Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection

适体 纳米孔 氨基酸 苯丙氨酸 化学 碱基 分子识别 组合化学 生物分子 酪氨酸 纳米技术 生物物理学 分子 材料科学 生物化学 DNA 生物 有机化学 遗传学
作者
Tilman Schlotter,Tom Kloter,Julian Hengsteler,Kyung-Ae Yang,Lijian Zhan,Sujeni Ragavan,Haiying Hu,Xinyu Zhang,Jens Duru,János Vörös,Tomaso Zambelli,Nako Nakatsuka
出处
期刊:ACS Nano [American Chemical Society]
卷期号:18 (8): 6286-6297 被引量:2
标识
DOI:10.1021/acsnano.3c10679
摘要

Single-molecule proteomics based on nanopore technology has made significant advances in recent years. However, to achieve nanopore sensing with single amino acid resolution, several bottlenecks must be tackled: controlling nanopore sizes with nanoscale precision and slowing molecular translocation events. Herein, we address these challenges by integrating amino acid-specific DNA aptamers into interface nanopores with dynamically tunable pore sizes. A phenylalanine aptamer was used as a proof-of-concept: aptamer recognition of phenylalanine moieties led to the retention of specific peptides, slowing translocation speeds. Importantly, while phenylalanine aptamers were isolated against the free amino acid, the aptamers were determined to recognize the combination of the benzyl or phenyl and the carbonyl group in the peptide backbone, enabling binding to specific phenylalanine-containing peptides. We decoupled specific binding between aptamers and phenylalanine-containing peptides from nonspecific interactions (e.g., electrostatics and hydrophobic interactions) using optical waveguide lightmode spectroscopy. Aptamer-modified interface nanopores differentiated peptides containing phenylalanine vs. control peptides with structurally similar amino acids (i.e., tyrosine and tryptophan). When the duration of aptamer–target interactions inside the nanopore were prolonged by lowering the applied voltage, discrete ionic current levels with repetitive motifs were observed. Such reoccurring signatures in the measured signal suggest that the proposed method has the possibility to resolve amino acid-specific aptamer recognition, a step toward single-molecule proteomics.
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