STM of metal embedded and coated DNA and DNA-protein complexes

Bare and Pt/Ir/C-coated DNA has been analysed using scanning tunnelling microscopy (STM). To achieve reproducible imaging of bare DNA on mica ethanol/air-dried molecules were embedded in Pt/C. By peeling the metal film off the mica, the previously mica-exposed side of the Pt/C-film with the embedded DNA molecules was accessible for STM analysis. By applying this replica/anchoring technique only hollow trenches in the metal film, and not the DNA itself, could be visualized. The gaps averaged 3.1 nm (+/- 0.9 nm) wide and 1 nm (+/- 0.5 nm) deep. Using scanning force microscopy it could be confirmed that the DNA remained in the Pt/C film during the peel-off procedure. For STM, DNA fragments were also coated with 0.7-1 nm Pt/Ir/C. Owing to the high Z-resolution the STM samples were coated at a high elevation angle (65 degrees), thereby minimizing the problem of self-shadowing. Coating by Pt/Ir/C allowed routine imaging and quantitative analysis of both ethanol/air- and freeze-dried DNA under atmospheric conditions. After ethanol/air drying measured values for DNA width and height were 5.1 nm (+/- 1.8 nm) and 0.9 nm (+/- 0.2 nm), respectively. Freeze-dried DNA averaged 4.2 nm (+/- 1.3 nm) wide and 1.1 nm (+/- 0.1 nm) high. A Pt/Ir/C-coating was also applied to visualize DNA-protein interaction using STM.