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Free-standing nanocrystalline graphite (NCG) membranes directly grew on SiN x substrates with the aid of the catalyst-free chemical vapor deposition method. A new type of NCG nanopore was formed in the NCG membrane via controlled dielectric breakdown in KCl electrolyte. The electrical properties, especially the ionic conductance of the NCG nanoporewere examined under different physical parameters (pore size, ion strength, and pH condition). Due to their impressive transport properties, we first realized DNA sensing using the NCG nanopores. [Display omitted] • A nanopore was formed in a free-standing nanocrystalline graphite 2D membrane via controlled dielectric breakdown. • Nonlinear but symmetric I–V curves of the NCG nanopore indicate the existence of internal electrostatic potential. • DNA translocation caused stochastic upward current pulses. • The dsDNA translocation speed was slowed down compared to other nanopores. [ABSTRACT FROM AUTHOR]

[Display omitted] • Establishment of a cost-effective nanopore platform for NCL identification at low LOD with trace amount of sample. • Discrimination of single-molecule topologies of DNA/RNA G4 with distinct sequences while closed in sequence length. • Proof of the well-binding properties of NCL with G4 folded from both DNA and RNA. • Recognition of NCL and NCL/G4 complex in human serum. DNA/RNA quadruplexes (G4) are significant secondary structures that exist in human genes, playing essential part in transcription and replication. Nucleolin (NCL) is a ubiquitous protein mainly found in the human nucleus. It is frequently overexpressed in cancer cells and displays a remarkable preference for DNA/RNA G4 binding, playing a crucial role in controlling nucleic acid metabolism and chromatin structure. Additionally, NCL is involved in microRNA (miRNA) biogenesis.This work presents the discrimination of DNA/RNA G4 topologies harboring close sequence length with size-matched nanopore devices. The single-molecule identification of NCL under various parameters was implemented, and a low detection limit of 0.5 nM was achieved, NCL could specifically bind with DNA G4 AS1411 and RNA G4 (rG4) from pre-miRNA 92b and pre-miRNA 149, forming stable complexes that demonstrate distinct nanopore translocation properties. The augmentation of the molar ratio of G4 to NCL induces elevated complex formation. Recognition of both NCL and NCL-G4 complex in human serum is realized. Our work established a precise platform for the differentiation of nucleic acid secondary structure with similar conformation, we also proved the binding behaviors between NCL and DNA/RNA G4, as well as the serum interference test, which is valuable for the investigation of the interactions between proteins and nucleic acids as well as for further understanding the mechanism of the NCL-related diseases processes. [ABSTRACT FROM AUTHOR]

Solid-state nanopores are considered an attractive basis for single-molecule DNA sequencing. At present, one obstacle to be overcome is the improvement of their temporal resolution, with the DNA molecules remaining in the sensing volume of the nanopore for a long period of time. Here, we used a composite system of a concentration gradient of LiCl in solution and a nanofiber mesh to slow the DNA perforation speed. Compared to different alkali metal solutions with the same concentration, LiCl can extend the dwell time to 20 ms, five times longer than NaCl and KCl. Moreover, as the concentration gradient increases, the dwell time can be tuned from dozens of milliseconds to more than 100 ms. When we introduce a nanofiber mesh layer on top of the pore in the asymmetric solution, the DNA molecules get retarded by 162–185 μ s/nt, which is three orders of magnitude slower than the bare nanopore. At the same time, because the molecule absorption region becomes larger at the pore vicinity, the higher molecule capture rate improves the detection efficiency. [ABSTRACT FROM AUTHOR]

[Display omitted] • The system utilizes the specific affinity between aptamer and CEA. • The nanopore detect the DNA instead of directly detecting the translocation of CEA. • We realized the detection of CEA with a concentration as low as 0.1 nM. • The biosensor could be utilized in real serum sample analysis. 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 Fe 3 O 4 and CEA, rather than directly detecting the translocation of CEA through the nanopore. The aptamer-modified magnetic Fe 3 O 4 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. [ABSTRACT FROM AUTHOR]

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 Fe 3 O 4 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. [Display omitted] • MUC1-aptamer and DNAzyme hybridization reaction was used as sensing platform. • 3D DNA walker nanoprobe was used for both MUC1 recognition and signal amplification. • MUC1 was detected indirectly by cutting the DNA fragments. • The α-HL nanopore biosensor could be utilized in real sample analysis. [ABSTRACT FROM AUTHOR]

With the advantages of simple equipment and in-situ preparation of nanopores, the CBD method has been widely concerned by researchers. In this work, a fluorescence platform was set up to directly observe the λ-DNA motions near the CBD prepared different kinds of SiN x nanopores. At first, for the one nanopore film, the λ-DNA post-translocation motion was observed. Then, for the multiple nanopores film, the current modulation phenomena of each nanopore after the DNA clogged the pores was observed. When the distance of asymmetric pores is less than the length of λ-DNA, the larger nanopores are easy to be blocked preferentially by considering the tug-of-war on λ-DNA; when the asymmetric porous distance is larger than the DNA two polymer length, due to the forming a folded structure, the smaller nanopores are preferentially blocked. These results reveal that the clogging phenomena during the DNA translocation analysis for the nanopores are varied, and it should be considered for CBD-prepared nanopores. A fluorescence platform was set up to directly observe the λ-DNA motions near the CBD prepared different kinds of SiNx nanopores and reveals the clogging phenomena during the DNA translocation analysis for the nanopores. [Display omitted] • CBD prepared different kinds of SiNx nanopores. • directly observe the λ-DNA motions near nanopores. • the clogging phenomena during the DNA translocation analysis. [ABSTRACT FROM AUTHOR]