Functionalization of cantilever tips with nucleotides by the phosphoramidite method.

In atomic force microscopy (AFM) a sharp cantilever tip is used to scan surfaces at the atomic level. One further application is force spectroscopy, in which force-distance curves between binding partners located on the cantilever and substrate surface are determined. This requires specifically immobilized molecules. Herein we describe the covalent binding of single adenosine and thymidine nucleotides on an amino-PEGylated cantilever tip by the phosphoramidite method. Force-distance curves between these cantilever tips and gold surfaces were recorded. The rupture forces of the coordination bond between the primary amine of adenosine and the undercoordinated gold atoms were determined to be 145 pN, which is in agreement with previously published data. The force-distance curves of thymidine-functionalized tips did not show rupture events, because this nucleotide does not possess a primary amine function. Nucleotide-functionalized tips could aid in the understanding of binding mechanisms of nucleotide binding molecules such as polymerases immobilized on surfaces or membranes.

Electric glue: electrically controlled polymer-surface adhesion.

Polymer-surface interactions provide a basis for nanoscale design and for understanding the fundamental chemistry and physics at these length scales. Controlling these interactions will provide the foundation for further manipulation, control, and measurement of single molecule processes. It is this direction of control over nanoscale polymer-surface interactions that we explore with electric glue. The adhesion between surfaces and single molecules is manipulated based on an externally controlled potential in electric glue.

Electrically induced bonding of DNA to gold.

The development of single-molecule techniques has afforded many new methods for the observation and assembly of supramolecular structures and biomolecular networks. We previously reported a method, known as the single-molecule cut-and-paste approach, to pick up and deposit individual DNA strands on a surface. This, however, required pre-functionalization of the surface with DNA strands complementary to those that were to be picked up and then deposited. Here we show that single molecules of double-stranded DNA, bound to the tip of an atomic force microscope, can be deposited on a bare gold electrode using an electrical trigger (surface potential cycling). The interactions between the DNA and the electrode were investigated and we found that double-stranded DNA chemisorbs to the gold electrode exclusively at its end through primary amine groups. We corroborated this finding in experiments in which only a single adenosine nucleotide on a polyethylene glycol spacer was 'electrosorbed' to the gold electrode.

Placement and orientation of individual DNA shapes on lithographically patterned surfaces.

Artificial DNA nanostructures show promise for the organization of functional materials to create nanoelectronic or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter 'staple strands', can display 6-nm-resolution patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in solution and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here we describe the use of electron-beam lithography and dry oxidative etching to create DNA origami-shaped binding sites on technologically useful materials, such as SiO(2) and diamond-like carbon. In buffer with approximately 100 mM MgCl(2), DNA origami bind with high selectivity and good orientation: 70-95% of sites have individual origami aligned with an angular dispersion (+/-1 s.d.) as low as +/-10 degrees (on diamond-like carbon) or +/-20 degrees (on SiO(2)).