  The potential of a double nanopore system to determine DNA barcodes has been
demonstrated experimentally. By carrying out Brownian dynamics simulation on a
coarse-grained model DNA with protein tag (barcodes) at known locations along
the chain backbone, we demonstrate that due to large variation of velocities of
the chain segments between the tags, it is inevitable to under/overestimate the
genetic lengths from the experimental current blockade and time of flight data.
We demonstrate that it is the tension propagation along the chain's backbone
that governs the motion of the entire chain and is the key element to explain
the non uniformity and disparate velocities of the tags and DNA monomers under
translocation that introduce errors in measurement of the length segments
between protein tags. Using simulation data we further demonstrate that it is
important to consider the dynamics of the entire chain and suggest methods to
accurately decipher barcodes. We introduce and validate an interpolation scheme
using simulation data for a broad distribution of tag separations and suggest
how to implement the scheme experimentally.
