Scanning Tunneling Microscopy of Nucleic Acids

Abstract

The scanning tunneling microscope (STM) has been used to measure properties of poly(rA).poly(rU) and DNA, such as helical pitch, half-period oscillations that were interpreted as the alternation between the major and minor grooves, and interhelical spacing. Average pitches were measured by two-dimensional Fourier transforms and by topographic profiles along the fiber axes. Values were typically 7 percent less than standard dimensions of A-form RNA and B-form DNA fibers. This result is compatible with the mild dehydration that occurred under air-drying conditions. More extensive dehydration typically led to 19 percent shrinkage. Analysis of specific regions allowed local variations in helical pitch as small as 1 angstrom to be detected, thus demonstrating that the STM can visualize functionally significant modulations of nucleic acid structure.