Single Molecule DNA Biophysics with Atomic Force Microscopy

Structural and functional properties of double stranded deoxyribonucleic acid (dsDNA) are investigated by atomic force microscopy (AFM) on a single molecule level. Here, we characterize different linear and circular DNA systems in terms of their geometry and topology, and visualize enzyme binding of restriction endonuclease Hae III to DNA. Manipulation of single DNA molecules is demonstrated by dissecting individual DNA strands. Furthermore, the elastic response of single DNA molecules to an externally applied force is investigated by AFM force spectroscopy experiments. This gives information about structural properties of the DNA double helix. Specifically, transition from B-form to S-form DNA and a melting transition from double stranded to single stranded DNA is observed. This allows monitoring of specific interaction and binding of small intercalator molecules such as ethidium bromide (EtBr) to DNA by means of a mechanical, non-fluorescent detection scheme.