Bin Meng

Nanopore sequencing for full-length proteins is daunting due to inaccuracy of fingerprinting amino acids with ionic current and lack of theoretical models. Here, we demonstrate that nanopores drilled in 5 nm-thick membranes with constriction diameter <1 nm, i.e., subnanopores, can site-specifically read the primary structure of amyloid-β (Aβ) isoforms after 50-fold coverage. Molecular dynamics simulations reveal that charged side chains near the constriction swing and modulate the volume exclusion of neighboring residues, resulting in a sequence context-dependent signal altered between translocation orientations. Orientation of individual label-free molecules is inferred by clustering, which yields high-fidelity empirical consensus that strongly correlates with computational trajectories (PCC = 0.78 ± 0.03). A homemade self-supervised learning method categorizes Aβ42 and Aβ40 at the single-molecule level (AUC = 0.88 ± 0.02) and predicts the mole fraction in agreement with actual ratios. Solid-state subnanopores offer a straightforward strategy for proteoform single-molecule classification and sequence extraction in mixtures.

Proteoforms are proteins derived from highly related genes or post translational modifications (PTMs) of the same protein. They share extremely similar primary structures but have varying functions. Unfortunately, protein de novo sequencing including specific PTM/mutation detection is still challenging. Herein, a nanopore‐based technique is reported to resolve the amino acid order of amyloid‐β (Aβ_1‐42) with site specificity. Subnanopores are sputtered in 5 nm‐thick inorganic membranes with a sensing depth of 0.66 nm inferred by finite element analysis. Denatured molecules at 0.45 ng mL⁻¹ translocate through subnanopores while the current traces are sampled at 500 kHz with rms noise 1‐42 at single residue resolution, with Pearson Correlation Coefficients (PCCs) of 0.81 ± 0.03 and 0.92 ± 0.03 before and after dynamic time warping (DTW). A scrambled version of Aβ_1‐42 is tested for validation purposes. Deep learning classification reveals that different polypeptides generate distinct translocation fluctuating patterns, but variations become imperceptible for the same species measured across nanopores (Area Under the Curve, AUC 0.93 ± 0.05 vs 0.64 ± 0.12). Lastly, important PTMs and mutations are site‐specifically located along the primary structure, implying new potential clinical applications.

This paper reports a handy technical scheme to decorate atomic force microscopy (AFM) tips toward tip-enhanced Raman spectroscopy (TERS) applications. The major attraction of these homemade tips lies in that silver decoration can be confined at the apex of commercial tips by the means of an AFM-controlled electrochemical reaction. The reduction of Ag⁺ occurs in a highly sealed environment to secure the metal coating efficiency. Key factors include silver nitrate solution to provide Ag⁺, ambient relative humidity and temperature in a humidity cell, electric potential bias, and tip-surface distance. Subsequently, these silver-coated tips are evaluated for TERS measurement of carbon nanotubes (CNTs) so that both morphological and chemical characteristics of CNTs are concurrently obtained. The Raman spectra reveal that our plasmonic tip competently possesses an ∼30-fold local field signal increase and the corresponding TERS image laterally resolves at the single-pixel level.