Riehn Lab

We are exploring how DNA behaves in volumes comparable or small relative to its persistence length (about 50-60 nm, crudely the "average bending radius") of the molecule. We are then using this knowledge to design devices in which molecular biology techniques are performed on a single-molecule basis, and more efficiently than in conventional bulk methods.

To see the importance, one needs to know that DNA is a semiflexible polymer, and forms random coil in solution. Hence, not much can be said about a short DNA molecule just by looking at it with an ordinary microscope. Using an electron microscope, the finer structure becomes apparent, but translating a spatial position into a genomic position is nearly impossible even for an ordinary piece of viral DNA.

The problem can be overcome by stretching DNA molecules, which we do inside nanochannels. Once the channel width becomes comparable in size to the persistence length of DNA, molecules are stretched out to a well-defined faction of their contour length. It then becomes possible to directly observe the length of DNA, image binding of proteins to DNA, or to monitor site-selective biochemistry.

Model of a 100-nm channel with DNA confined in it.	Cross-section of a nanochannel in a fused silica device. Dimensions 80 nm x 90 nm, measured by SEM.

We have found that the ultimate obtainable genomic resolution of DNA-nanochannel measurements should be one basepair. Since molecules in nanochannels are allowed to find an equilibrium geometry, and fluctuate, multiple independent measurements on the same molecule can be taken and averaged. For long measurements the equilibrium value could thus be arbitrarily well defined.

Time trace of sequence-specific cutting of DNA inside nanochannel. On the left are individual screenshots of DNA inside the channel, and on the right are stacks of line intensities along the respective molecules.