Dynamics of DNA Clogging in Hafnium Oxide Nanopores

Enhancing RBP4 protein detection in clinical urine samples with solid-state nanopores through optimized sandwich immunoassay techniques

Nanopore technology is a promising single-molecule sensing platform that can identify substances through the precise monitoring of changes in ion currents. However, protein detection in clinical samples using solid-state nanopores remains challenging due to their heterogeneously charged spherical structure, which results in signals with extremely low signal-to-noise ratios (SNR) and low capture rates that are difficult to analyze. In this study, we employed a double-antibody sandwich technique to specifically capture and amplify the target antigen, which significantly improves the SNR and effectively distinguishes the target signal from background interference. Key factors including buffer composition, voltage, antibody concentration, and pore dimensions were systematically optimized to further improve capture efficiency. The optimized approach enabled precise and reliable detection of retinol-binding protein 4 (RBP4) with an excellent linear response within the range of 55 fM to 5.5 pM. Moreover, our method facilitates quantitative detection of RBP4 in clinical urine samples within 40 min, and achieves 100% accuracy in distinguishing between 11 urine samples from chronic kidney disease (CKD) patients and healthy donors, highlighting its robustness and specificity. Our research not only paves a new pathway for efficient RBP4 detection, but also provides valuable insights into the application of nanopore technology for the clinical diagnosis of protein biomarkers.

Addressing Buffer, Size, and Clogging Challenges in LAMP-Coupled Solid-State Nanopores for Point-of-Care Testing

Loop-mediated isothermal amplification (LAMP) is a promising method for point-of-care nucleic acid testing due to its simplicity, rapidity, and high sensitivity. Coupling LAMP with solid-state nanopores enables label-free, single-molecule sensing, enhancing diagnostic accuracy. However, conventional LAMP-coupled nanopore protocols require high-salt buffers (>1 M) to improve signal strength and translocation frequency, complicating workflows and increasing contamination risks. In native LAMP buffers (50 mM KCl), electroosmotic flow (EOF) hinders amplicon transport in sub-10 nm pores, while large amplicons increase the risk of clogging. These challenges limit event rates, data throughput, and device reliability. To address these limitations, we developed a glass nanopore device optimized for direct sensing of amplicons in native buffers, featuring integrated declogging capabilities. Our results revealed that 200 nm pores provided the best balance between minimizing EOF interference and maintaining strong signal strength, achieving the highest event rates. Smaller pores (<100 nm) had low event rates due to EOF effects, while larger pores (>1 μm) showed weakened signal strength. We discovered that clogging in low-salt conditions differs from high-salt environments, with physical vibration effectively resolving clogging in low-salt settings. This led to the integration of an automated vibration motor, extending nanopore lifespan and ensuring continuous data acquisition. Our clog-free, native-buffer sensing platform demonstrated a sensitivity of 0.12 parasite/μL using Plasmodium vivax (P. vivax) as a model organism, exceeding the threshold for detecting asymptomatic infections. These advancements highlight the potential of our nanopore device for rapid, reliable, and user-friendly diagnostics for point-of-care testing.

Regulation of Protein Transport in Functionalized PET Nanopores

Facilitated translocation is a critical mechanism for transporting substances in biological systems, where molecular and ionic species move across the biological membrane with the help of specific transmembrane protein ion channels. In this work, we systematically examined protein transport in three poly(ethylene terephthalate) (PET) nanopores modified with different types of surface functions (hydroxyl, phenyl, and amine). We found that the event signature as well as the kinetics and thermodynamics of protein movement in the PET nanopore varied significantly with the change in the surface function in the pore. In addition to the electrophoretic effect, other factors such as diffusion, electro-osmotic effect, ion selectivity of the channel, and affinity strength between the protein species and the surface functional group of the nanopore also play significant roles in the protein transport. Although properly functionalized individual PET nanopores can be used as stochastic elements for rapid protein differentiation and characterization, enhanced resolution and accuracy could be accomplished by employing an array of PET nanopores having different inner surface functional groups to characterize proteins based on their collective responses. Given the important roles proteins play in living organisms and their applications as biomarkers in early disease diagnosis and prognosis, the pattern-recognition solid-state nanopore-sensing strategy for protein detection and characterization developed in this work may find useful applications in various fields.

Ion transport based structural description for in situ synthesized SBA-15 nanochannels in a sub-micropipette

Construction of nanoporous arrays can greatly facilitate their development in the fields of sensing, energy conversion, and nanofluidic devices. It is important to characterize the structure and understand the ion transport behaviour of a nanoporous array, especially those prepared by in situ synthesis, which are difficult to be characterized by conventional methods. Herein, an inorganic and non-crystalline mesoporous silica SBA-15 is selected as a template, where a combination (GP-SBA-15) of a sub-micropipette and SBA-15 is constructed by in situ synthesis, and the multichannel array structure of GP-SBA-15 is illustrated by its ion transport properties from current-voltage responses. Experiments of linear scan voltammetry and chronoamperometry show a rapid accumulation and slow redistribution of ions in the surface-charged nanochannels, and the high/low currents originate from the accumulation/depletion of ions in the channels. The finite element simulation is introduced to calculate the effects of surface charge and pore size on ion rectification and ion concentration distribution. In addition, the short straight channels and long bending channels present in GP-SBA-15 are demonstrated by the voltage-independent resistance pulse signals in the translocation of BSA. This study shows that electrochemical means effectively provide insight into ion transport, achieve structural description and reveal the sensing potential of GP-SBA-15.

Self-Limited Formation of Bowl-Shaped Nanopores for Directional DNA Translocation

Solid-state nanopores of on-demand dimensions and shape can facilitate desired sensor functions. However, reproducible fabrication of arrayed nanopores of predefined dimensions remains challenging despite numerous techniques explored. Here, bowl-shaped nanopores combining properties of ultrathin membrane and tapering geometry are manufactured using a self-limiting process developed on the basis of standard silicon technology. The upper opening of the bowl-nanopores is 60-120 nm in diameter, and the bottom orifice reaches sub-5 nm. Current-voltage characteristics of the fabricated bowl-nanopores display insignificant rectification indicating weak ionic selectivity, in accordance to numerical simulations showing minor differences in electric field and ionic velocity upon the reversal of bias voltages. Simulations reveal, concomitantly, high-momentum electroosmotic flow downward along the concave nanopore sidewall. Collisions between the left and right tributaries over the bottom orifice drive the electroosmotic flow both up into the nanopore and down out of the nanopore through the orifice. The resultant asymmetry in electrophoretic-electroosmotic force is considered the cause responsible for the experimentally observed strong directionality in λ-DNA translocation with larger amplitude, longer duration, and higher frequencies for the downward movements from the upper opening than the upward ones from the orifice. Thus, the resourceful silicon nanofabrication technology is shown to enable nanopore designs toward enriching sensor applications.