(250h) Diffusion and Mobility of ssDNA Confined in a Nanopore Under a Ratcheting Force from an Enzyme

The idea of DNA sequencing based on single-file translocation of the DNA through nanopores under the action of electric fields has received much attention over the past two decades due to the societal need for high speed and high-throughput sequencing. However, interrogating individual bases as they traverse through the pore with the required signal to noise ratio has been a major problem, as the typical speeds are too high. Recently, the use of phi29 polymerase in conjunction with a protein pore (alpha-hemolysin) in the presence of an electric field has been shown to slow down the polymer translocation speed enabling reasonably successful base-calling. We have evaluated the signal-to-noise ratio of such a construct by performing Langevin Dynamics simulations on models of this construct. By monitoring the contributions of the conformational fluctuations of the polymer, we have computed the diffusional behavior of monomers of the chain under varying speeds of the polymerase activity and externally imposed voltage gradients. The fractal dimensions of polymer dynamics at different stages of translocation are also obtained. Our simulations show that even if the translocation speed is slowed considerably by using the polymerase-nanopore construct, the conformational fluctuations of ssDNA inside the pore are always present at high levels resulting in high levels of noise in the detection signal. We report a strategy to reduce the noise by specifically binding the wiggling tail of the polymer outside the pore with specific proteins in order to suppress the conformational fluctuations inside the pore.