Experimental Observations of DNA Vertex Pinning: Effect of Adsorbed Polymer Type and Electric Field Reversal

Trapping, linearization, and imaging of single-molecule DNA are critical for fundamental biophysical studies and genomic analysis. DNA vertex pinning is a promising technique for this purpose, offering operational simplicity and high throughput. This method adsorbs neutral polymers onto a microchannel surface and uses applied electric fields to drive DNA to interact with and become trapped by the neutral polymer. Quantitative studies are required to characterize its dynamics over a broader range of conditions. Investigated are the impact of parameters such as electric field strength, neutral polymer type, polymer concentration, and the behavior under reversals of the electric field direction. Identified are parameter sets that enable stable and effective pinning. Hypotheses are proposed to explain trends in saturation with electric field strength and behavior under electric field reversal. Furthermore, data show that DNA vertex pinning is possible under pressure-driven flow in the absence of an electric field. This work helps establish a foundation for the design and operation of microfluidic devices that achieve DNA vertex pinning and offers experimental evidence that may be useful in the study of underlying physical mechanisms.