DNA sequencing with stacked nanopores and exonuclease: a simulation-based analysis

Experiments (Clarke et al., Nat. Nanotech., 2009, 4, 265-270) have shown that DNA could be sequenced using a nanopore-based electrolytic cell in which an exonuclease enzyme in the cis chamber cleaves the leading base of a strand of DNA. The base is identified (with a reported accuracy that exceeds 99%) by the level of the current blockade it causes in the pore; a biological adapter inside slows down the base to lower the detection bandwidth required. This approach, which has been mathematically modeled, analyzed, and simulated (Reiner et al., J. Chem. Phys., 2012, 137, 214903; Brady and Reiner, ibid., 2015, 143, 074904), is error-prone because bases may be lost to diffusion or enter the pore out of order. Here a modified cell with three stacked nanopores (UNP, MNP, and DNP) and the enzyme attached to the trans side of UNP is proposed. Translocation of a base is simulated with the random walk of a dimensionless particle; the results show that bases translocate through MNP and DNP in sequence order without loss. If this holds in practice then with a suitably designed adapter and compatible enzyme turnover rates base calling accuracy would be limited only by the accuracy of base discrimination. Potential implementation issues are discussed.