DNA sequencing with a nanopore and a sub-nanometer stop-and-go positioning system for incremental base identification

A recent report (doi: 10.26434/chemrxiv-2025-gsw8x) described a proposal for peptide synthesis with a nanopore and a sub-nanometer precision mechanical positioning system. Here a similar device is proposed for sequencing of single-stranded DNA. One end of a homonucleotide header is bound to a fixed surface and the other is attached to the strand; the surface is mounted on a platform in the cis chamber of an electrolytic cell (e-cell). The platform can be moved with a precision of 0.1-0.15 nm; movement times are ~1 μs. The free end of the DNA strand is threaded through the pore into the trans chamber of the e-cell; a voltage across the pore and hydraulic pressure ensure that the header-strand inside cis and the pore remains stretched at all times. Alternatively the trans end also can be tethered to a second platform through a homonucleotide trailer to allow coordinated stretching and moving of the full header-strand-trailer. The blockade current through the pore is measured over a desired period of time (≥ 1 ms); the platform is retracted by 3.5 Å; the process is repeated. With such stop-and-go control the measurement bandwidth can be as low as desired. A pore of length L Å holds M = ⌈L/3.5⌉ bases, the M-th base can be determined from the measured blockade current and the preceding M-1 bases (obtained from the previous M-1 reads). This Markov-like measurement process is analyzed quantitatively and the current precision required for incremental next-base identification is given for biological pores (such as MspA) and synthetic pores (such as Si3N4, which has a considerably higher current capability). A similar structure with piezo-electric sensors has been used earlier to discriminate among three types of homonucleotides (doi: 10.1038/s41598-017-08290-6); the experiences detailed in that report suggest that the method proposed here can be similarly translated into practice. This is a long read single molecule method; it may potentially be used for the detection of some types of post-translational modifications (PTMs), such as phosphorylation, in DNA.