Ratcheting charged polymers through symmetric nanopores using pulsed fields: Designing a low pass filter for concentrating DNA

Abstract

We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation and pulsed fields. Using Langevin Dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses can significantly enhance the device efficiency. The process itself can be performed with many pores in parallel, and it should be possible to integrate it directly into nanopore sequencing devices, increasing its potential utility.