Slowing down DNA translocation through a nanopore in lithium chloride

The charge of a DNA molecule is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial reduction of the DNA charge due to counterion binding by means of nanopore translocation experiments and all-atom molecular dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA molecule through a solid-state nanopore strongly increases as the counterions decrease in size from K(+) to Na(+) to Li(+), both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li(+) and Na(+) bind DNA stronger than K(+). These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resolution in nanopore applications.     

p-n Semiconductor membrane for electrically tunable ion current rectification and filtering

We show that a semiconductor membrane made of two thin layers of opposite (n- and p-) doping can perform electrically tunable ion current rectification and filtering in a nanopore. Our model is based on the solution of the 3D Poisson equation for the electrostatic potential in a double-cone nanopore combined with a transport model. It predicts that, for appropriate biasing of the membrane-electrolyte system, transitions from ohmic behavior to sharp rectification with vanishing leakage current are achievable. Furthermore, ion current rectifying and filtering regimes of the nanopore correspond to different charge states in the p-n membrane, which can be tuned with appropriate biasing of the n- and p- layers.     

Slowing DNA translocation in a solid-state nanopore

Reducing a DNA molecule's translocation speed in a solid-state nanopore is a key step toward rapid single molecule identification. Here we demonstrate that DNA translocation speeds can be reduced by an order of magnitude over previous results. By controlling the electrolyte temperature, salt concentration, viscosity, and the electrical bias voltage across the nanopore, we obtain a 3 base/micros translocation speed for 3 kbp double-stranded DNA in a 4-8 nm diameter silicon nitride pore. Our results also indicate that the ionic conductivity inside such a nanopore is smaller than it is in bulk.     

Simulation of ionic current through the nanopore in a double-layered semiconductor membrane

We study the effects of different nanopore geometries (double-conical, single-conical, cylindrical) on the electrostatic potential distribution and ionic conductivity in a double-layered semiconductor nanopore device as functions of the applied membrane bias. Ionic current-voltage characteristics as well as their rectification ratios are calculated using a simple ion transport model. Based on our calculations, we find that the double-layered semiconductor membrane with a single-conical nanopore with a narrow opening in the n-Si layer exhibits the largest range of available potential variations in the pore and, thus, may be better suited for control of polymer translocation through the nanopore.     

Interdigitated electrode-induced phase grating with an electrically switchable and tunable period

A new design for an adjustable electro-optic phase grating inside a waveguide is proposed. The electric field and the refractive-index distribution induced inside a waveguide by voltage applied to double-sided periodic interdigitated electrode arrays are calculated rigorously on the basis of an original analytical technique. The modeling was carried out with the Mathcad software. It is shown that the fundamental periodicity of the induced grating inside the waveguide can be switched between l and 2l by application of the appropriate voltage, where l is the spatial periodicity of the interdigitated electrodes. One can also fine tune the peak grating reflectivity by changing the constant component of the induced refractive index with the help of the constant component of the electric field inside the waveguide. The suggested design can be used as a basic idea for a variety of optical communication networking applications, including switching, modulation, deflection, and data processing.     

DNA tunneling detector embedded in a nanopore

We report on the fabrication and characterization of a DNA nanopore detector with integrated tunneling electrodes. Functional tunneling devices were identified by tunneling spectroscopy in different solvents and then used in proof-of-principle experiments demonstrating, for the first time, concurrent tunneling detection and ionic current detection of DNA molecules in a nanopore platform. This is an important step toward ultrafast DNA sequencing by tunneling.     

Charging capacity of a sharp p-n junction in a variband semiconductor

The barrier capacitance of a sharp p-n junction in a variband semiconductor with coordinate-independent bandgap gradient and electron affinity was calculated. It is shown that the square inverse barrier capacitance is a linear function of the applied voltage and that the cutoff voltage may significantly exceed the contact potential difference.     

A ligand-gated ion-channel mimetic nanopore membrane with an on-board transmembrane microbattery

We have been investigating synthetic nanopore membranes that mimic the function of ligand-gated ion channels. We showed previously that the transmembrane ion current in a hydrophobic alumina nanopore membrane can be switched from an "off" state to an "on" state by exposure of the membrane to hydrophobic ionic surfactants. In these prior experiments, external electrodes and an external power supply were used to drive the ion current when the membrane was in its "on" state. In biological channels there are no electrodes, and the ion current is driven by an electrochemical potential difference across the cell membrane. In this article we mimic this function of the ligand-gated ion channel by applying a porous battery cathode film to one face of the hydrophobic alumina membrane and a porous battery anode film to the other face. Hence, in analogy to the naturally occurring channel case, we have a membrane with a built in electrochemical potential difference across the membrane. We show here that in the absence of the ligand (again, a hydrophobic ionic surfactant), the membrane is in its "off" state, and the electrochemical potential difference cannot be utilized to drive a transmembrane ion current. In contrast, when the ligand is detected, the membrane switches to its "on" state and the transmembrane battery discharges, producing a corresponding transmembrane ion current.     

Detecting single stranded DNA with a solid state nanopore

Voltage biased solid-state nanopores are used to detect and characterize individual single stranded DNA molecules of fixed micrometer length by operating a nanopore detector at pH values greater than approximately 11.6. The distribution of observed molecular event durations and blockade currents shows that a significant fraction of the events obey a rule of constant event charge deficit (ecd) indicating that they correspond to molecules translocating through the nanopore in a distribution of folded and unfolded configurations. A surprisingly large component is unfolded. The result is an important milestone in developing solid-state nanopores for single molecule sequencing applications.     

