Cut-and-paste single molecule nanotechnology using DNA

Regular readers of Nanodot will be aware that the nanotech uses of the exquisite molecular recognition properties of DNA include both the programmed assembly of nanoparticles (which is not atomically precise) and structural DNA nanotechnology (the atomically precise assembly of nanometer scale structures from DNA strands). A group of German scientists have developed a new slant on DNA nanotechnology by using atomic force microscopy to assemble a DNA scaffold on a surface to which molecular building blocks can then bind. The pattern of molecular building blocks thus assembled can be arbitrarily complex, with individual building blocks spaced about 50 nm apart. The precision of assembly is essentially the lateral precision of the AFM, about 6 nm. So the building blocks are atomically precise but the larger structure is only precise on a larger scale. The technology is described in a Nanowerk Spotlight written by Michael Berger, which includes a movie showing the assembly of a rather intricate flower pattern about 10 µmeters across. From “Nanotechnology cut and paste with single molecules“

Using a hybrid approach that combines the precision of an atomic force microscope (AFM) with the selectivity of DNA interactions, researchers in Germany have successfully demonstrated a technique that fills the gap between top-down and bottom-up since it allows for the control of single molecules with the precision of atomic force microscopy and combines it with the selectivity of self-assembly.

“In the past, great efforts have been put into creating DNA structures like the so called DNA origami or crystals composed of nanoparticles” Dr. Hermann E. Gaub tells Nanowerk. “However, these approaches exclusively rely on self-assembly and are purely bottom-up. They don’t allow control over single molecules and the structures that are formed are predetermined by the design of the experiment.”

Gaub, head of the Biophysics and Molecular Materials Group in the Physics Department at the Ludwig-Maximilians-University (LMU) of Munich, together with Elias Puchner and colleagues from the university’s Center for Nanoscience and the Center for Integrated Protein Science Munich, combined the precision of atomic force microscopy with the selectivity of DNA interaction to create freely programmable nanopatterns of DNA-oligomers on a surface and in aqueous environment.

What the LMU researchers did was create a DNA scaffold by picking biotin bearing DNA oligomers with an AFM tip and depositing them, one by one, in a desired pattern on a surface, basically creating a pattern of attachment points for fluorescent semiconductor nanoparticles conjugated with streptavidin. The small bacterial protein streptavidin is commonly used for the detection of various biomolecules and it binds with high affinity to the vitamin biotin. The strong streptavidin-biotin bond can be used to attach various biomolecules to one another or onto a solid support.

When the sample with the DNA scaffold is incubated with a solution of fluorescent nanoparticles, a rapid self-assembly process of these particles on the predefined scaffold takes place. Watch a movie of this process here.

Berger quotes Gaub that extension of the technique to assembly in three dimensions “appears challenging but achievable”. The technique was introduced in Science earlier this year (abstract) and recently elaborated in Nano Letters (abstract).

A subtle but crucial point that makes the technique workable is only clearly illustrated in the online supplementary material to the Science paper. The molecular building block is a single strand of DNA to which other molecules (biotin, a fluorophore, etc.) can be attached. One end of the DNA strand binds to an anchor DNA strand on the surface; the other, shorter end binds to a DNA strand on the AFM tip. The AFM tip moves the molecular building block from an anchor strand in the “depot” area of the surface to an anchor strand in the “target” area where the structure is to be assembled. The key to the technique working is that the anchor strand is linked to the surface by its 5′ end in the depot region and by its 3′ end in the target region. As can be seen in the illustration, this sets up the binding of the molecular building block to the depot region in an “unzip” geometry in which the duplex can be broken one base pair at a time, thus requiring a relatively small retraction force on the AFM tip, while binding to the target region is in a “shear” geometry which requires a greater force to pull the duplex apart. Consequently the AFM tip can remove the building block from the depot area, but leave it on the target area when the tip retracts. The authors report that, amazingly, one cantilever tip was used to transport over 5000 units from the depot to the target area.
—Jim