm their previous observations of sliding: a longitudinal movement of RNA polymerase along fixed, extended DNA (Science 262, 1561, 1993).


If the protein molecule track a DNA groove, translational movement of DNA over the enzyme-laden surface rotate DNA as a screw penetrating a fixed nut, and the DNA rotate the bead held by laser tweezers. This figure illustrates the principle of detection, and the DNA end opposite to the bead is actually fixed on the surface so that the sliding complex is frequently formed. A drawback of this fixing is that groove tracking rotates the bead not unidirectionally but continuously in both directions, as seen in the movie.
an example	a control with no DNA	(Quicktime movie)
Movement of the fluorescent sphere in real speed. Further controls with heparin or without the surface movement showed no significant rotational motion.