DNA strands attached inside single conical nanopores: ionic pore characteristics and insight into DNA biophysics

Nanochannel-based biosensor for ultrasensitive and label-free detection of thymidine kinase activity

Thymidine Kinase 1 (TK1) is a pivotal enzyme in fundamental biochemistry and molecular diagnosis, but recognition and molecule detection is a challenging task. Here, we constructed a DNA-integrated hybrid nanochannel sensor for TK1 activity and inhibition assay. Single-stranded DNA containing thymidine was used as a substrate to functionalize the nanochannels, restricting the ion current through channels. With kinase, the thymidine at the termini of the substrate DNA is phosphorylated, elevating surface charge density and mitigating the pore-obstruction effect by increasing transmembrane ion current. The kinase-induced distinctness can be accurately monitored by this hybrid nanodevice, which benefits from its high sensitivity to the change of surface charge. The excellent analytical performance in both kinase enzyme activity and inhibition analysis resulted in efficient and selective evaluation in human serum. Furthermore, compared to current approaches, it greatly simplifies and offers a direct method of analysis, making it a promising sensor technology for cancer management as well as the activities of multiple types of nucleic acid kinases.

Structure and Dynamics of dsDNA in Cell-like Environments

Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA's structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.

Protein and DNA Yield Current Enhancements, Slow Translocations, and an Enhanced Signal-to-Noise Ratio under a Salt Imbalance

Nanopores are a promising single-molecule sensing device class that captures molecular-level information through resistive or conductive pulse sensing (RPS and CPS). The latter has not been routinely utilized in the nanopore field despite the benefits it could provide, specifically in detecting subpopulations of a molecule. A systematic study was conducted here to study the CPS-based molecular discrimination and its voltage-dependent characteristics. CPS was observed when the cation movement along both electrical and chemical gradients was favored, which led to an ∼3× improvement in SNR (i.e., signal-to-noise ratio) and an ∼8× increase in translocation time. Interestingly, a reversal of the salt gradient reinstates the more conventional resistive pulses and may help elucidate RPS-CPS transitions. The asymmetric salt conditions greatly enhanced the discrimination of DNA configurations including linear, partially folded, and completely folded DNA states, which could help detect subpopulations in other molecular systems. These findings were then utilized for the detection of a Cas9 mutant, Cas9d10a─a protein with broad utilities in genetic engineering and immunology─bound to DNA target strands and the unbound Cas9d10a + sgRNA complexes, also showing significantly longer event durations (>1 ms) than typically observed for proteins.

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.

Biomimetic Nanochannels: From Fabrication Principles to Theoretical Insights

Biological nanochannels which can regulate ionic transport across cell membranes intelligently play a significant role in physiological functions. Inspired by these nanochannels, numerous artificial nanochannels have been developed during recent years. The exploration of smart solid-state nanochannels can lay a solid foundation, not only for fundamental studies of biological systems but also practical applications in various fields. The basic fabrication principles, functional materials, and diverse applications based on artificial nanochannels are summarized in this review. In addition, theoretical insights into transport mechanisms and structure-function relationships are discussed. Meanwhile, it is believed that improvements will be made via computer-guided strategy in designing more efficient devices with upgrading accuracy. Finally, some remaining challenges and perspectives for developments in both novel conceptions and technology of this inspiring research field are stated.

Multi-resistive pulse sensor microfluidic device

Resistive pulse sensors have been used to characterise everything from whole cells to small molecules. Their integration into microfluidic devices has simplified sample handling whilst increasing throughput. Typically, these devices measure a limited size range, making them prone to blockages in complex sample matrixes. To prolong their life and facilitate their use, samples are often filtered or prepared to match the sample with the sensor diameter. Here, we advance our tuneable flow resistive pulse sensor which utilises additively manufactured parts. The sensor allows parts to be easily changed, washed and cleaned, its simplicity and versatility allow components from existing nanopore fabrication techniques such as glass pipettes to be integrated into a single device. This creates a multi-nanopore sensor that can simultaneously measure particles from 0.1 to 30 μm in diameter. The orientation and controlled fluid flow in the device allow the sensors to be placed in series, whereby smaller particles can be measured in the presence of larger ones without the risk of being blocked. We illustrate the concept of a multi-pore flow resistive pulse sensor, by combining an additively manufactured tuneable sensor, termed sensor 1, with a fixed nanopore sensor, termed sensor 2. Sensor 1 measures particles as small as 10 μm in diameter, whilst sensor 2 can be used to characterise particles as small as 100 nm, depending upon its dimensions. We illustrate the dual pore sensor by measuring 1 and 10 μm particles simultaneously.

