Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore.

Precise identification and quantification of amino acids is crucial for many biological applications. Here we report a copper(II)-functionalized Mycobacterium smegmatis porin A (MspA) nanopore with the N91H substitution, which enables direct identification of all 20 proteinogenic amino acids when combined with a machine-learning algorithm. The validation accuracy reaches 99.1%, with 30.9% signal recovery. The feasibility of ultrasensitive quantification of amino acids was also demonstrated at the nanomolar range. Furthermore, the capability of this system for real-time analyses of two representative post-translational modifications (PTMs), one unnatural amino acid and ten synthetic peptides using exopeptidases, including clinically relevant peptides associated with Alzheimer's disease and cancer neoantigens, was demonstrated. Notably, our strategy successfully distinguishes peptides with only one amino acid difference from the hydrolysate and provides the possibility to infer the peptide sequence.

Recent progress of biosensors for the detection of lung cancer markers.

Lung cancer is one of the most common cancers worldwide and the leading cause of death. Early screening of lung cancer is exceptionally essential for later treatment. Abnormal lung cancer tumor markers are validated to assess their diagnostic utility in non-small cell lung cancer (NSCLC) patients. Therefore, tumor markers can be identified in the early stage of lung cancer through biosensor technology and timely diagnosis. This review discusses cutting-edge methods for detecting various types of lung cancer tumor markers using multiple biosensors. The biosensors working at the molecular level are mainly introduced, which can be divided into three categories according to the types of markers: DNA biosensors, RNA biosensors, and protein biosensors. This review focuses on critical electrochemical methods such as electrochemical impedance spectroscopy (EIS), field-effect transistors (FET), cyclic voltammetry (CV), necessary optical sensors such as surface enhancement Raman spectroscopy (SERS), surface-plasmon resonance (SPR), fluorescence methods, and some novel sensing platforms such as biological nanopore and solid-state nanopore sensors and these sensors detect lung cancer tumor markers, such as microRNA (miRNA), DNA mutations (EGFR, KRAS and p53), DNA methylation, circulating tumor DNA (ctDNA), cytokeratin fragment 21-1 (CYFRA21-1), carcinoembryonic antigen (CEA), matrix metallopeptidase 9 (MMP-9), and vascular endothelial growth factor (VEGF). The advantages and disadvantages of different methods are summarized and prospected on this basis, which provides important insights for developing pioneering optoelectronic biosensors for the early diagnosis of lung cancer.

Label-free high-precise nanopore detection of endopeptidase activity of anthrax lethal factor regulated by diverse conditions.

Endopeptidase activity of anthrax lethal factor (aLF) prevents the destroy of anthracis spore intracellularly by host macrophages, meanwhile disables the signaling pathways extracellularly that leads to host lethality. Hence, inhibitory of this activity is expected to be an alternative option to cure anthrax infection. Herein, we fabricated a nanopore platform via transmembrane pore construction in vitro, which allows precise mimics, monitoring of intercellular proteinic transport and enables the quantitative detection of aLF endopeptidase activity towards MAPKK signaling protein at single molecule level. Next, we inhibited the aLF activity via screening approaches of protein-metal ion acquisition and other condition controlment (proton/hydroxide strength, adapted temperature, ionizing irradiation), which were identified by nanopore electrokinetic study. Upon the results, we found that Ca2+, Mg2+, Mn2+, Ni2+ collaborating with Zn2+ promote aLF activity efficiently. In contrary, Cd2+, Co2+, Cu2+ have great inhibitory effect. Result further revealed that, the speed of aLF endopeptidase activity with different ions functions as the nanopore signal frequency in linear manner, which enables evident distinction of those divalent ions using this proteinase assay. We also found the higher strength of the proton or hydroxide, the higher the inhibitory to aLF activity. Besides, adapted temperature and γ-ray also play integral roles in inhibiting this activity. Our results lay experimental basis for accurate detection of aLF activity, meanwhile provide new direction to screening novel stimuli-responsive inhibitors specific to aLF.

DNA nanostructure-assisted detection of carcinoembryonic antigen with a solid-state nanopore.

In this paper, a novel detection technique for tumor marker carcinoembryonic antigen (CEA) has been developed by using a solid-state nanopore as a tool. The system utilizes the specific affinity between aptamer-modified magnetic Fe3O4 and CEA, rather than directly detecting the translocation of CEA through the nanopore. The aptamer-modified magnetic Fe3O4 was hybridized with tetrahedral DNA nanostructures (TDNs), and TDNs were released after CEA was added. We investigate the translocation behavior of individual TDNs through solid-state nanopores. The frequency of the blockage signals for TDNs is recorded for indirect detection of CEA. We realized the detection of CEA with a concentration as low as 0.1 nM and proved the specificity of the interaction between the aptamer. In addition, our designed nanopore sensing strategy can detect CEA in real samples.

Highly sensitive α-hemolysin nanopore detection of MUC1 based on 3D DNA walker.

Mucin 1(MUC1) is an effective marker of breast cancer, so it is of great significance to develop a simple, sensitive and highly selective MUC1 detection sensor. Herein, we constructed a label-free nanopore biosensor for rapid and highly sensitive detection of MUC1. The presence of MUC1 triggered the modification of the DNAzyme walking chain on the surface of Fe3O4 nanoparticles and separation from the aptamer. In the presence of Zn2+, DNAzyme catalyzed hydrolytic cleavage of the hairpin substrate at the scissile rA. The DNAzyme was divided into two fragments and ssDNA was released. ssDNA products from the hairpin substrate can generate a current blocking signal during α-hemolysin nanopore testing. The frequency of signature events showed a linear response toward the concentration of MUC1 in the range of 0.01 nM-100 nM. The sensing system also exhibited high selectivity against other protein and can be used for the detection of real sample.