Threading Macromolecules

The ability to precisely control the transport of single DNA molecules through a nanoscale channel is critical to DNA sequencing and mapping technologies that are currently under development. Threading a macromolecule such as genomic DNA through a nanopore or nanochannel forces its extension and ensures the sequential passage of molecular segments through a nanoscale volume. Electrical or optical probing of this volume produces a highly localized signal that can be correlated to the structure or nucleotide sequence of the DNA.

The transport of DNA molecules through these nanoscale conduits is most often achieved by applying an electric field across the conduit, which induces an electrostatic force on the negatively charged DNA and pulls it into the confines of the nanopore or nanochannel. This force must be sufficient to overcome the free-energy barrier to DNA entry into the nanopore or nanochannel that results from the reduced conformational entropy of the confined macromolecule. Control over transport dynamics in turn affects the throughput and resolving power of such platforms vis-à-vis the efficiency with which DNA molecules are introduced to the nanoscale region and the speed with which the DNA passes through the detection volume. By incorporating a three-dimensional nanofunnel at the nanochannel entrance, DNA can be more efficiently introduced into the nanochannel without an increase in the nanochannel electric field.

In a paper published in Nature Communications, the Ramsey and Rubinstein groups describe the fabrication of nanochannels having three-dimensional nanofunnel entrances of various shapes using FIB-milling, visualization of DNA behavior in these nanofunnels, and modeling of this behavior to better understand how controlling the geometry of the nanochannel entrance can enhance the electrokinetic manipulation of DNA molecules in nanofluidic platforms.

Individual DNA molecules are imaged as they attempt to overcome the entropic barrier to nanochannel entry. Theoretical modeling of this behavior reveals the pushing and pulling forces that result in up to a 30-fold reduction in the threshold electric field needed to initiate nanochannel entry. In some cases, DNA molecules are stably trapped and axially positioned within a nanofunnel at sub-threshold field strengths, suggesting the utility of nanofunnels as force spectroscopy tools. These applications illustrate the benefit of finely tuning nanoscale conduit geometries, which can be designed using the theoretical model developed here.