Detection and Separation of DNA and Silver Nanoparticles Using a Solid-State Nanopore

Abstract

Nanopore sensors, a new generation of single-molecule sensors, are increasingly used to detect and analyze various analytes and have great potential for rapid gene sequencing. However, there are still some problems in the preparation of small diameter nanopores, such as imprecise pore size and porous defects, while the detection accuracy of large-diameter nanopores is relatively low. Therefore, how to achieve more precise detection of large diameter nanopore sensors is an urgent problem to be studied. Here, SiN nanopore sensors were used to detect DNA molecules and silver nanoparticles (NPs) separately and in combination. The experimental results show that large-size solid-state nanopore sensors can identify and discriminate between DNA molecules, NPs, and NP-bound DNA molecules clearly according to resistive pulses. In addition, the detection mechanism of using NPs to assist in identifying target DNA molecules in this study is different from previous reports. We find that silver NPs can simultaneously bind to multiple probes and target DNA molecules and generate a larger blocking current than free DNA molecules when passing through the nanopore. In conclusion, our research indicates that large-sized nanopores can distinguish the translocation events, thereby identifying the presence of the target DNA molecules in the sample. This nanopore-sensing platform can produce rapid and accurate nucleic acid detection. Its application in medical diagnosis, gene therapy, virus identification, and many other fields is highly significant.

Figure 1

(A) SEM image of a SiN nanopore with a diameter of 45 nm; (B) SEM image of NPs with a diameter of about 20 nm; (C) scheme of a nanopore sensor detecting a DNA molecule translocating through the nanopore.

Figure 2

(A) Ionic current diagram for detection of NPs; (B) scatter diagram of the ionic current through nanopores; (C) amplitude distribution of the current blockade during the sample translocation through the nanopore; (D) dwell time distribution of the current histogram of the current blockade during the sample translocation through the nanopore.

Figure 3

NP translocation events through the nanopore. (A) Scatter diagram of ionic current in the bias voltage range of 100–400 mV; (B) histograms of dwell time under different bias voltages; and (C) amplitude distribution histogram of NP samples under different bias voltages. (D) Mean amplitude of ionic pulses.

Figure 4

(A) SEM image of SiN nanopores with a diameter of 30 nm; (B) ionic current trace for detection of DNA; (C) ionic current trace for detection of NPs; and (D) ionic current trace for detection of NPs and DNA mixed samples.

Figure 5

(A–C) DNA translocation through the nanopore. (A) Scatter diagram of ionic current; (B) amplitude distribution histogram of ionic current; (C) histogram of translocation time distribution; (D–F) mixed samples of NPs and DNA translocation through the nanopore. D. Scatter diagram of ionic current; E. amplitude distribution histogram of ionic current; F. histogram of translocation time distribution

Figure 6

Scatter diagram of translocation ionic current of DNA-particle conjugated samples and free DNA molecule samples detected by the nanopore sensor.