An optically fabricated gradient nanochannel array to access the translocation dynamics of T4-phage DNA through nanoconfinement

Abstract

It has been widely recognized that nanostructures in natural biological materials play important roles in regulating life machinery. Even though nanofabrication techniques such as two-photon polymerization (TPP) provide sub-100 nm fabrication resolution, it remains technologically challenging to produce 3D nanoscale features modeling the complexity in vivo. We herein demonstrate that a nanochannel array carrying different sizes and nanostructures with gradually transitioning dimensions can be easily produced on a slightly tilted nano-stage. Using the gradient nanochannel array, we systematically investigate the factors affecting the dynamics of DNA translocation through nanoconfinement, including the size of biomolecules and geometrical features of the physical environment, which resembles the selectivity of nanopores in the cell membrane. It is observed that T4-phage DNA shows distinctive conformational transition dynamics during translocation through nanochannels driven by electric field or flow, and the deformation energy required for DNA to enter the nanochannels depends on both chemical environmental conditions, i.e., the ionic strength regulating DNA persistence length and nanochannel dimension. In the electric field, DNA repeatedly gets stretched and compressed during its migration through the nanochannel, reflected by elevated fluctuation in extension, which is substantially greater than the thermal fluctuation. However, driven by flow, DNA remains stretched during translocation through nanochannels, and shows variances in extension of merely a few hundred nanometers. These results indicate that the optically fabricated gradient nanochannel array is a suitable platform for optimizing the experimental conditions for biomedical applications such as gene mapping, and verify that production of complex three dimensional (3D) nanostructures can be greatly simplified by including slight inclination during TPP fabrication.