Controlling the velocity of DNA base in nanopores using flossing

One of the challenging problems associated with the ionic current based DNA sequencing methods is the control of DNA base motion inside nanopores. For accurate base calling, the velocity of the DNA base inside the nanopore needs to be slow enough to be detected and the fluctuations associated with its motion needs to be small. We propose a DNA flossing technique for controlling the DNA base motion inside the nanopore and we demonstrate this using Langevin dynamics simulation. In this proposed technique, the single stranded DNA is covalently linked to symmetric flexible polycations at both ends. Such a chain can be captured by the nanopore using high bias. Once captured, the DNA is electrophoretically moved back and forth indefinite number of times. Using square wave alternating voltage the velocity of the DNA base is demonstrated to slow down by an order of magnitude at high frequencies of the alternating voltage. By varying the polycation length, magnitude and frequency of the applied alternating voltage, individual DNA base motion has been monitored while translocating through the nanopore. DNA base dynamics inside the nanopore as a function of these parameters helps us to understand the physics and practicality of flossing technique for genome sequencing applications.