Rapid quantification of prion proteins using resistive pulse sensing

Prion diseases are a group of fatal transmissible neurological conditions caused by the change in conformation of intrinsic cellular prion protein (PrP^C). We present a rapid assay using aptamers and resistive pulse sensing, RPS, to extract and quantify PrP^C from complex sample matrices. We functionalise the surface of superparamagnetic beads, SPBs, with a DNA aptamer. First SPB's termed P-beads, are used to pre-concentrate the analyte from a large sample volume. The PrP^C protein is then eluted from the P-beads before aptamer modified sensing beads, S-beads, are added. The velocity of the S-beads through the nanopore reveals the concentration of the PrP^C protein. The process is done in under an hour and allows the detection of picomol's of protein.

Surface coatings for solid-state nanopores

Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.

Rod-Cell-Mimetic Photochromic Layered Ion Channels with Multiple Switchable States for Controllable Ion Transport

The controllable ion transport in the photoreceptors of rod cells is essentially important for the light detection and information transduction in visual systems. Herein, inspired by the photochromism-regulated ion transport in rod cells with stacking structure, layered ion channels have been developed with a visual photochromic function induced by the alternate irradiation with visible and UV light. The layered structure is formed by stacking spiropyran-modified montmorillonite 2D nanosheets on the surface of an alumina nanoporous membrane. The visual photochromism resulting from the photoisomerization of spiropyran chromophores reversibly regulates the ion transport through layered ion channels. Furthermore, the cooperation of photochromism and pH value achieves multiple switchable states of layered ion channels for the controllable ion transport mimicking the biological process of the visual cycle. The ion transport properties of these states are explained quantitatively by a theoretical calculation based on the Poisson and Nernst-Plank (PNP) equations.

Functionalization of single solid state nanopores to mimic biological ion channels: A review

In nature, ion channels are highly selective pores and act as gate to ensure selective ion transport, allowing ions to cross the membrane. By mimicking them, single solid state nanopore devices emerge as a new, powerful class of molecule sensors that allow for the label-free detection of biomolecules (DNA, RNA, and proteins), non-biological polymers, as well as small molecules. In this review, we exhaustively describe the fabrication and functionalization techniques to design highly robust and selective solid state nanopores. First we outline the different materials and methods to design nanopores, we explain the ionic conduction in nanopores, and finally we summarize some techniques to modify and functionalize the surface in order to obtain biomimetic nanopores, responding to different external stimuli.

Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine

Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.

Protein detection using tunable pores: resistive pulses and current rectification

We present the first comparison between assays that use resistive pulses or rectification ratios on a tunable pore platform. We compare their ability to quantify the cancer biomarker Vascular Endothelial Growth Factor (VEGF). The first assay measures the electrophoretic mobility of aptamer modified nanoparticles as they traverse the pore. By controlling the aptamer loading on the particle surface, and measuring the speed of each translocation event we are able to observe a change in velocity as low as 18 pM. A second non-particle assay exploits the current rectification properties of conical pores. We report the first use of Layer-by-Layer (LbL) assembly of polyelectrolytes onto the surface of the polyurethane pore. The current rectification ratios demonstrate the presence of the polymers, producing pH and ionic strength-dependent currents. The LbL assembly allows the facile immobilisation of DNA aptamers onto the pore allowing a specific dose response to VEGF. Monitoring changes to the current rectification allows for a rapid detection of 5 pM VEGF. Each assay format offers advantages in their setup and ease of preparation but comparable sensitivities.

A flexible polymer confined inside a cone-shaped nano-channel

The nano-scale confinement of polymers in cone-shaped geometries occurs in many experimental situations. A flexible polymer confined in a cone-shaped nano-channel is studied theoretically and by using molecular dynamics simulations. Distribution of the monomers inside the channel, configuration of the confined polymer, the entropic force acting on the polymer, and their dependence on the channel and the polymer parameters are investigated. The theory and the simulation results are in very good agreement. The entropic force on the polymer that results from the asymmetric shape of the channel is measured in the simulations and its magnitude is found to be significant relative to thermal energy. The obtained dependence of the force on the channel parameters may be useful in the design of cone-shaped nano-channels.

