Bioinformatics and Biomedical Engineering

Newer methodologies that are quick, label-free, reliable, and low-cost for DNA sequencing and identification are currently being explored. High frequency based-scattering parameters provide a reliable measurement platform and technique to characterize DNA bases. Using a modeling approach, this work investigates the utilization of high frequency-selective structure coupled with nanopore technology for nucleotide identification and sequencing. The model envisions a coplanar waveguide structure harboring a small hole with an internal diameter of the order of several nanometers to demonstrate the potential use of high frequency to identify and sequence DNA. When DNA molecule enters the pore, it should cause disturbance in the electromagnetic field. This disturbance should result in a shift in the resonance frequency and its corresponding characteristics, thus enabling nucleotide identification. The frequency response of four different single DNA strands composed exclusively of either A, C, G or T were measured and characterized to extract the corresponding dielectric constants and their corresponding base paired strands. These dielectric constant values were then used to model the presence of the corresponding DNA molecules in the nanopore. The conducted simulations revealed distinctions between the single and double-stranded DNA molecules due to their different and distinct electrical properties.