Figure 1.

(a) Schematic diagram of a dsDNA captured in between two nanopores drilled through an infinitely extended material with thickness $h_{\mathit{pore}}$ and at a separation distance $d_{\mathit{LR}}$. External bias forces ${\overrightarrow{f}}_L$ and ${\overrightarrow{f}}_R$ are applied to the monomers in the left and right nanopore respectively. The colored beads are tags attached to the nucleotides and have different mass and solvent friction different from the rest of the monomers. Keeping the tug of war force at a fixed value, the force ${\overrightarrow{f}}_L$ and ${\overrightarrow{f}}_R$ are applied and varied so that DNA in between the pore has a bias $\mathrm{\Delta }{\overrightarrow{f}}_{\mathit{LR}}={\overrightarrow{f}}_L-{\overrightarrow{f}}_R$ to floss it from one pore to the other. (b) Positions of the protein tags along the dsDNA. Figures (c)–(f) show the translocation of the tags from $L\to R$ direction during scanning. The progressive uncoiling of the dsDNA contour length at the cis side and recoiling at the trans side due to the tension propagation (as observed from the simulation trajectories and the movies) are important elements to be considered to calculate the barcodes accurately (Supplementary Fig. S2). (g) Demonstration of flossing the DNA keeping it captured in the double nanopore system. The configuration shows a translocation taking place from $R\to L$ direction so that $\mathrm{\Delta }{\overrightarrow{f}}_{\mathit{LR}}>0$ and the last tag is on the right chamber. (h) Shows a snapshot a while later when the last tag has completed the translocation through both the pores, at which point the differential voltage is reversed so that $\mathrm{\Delta }{\overrightarrow{f}}_{\mathit{RL}}>0$ and the translocation proceeds in the $L\to R$ direction. (i) Dwell time of ${\mathbf{T}}_{\mathbf{7}}$ is calculated by recording the time difference between arrival $t_{1i}^{L\to R}(7)$ and exiting time $t_{1f}^{L\to R}(7)$ within the left nanopore thickness for $L\to R$ translocation (see Eq. 1). (j) Illustration depicts the time of flight (tof) of ${\mathbf{T}}_{\mathbf{7}}$ is measured as the time taken to reach to right pore from left pore for $L\to R$ motion. (k) Demonstration of calculation of tag time delay $\mathrm{\Delta }{(\tau )}_{87}^{L\to R}=t_{\mathit{iR}}^{L\to R}(7)-t_{\mathit{iR}}^{L\to R}(8)$ for tags $T_7$ and $T_8$ at the right pore. The similar quantity for $R\to L$ translocation $\mathrm{\Delta }{(\tau )}_{78}^{R\to L}=t_{\mathit{iL}}^{R\to L}(8)-t_{\mathit{iL}}^{R\to L}(7)\ne \mathrm{\Delta }{(\tau )}_{87}^{L\to R}$ as of the asymmetric tag positions along the chain. Figure (c)–(h) are generated using VMD²⁶. Please also refer to the movie in the Supplemantary Information.