Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control

Coupled nanopores for single-molecule detection

Rapid sensing of molecules is increasingly important in many studies and applications, such as DNA sequencing and protein identification. Here, beyond atomically thin 2D nanopores, we conceptualize, simulate and experimentally demonstrate coupled, guiding and reusable bilayer nanopore platforms, enabling advanced ultrafast detection of unmodified molecules. The bottom layer can collimate and decelerate the molecule before it enters the sensing zone, and the top 2D pore (~2 nm) enables position sensing. We varied the number of pores in the bottom layer from one to nine while fixing one 2D pore in the top layer. When the number of pores in the bottom layer is reduced to one, sensing is performed by both layers, and distinct T- and W-shaped translocation signals indicate the precise position of molecules and are sensitive to fragment lengths. This is uniquely enabled by microsecond resolution capabilities and precision nanofabrication. Coupled nanopores represent configurable multifunctional systems with inter- and intralayer structures for improved electromechanical control and prolonged dwell times in a 2D sensing zone.

Free-energy landscape of a polymer in the presence of two nanofluidic entropic traps

Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the underlying free-energy landscape. In this study we use computer simulations to explicitly calculate the free energy and test the approximations employed in such analytical models. Specifically, Monte Carlo simulations were used to study a polymer confined to complex geometry consisting of a nanoslit with two square nanopits embedded in one of the surfaces. The two-dimensional weighted histogram analysis method is used to calculate the free energy, F, as a function of the sum (λ_{1}) and the difference (λ_{2}) of the length of the polymer contour contained in the two nanopits. We find the variation of the free-energy function with respect to confinement dimensions to be comparable to the analytical predictions that employ a simplistic theoretical model. However, there are some noteworthy quantitative discrepancies, particularly between the predicted and observed variation of F with respect to λ_{1}. Our study provides a useful lesson on the limitations of using simplistic analytical expressions for polymer free-energy landscapes to interpret results for experiments of DNA confined to a complex geometry and points to the value of carrying out accurate numerical calculations of the free energy instead.

Ten Thousand Recaptures of a Single DNA Molecule in a Nanopore and Variance Reduction of Translocation Characteristics

Nanopores have emerged as highly sensitive biosensors operating at the single-molecule level. However, the majority of nanopore experiments still rely on averaging signals from multiple molecules, introducing systematic errors. To overcome this limitation and obtain accurate information from a single molecule, the molecular ping-pong methodology provides a precise approach involving repeated captures of a single molecule. In this study, we have enhanced the molecular ping-pong technique by incorporating a customized electronic system and control algorithm, resulting in a recapture number exceeding 10,000. During the ping-pong process, we observed a significant reduction in the variance of translocation characteristics, providing fresh insights into single-molecule translocation dynamics. An inhomogeneous translocation velocity of folded DNA has been revealed, illustrating a strong interaction between the molecule and the solid-state nanopore. The results not only promise heightened experimental efficiency with reduced sample volume but also increase the precision in statistical analysis of translocation events, marking a significant stride toward authentic single-molecule nanopore sensing.

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.

DNA Barcodes Using a Dual Nanopore Device

We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.

DNA Carrier-Assisted Molecular Ping-Pong in an Asymmetric Nanopore

Nanopore analysis relies on ensemble averaging of translocation signals obtained from numerous molecules, requiring a relatively high sample concentration and a long turnaround time from the sample to results. The recapture and subsequent re-reading of the same molecule is a promising alternative that enriches the signal information from a single molecule. Here, we describe how an asymmetric nanopore improves molecular ping-pong by promoting the recapture of the molecule in the trans reservoir. We also demonstrate that the molecular recapture could be improved by linking the target molecule to a long DNA carrier to reduce the diffusion, thereby achieving over 100 recapture events. Using this ping-pong methodology, we demonstrate its use in accurately resolving nanostructure motifs along a DNA scaffold through repeated detection. Our method offers novel insights into the control of DNA polymer dynamics within nanopore confinement and opens avenues for the development of a high-fidelity DNA detection platform.

Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device

We report Brownian dynamics simulation results with the specific goal to identify key parameters controlling the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. First, we validate the simulation scheme in silico by reproducing and explaining the physical origin of the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on a 48 kbp long dsDNA at the left and the right pore. We study the effect of the electric field inside and beyond the pores, critical to discriminate the protein tags based on their effective charges and masses revealed through a generic power-law dependence of the average dwell time at each pore. The simulation protocols monitor piecewise dynamics at a sub-nanometer length scale and explain the disparate velocity using the concepts of nonequilibrium tension propagation theory. We further justify the model and the chosen simulation parameters by calculating the Péclet number which is in close agreement with the experiment. We demonstrate that our carefully chosen simulation strategies can serve as a powerful tool to discriminate different types of neutral and charged tags of different origins on a dsDNA construct in terms of their physical characteristics and can provide insights to increase both the efficiency and accuracy of an experimental dual-nanopore setup.