Single Molecular Nanopores as a Label-Free Method for Homogeneous Conformation Investigation and Anti-Interference Molecular Analysis

In this paper, we propose a reciprocal strategy that, on the one hand, explores the ability of solid-state nanopores in a homogeneous highfidelity characterization of nucleic acid assembly and, on the other hand, the formed nucleic acid assembly with a large size serves as an amplifier to provide a highly distinguished and anti-interference signal for molecular sensing. Four hairpin hybridization chain reaction (HCR) with G-rich tail tags is taken as the proof-of-concept demonstration. G-rich tail tags are commonly used to form Gquadruplex signal probes on the side chain of HCR duplex concatemers. When such G-tailed HCR concatemers translocate the nanopore, abnormal, much higher nanopore signals over normal duplexes can be observed. Combined with atomic force microscopy, we reveal the G-rich tail may easily induce the intermolecular interaction between HCR concatemers to form branched assembly structure (BAS). To the best of our knowledge, this is the first evidence for the formation BAS of the G tailed HCR concatemers in a homogeneous solution. Systematic nanopore measurements further suggest the formation of these BASs is closely related to the types of salt ions, the amount of G, the concentration of substrate hairpins, the reaction time, and so forth. Under optimized conditions, these BASs can be grown to just the right size without being too large to block the pores, while producing a current 14 times that of conventional double-stranded chains. Here, these very abnormal large current blockages have, in turn, been taken as an anti-interference signal indicator for small targets in order to defend the high noises resulting from co-existing big species (e.g., enzymes or other long double-stranded DNA).

Automated summary

In this paper, a reciprocal strategy is proposed that utilizes solid-state nanopores for precise characterization of nucleic acid assembly and utilizes the formed assembly as an amplifier for molecular sensing with highly distinguished and anti-interference signal. The formation of branched assembly structures (BAS) of G-tailed hairpin hybridization chain reaction (HCR) concatemers in a homogeneous solution is demonstrated. These BASs can be controlled to the optimal size to avoid pore blockage and produce a current 14 times higher than conventional double-stranded chains, which serve as an anti-interference signal for small targets.