Localized Nanoscopic Surface Measurements of Nickel-Modified Mica for Single-Molecule DNA Sequence Sampling

Cleaved cation derivatized Muscovite mica is utilized extensively in atomic force microscopy (AFM) imaging because of its flatness over large areas (millimeter cleavage planes with local root-mean-square roughness < 0.3 nm), ease of preparation, and ability to adsorb charged biomolecules such as DNA (work by Hansma and Laney, Cuthold, et al. and McMaster et al.). In particular, NiCl2 treatment has become a common method for controlling DNA adsorption on mica substrates while retaining the mica's ultraflat surface (work by Pietrement et al.). While several studies have modeled the mica/metal ion DNA system using macroscopic colloidal theory (DLVO, etc., Pietrement et al.), Sushko et al., Pastre et al., and Cheng et al.,), nickel/mica's physicochemical properties have not been well characterized on the nanoscale. Efforts to manipulate and engineer DNA nanostructures would benefit greatly from a better understanding of the surface chemistry of nickel/mica. Here we present in situ nanometer- and attogram-scale measurements and thermodynamic simulation results that show that the surface chemistry of nickel-treated mica is more complex than generally appreciated by AFM practitioners because of metal ion speciation effects present at neutral pH. We also show that, under certain preparations, nickel/mica allows in situ nanoscopic nucleotide sequence mapping within individual surface adsorbed DNA molecules by permitting localized controlled desorption of the double helix by soluble DNA binding enzymes. These results should aid efforts to precisely control the DNA/mica binding affinity particularly at the physiological pH ranges required by enzymatic biochemistry (pH 7.0 - 8.5), and facilitate the development of more complex and useful biochemical manipulations of adsorbed DNA such as single-molecule sequencing.