The temporal resolution and single-molecule manipulation of a solid-state nanopore by pressure and voltage

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. In a previous publication, we discovered a hairpin unraveling mechanism, namely, the pulley effect, in a pressure-driven translocation system. In this paper, we further investigate the pulley effect in the presence of pressure-driven fluid flow and an opposing force provided by an electrostatic field as an approach to increase single-file capture probability. A hydrodynamic flow is used to move the polymer forward, and two oppositely charged electrostatic square loops are used to create an opposing force. By optimizing the balance between forces, we show that the single-file capture can be amplified from about 50% to almost 95%. The force location, force strength, and flow rate are used as the optimizing variables.

Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes

Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.

DNA Coil Dynamics and Hydrodynamic Gating of Pressure-Biased Nanopores

Nanopores are ideally suited for the analysis of long DNA fragments including chromosomal DNA and synthetic DNA with applications in genome sequencing and DNA data storage, respectively. Hydrodynamic fluid flow has been shown to slow down DNA transit time within the pore, however other influences of hydrodynamic forces have yet to be explored. In this report, a broad analysis of pressure-biased nanopores and the impact of hydrodynamics on DNA transit time, capture rate, current blockade depth, and DNA folding are conducted. Using a 10 nm pore, it is shown that hydrodynamic flow inhibits the early stages of linearization of DNA and produces predominately folded events which are initiated by folded DNA (2-strands) entering the pore. Furthermore, utilizing larger pores (30 nm) leads to unique DNA gating behavior in which DNA events can be switched on and off with the application of pressure. A computational model, based on combining electrophoretic drift velocities with fluid velocities, accurately predicts the pore size required to observe DNA gating. Hydrodynamic fluid flow generated by a pressure bias, or potentially more generally by other mechanisms like electroosmotic flow, is shown to have significant effects on DNA sensing and can be useful for DNA sensing technologies.

Ionic current magnetic fields in 3D finite-length nanopores and nanoslits

Deoxyribonucleic acid (DNA) encodes all genetic information, and in genetic disorders, DNA sequencing is used as an effective diagnosis. Nanopore/slit is one of the recent and successful tools for DNA sequencing. Passage of DNA along the pores creates non-uniform ionic currents which creates non-uniform electric and magnetic fields, accordingly. Sensing the electric field is usually used for sequencing application. We suggest to use the magnetic field induced by pressure-driven ionic currents as a secondary signal. We systematically compared the induced magnetic field of nanopores and nanoslits with equal cross-sectional area. The 3D magnetic field is numerically obtained by solving the Poisson-Nernst-Planck, Ampere, and Navier-Stokes equations. As expected, the maximum value of the maximum magnetic flux occurs near the wall and inside the channel, and increasing the pressure gradient along the pore/slit increases the flowrate and magnetic field, consequently. At a given pressure difference across the pore/slit, nanopores are better than nanoslits in sensing the magnetic flux. For example, by applying 2 MPa across the pore/slit, the maximum magnetic flux density for nanopore, nanoslit A R = 1 and nanoslit A R = 5 are 1.10 pT, 1.08 pT and 0.45 pT, accordingly. Also, at a given flowrate across the pore/slit, nanoslits are the better choice. It should be noted the external magnetic fields as small as pico-Tesla are detectable and measurable in voltage/pressure driven electrokinetic flow slits.

Graphical abstract

Wetting of nanopores probed with pressure

Nanopores are both a tool to study single-molecule biophysics and nanoscale ion transport, but also a promising material for desalination or osmotic power generation. Understanding the physics underlying ion transport through nano-sized pores allows better design of porous membrane materials. Material surfaces can present hydrophobicity, a property which can make them prone to formation of surface nanobubbles. Nanobubbles can influence the electrical transport properties of such devices. We demonstrate an approach which uses hydraulic pressure to probe the electrical transport properties of solid state nanopores. We show how pressure can be used to wet pores, and how it allows control over bubbles or other contaminants in the nanometer scale range normally unachievable using only an electrical driving force. Molybdenum disulfide is then used as a typical example of a 2D material on which we demonstrate wetting and bubble induced nonlinear and linear conductance in the regimes typically used with these experiments. We show that by using pressure one can identify and evade wetting artifacts.