Voltage-activated complexation of α-synuclein with three diverse β-barrel channels: VDAC, MspA, and α-hemolysin

DNAzyme-assisted the detection of rps27l mRNA in protein nanopores

Quantifying mRNA is crucial for elucidating the physiological condition of organisms in life science research and clinical diagnostics. Recently, nanopore technology has been demonstrated as a versatile tool with a myriad of applications and successful implementations for genomic analyte identification. However, its application in mRNA quantification encounters challenges such as the presence of numerous background species, low expression levels, and complex mRNA structures. Herein, we propose the implementation of a DNAzyme-assisted approach for rp27l mRNA quantification in MspA protein nanopores. The strategy involves converting the quantification of mRNA through a DNAzyme reaction, where the sequence of GR-5 DNAzyme is integrated into Probe 2 (P2). The sandwich structure (P1-T-P2) is constructed between the target molecules and two types of probes, enabling the identification of target molecules and the retention of the enzyme strand in magnetic fields. As a result, GR-5 DNAzyme not only effectively hydrolyzes the corresponding substrates to yield external probes for subsequent nanopore analysis but also functions as an ingenious molecular amplification method by persistently digesting excess substrates to produce abundant external probes. This sensor acquires the amplification capability and attains a high sensitivity with a detection limit of 40 pM within 15-min measurements, improving the sensitivity of protein nanopores for nucleic acid detection. Thus, the proposed DNAzyme-based protein nanopore sensor for rp27l mRNA quantification demonstrates remarkable advantages in its label-free, rapid, and sensitive nature, which promotes the performance of protein nanopores in genomic analyte detection. Moreover, this sensor may open a novel approach for mRNA quantification, significantly impacting disease diagnosis, customized treatment, and metabolic studies.

Counter-Intuitive Features of Particle Dynamics in Nanopores

Using the framework of a continuous diffusion model based on the Smoluchowski equation, we analyze particle dynamics in the confinement of a transmembrane nanopore. We briefly review existing analytical results to highlight consequences of interactions between the channel nanopore and the translocating particles. These interactions are described within a minimalistic approach by lumping together multiple physical forces acting on the particle in the pore into a one-dimensional potential of mean force. Such radical simplification allows us to obtain transparent analytical results, often in a simple algebraic form. While most of our findings are quite intuitive, some of them may seem unexpected and even surprising at first glance. The focus is on five examples: (i) attractive interactions between the particles and the nanopore create a potential well and thus cause the particles to spend more time in the pore but, nevertheless, increase their net flux; (ii) if the potential well-describing particle-pore interaction occupies only a part of the pore length, the mean translocation time is a non-monotonic function of the well length, first increasing and then decreasing with the length; (iii) when a rectangular potential well occupies the entire nanopore, the mean particle residence time in the pore is independent of the particle diffusivity inside the pore and depends only on its diffusivity in the bulk; (iv) although in the presence of a potential bias applied to the nanopore the "downhill" particle flux is higher than the "uphill" one, the mean translocation times and their distributions are identical, i.e., independent of the translocation direction; and (v) fast spontaneous gating affects nanopore selectivity when its characteristic time is comparable to that of the particle transport through the pore.

Blocker Effect on Diffusion Resistance of a Membrane Channel: Dependence on the Blocker Geometry

Being motivated by recent progress in nanopore sensing, we develop a theory of the effect of large analytes, or blockers, trapped within the nanopore confines, on diffusion flow of small solutes. The focus is on the nanopore diffusion resistance which is the ratio of the solute concentration difference in the reservoirs connected by the nanopore to the solute flux driven by this difference. Analytical expressions for the diffusion resistance are derived for a cylindrically symmetric blocker whose axis coincides with the axis of a cylindrical nanopore in two limiting cases where the blocker radius changes either smoothly or abruptly. Comparison of our theoretical predictions with the results obtained from Brownian dynamics simulations shows good agreement between the two.