DNA-modified polymer pores allow pH- and voltage-gated control of channel flux

Biological channels embedded in cell membranes regulate ionic transport by responding to external stimuli such as pH, voltage, and molecular binding. Mimicking the gating properties of these biological structures would be instrumental in the preparation of smart membranes used in biosensing, drug delivery, and ionic circuit construction. Here we present a new concept for building synthetic nanopores that can simultaneously respond to pH and transmembrane potential changes. DNA oligomers containing protonatable A and C bases are attached at the narrow opening of an asymmetric nanopore. Lowering the pH to 5.5 causes the positively charged DNA molecules to bind to other strands with negative backbones, thereby creating an electrostatic mesh that closes the pore to unprecedentedly high resistances of several tens of gigaohms. At neutral pH values, voltage switching causes the isolated DNA strands to undergo nanomechanical movement, as seen by a reversible current modulation. We provide evidence that the pH-dependent reversible closing mechanism is robust and applicable for nanopores with opening diameters of up to 14 nm. The concept of creating an electrostatic mesh may also be applied to different organic polymers.

Dynamic and electronic transport properties of DNA translocation through graphene nanopores

Graphene layers have been targeted in the last years as excellent host materials for sensing a remarkable variety of gases and molecules. Such sensing abilities can also benefit other important scientific fields such as medicine and biology. This has automatically led scientists to probe graphene as a potential platform for sequencing DNA strands. In this work, we use robust numerical tools to model the dynamic and electronic properties of molecular sensor devices composed of a graphene nanopore through which DNA molecules are driven by external electric fields. We performed molecular dynamic simulations to determine the relation between the intensity of the electric field and the translocation time spent by the DNA to pass through the pore. Our results reveal that one can have extra control on the DNA passage when four additional graphene layers are deposited on the top of the main graphene platform containing the pore in a 2 × 2 grid arrangement. In addition to the dynamic analysis, we carried electronic transport calculations on realistic pore structures with diameters reaching nanometer scales. The transmission obtained along the graphene sensor at the Fermi level is affected by the presence of the DNA. However, it is rather hard to distinguish the respective nucleobases. This scenario can be significantly altered when the transport is conducted away from the Fermi level of the graphene platform. Under an energy shift, we observed that the graphene pore manifests selectiveness toward DNA nucleobases.

Size and functional tuning of solid state nanopores by chemical functionalization

We demonstrate the possibility of using a simple functionalization procedure, based on an initial vapour-phase silanization, to control the size and functionality of solid state nanopores. The presented results show that, by varying the silanization time, it is possible to modify the efficiency of probe molecule attachment, thus shrinking the pore to the chosen size, while introducing a specific sensing selectivity. The proposed method allows us to tune the nanopore biosensor adapting it to the specific final application, and it can be efficiently applied when the pore initial diameter does not exceed a limit dimension related to the mean free path of the silane molecules at the working pressure.

Probing DNA-lipid membrane interactions with a lipopeptide nanopore

Association of DNA molecules with lipid bilayer membranes is of considerable interest for a large variety of applications in biotechnology. Here we introduce syringomycin E (SRE), a small pore-forming lipopeptide produced by the bacterium Pseudomonas syringae, as a facile sensor for the detection of DNA interactions with lipid membranes. SRE forms highly reproducible pores in cellular and artificial membranes. The pore structure involves bilayer lipids, which have a pronounced influence on open channel conductance and gating. SRE channels act as ionic diodes that serve as current rectifiers sensitive to the charge of the bilayer. We employ this intrinsic property to electronically monitor the association of DNA molecules with the membrane in a variety of different settings. We show that SRE can be used for quantitatively probing electrostatic interactions of DNA and DNA-cholesterol conjugates with a lipid membrane. Furthermore, we demonstrate that SRE channels allow monitoring of hybridization reactions between lipid-anchored probe strands and complementary strands in solution. In the presence of double-stranded DNA, SRE channels display a particularly high degree of rectification. Finally, the formation of multilayered structures assembled from poly-(L)-lysine and DNA oligonucleotides on the membrane was precisely monitored with SRE.

Controlling molecular transport through nanopores

Nanopores are emerging as powerful tools for the detection and identification of macromolecules in aqueous solution. In this review, we discuss the recent development of active and passive controls over molecular transport through nanopores with emphasis on biosensing applications. We give an overview of the solutions developed to enhance the sensitivity and specificity of the resistive-pulse technique based on biological and solid-state nanopores.