The morphology of duplex and quadruplex DNA on mica

Atomic force and low current scanning tunneling microscopy characterization of duplex and quadruplex DNA (“G-wire”) morphology adsorbed on to mica reveals very different topography. This observation contradicts similar dimensions for the two molecules as determined by spectroscopic techniques. In the work presented here, the diameter of duplex DNA, as measured by height above the mica background, was 25% of that observed by x-ray crystallographic methods. However, the G-wire diameter was similar to that determined by nuclear magnetic resonance and crystallographic methods. These observations appear to be independent of the residual buffer or scanning probe microscopy (SPM) technique used. The SPM observed widths of these molecules are similar and supports a model in which duplex DNA is pinned flat to the mica substrate. These morphological differences may be related to the variations in intermolecular forces with the mica substrate and intramolecular forces holding the polymers together.