DNA molecules and configurations in a solid-state nanopore microscope

A nanometre-scale pore in a solid-state membrane provides a new way of electronically probing the structure of single linear polymers, including those of biological interest in their native environments. Previous work with biological protein pores wide enough to let through and sense single-stranded DNA molecules demonstrates the power of using nanopores, but many future tasks and applications call for a robust solid-state pore whose nanometre-scale dimensions and properties may be selected, as one selects the lenses of a microscope. Here we demonstrate a solid-state nanopore microscope capable of observing individual molecules of double-stranded DNA and their folding behaviour. We discuss extensions of the nanopore microscope concept to alternative probing mechanisms and applications, including the study of molecular structure and sequencing.     

Application of semiconductor detectors with p-n junctions in nuclear instrument making

Conclusions It is possible to state from the factory and State test results that the equipment developed by us is, with respect to several of its parameters, as good as similar foreign makes. A further study and development of semiconductor detectors will make it possible in future to produce physicoelectronic equipment whose parameters will have new qualities suitable for solving a number of technical problems, such as analyzing substances by their -, -, and -radiation spectra, improving the operating characteristics of equipment for x-ray-chemical analysis, activation analysis, etc.The authors wish to express their gratitude to L. S. Gorn and E. B. Usha for their valuable suggestions and advice, to O. B. Podgornyi and O. B. Saratovskii for their assistance in adjusting the equipment and carrying out experiments, as well as to V. I. Lopovok and other designers who participated in the development of this instrument.Translated from Izmeritel'naya Tekhnika, No. 10, pp. 61–63, October, 1967.     

Detection of DNA sequences using an alternating electric field in a nanopore capacitor

Molecular dynamics simulations revealed that back-and-forth motion of DNA strands through a 1 nm diameter pore exhibits sequence-specific hysteresis that arises from the reorientation of the DNA bases in the nanopore constriction. Such hysteresis of the DNA motion results in detectable changes of the electrostatic potential at the electrodes of the nanopore capacitor and in a sequence-specific drift of the DNA strand under an oscillating transmembrane bias. A strategy is suggested for sequencing DNA in a nanopore using the electric field that alternates periodically in time.     

An explicit analytic solution for convective heat transfer in an electrically conducting fluid at a stretching surface with uniform free stream

An analytic technique, namely the homotopy analysis method, is applied to study the flow and heat transfer characteristics in an electrically conducting fluid near an isothermal sheet. The sheet is linearly stretched in the presence of a uniform free stream of constant velocity and temperature. The effects of free convection and internal heat generation or absorption are also considered. Within the framework of boundary layer approximations, the explicit, totally analytic and uniformly valid solutions governed by a set of three fully coupled, highly non-linear equations are obtained, which agree well with numerical results.     

Stretching DNA using the electric field in a synthetic nanopore

The mechanical properties of DNA over segments comparable to the size of a protein-binding site (3-10 nm) are examined using an electric-field-induced translocation of single molecules through a nanometer diameter pore. DNA, immersed in an electrolyte, is forced through synthetic pores ranging from 0.5 to 1.5 nm in radius in a 10 nm thick Si(3)N(4) membrane using an electric field. To account for the stretching and bending, we use molecular dynamics to simulate the translocation. We have found a threshold for translocation that depends on both the dimensions of the pore and the applied transmembrane bias. The voltage threshold coincides with the stretching transition that occurs in double-stranded DNA near 60 pN.     

Spontaneous stretching of DNA in a two-dimensional nanoslit

DNA molecules in silicon dioxide-glass fluidic nanoslits spontaneously extend at the lateral sidewalls of the slit. The nanoslit geometry, however, physically confines polymer molecules to two spatial dimensions; further reduction in configurational entropy resulting in axially stretched molecules arises spontaneously and appears to be electrostatically mediated. The observations not only shed light on electrostatic interactions of charged soft matter with like-charged confining walls but also offer a new method to stretch DNA in solution.     

Nucleotide identification and orientation discrimination of DNA homopolymers immobilized in a protein nanopore

Nanopores have been used as extremely sensitive resistive pulse sensors to detect analytes at the molecular level. There has been interest in using such a scheme to rapidly and inexpensively sequence single molecules of DNA. To establish reference current levels for adenine, cytosine, and thymine nucleotides, we measured the blockage currents following immobilization of single-stranded DNA polyadenine, polycytosine, and polythymine within a protein nanopore in chemical orientations in which either the 3' or the 5' end enters the pore. Immobilization resulted in low-noise measurements, yielding sharply defined current distributions for each base that enabled clear discrimination of the nucleotides in both orientations. In addition, we find that not only is the blockage current for each polyhomonucleotide orientation dependent, but also the changes in orientation affect the blockage currents for each base differently. This dependence can affect the ability to resolve polyadenine and polythymine; with the 5' end entering the pore, the separation between polyadenine and polythymine is double that observed for the 3' orientation. This suggests that, for better resolution, DNA should be threaded through the 5' end first in nanopore DNA sequencing experiments.     

Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore

Nanoscale pores have potential to be used as biosensors and are an established tool for analysing the structure and composition of single DNA or RNA molecules. Recently, nanopores have been used to measure the binding of enzymes to their DNA substrates. In this technique, a polynucleotide bound to an enzyme is drawn into the nanopore by an applied voltage. The force exerted on the charged backbone of the polynucleotide by the electric field is used to examine the enzyme-polynucleotide interactions. Here we show that a nanopore sensor can accurately identify DNA templates bound in the catalytic site of individual DNA polymerase molecules. Discrimination among unbound DNA, binary DNA/polymerase complexes, and ternary DNA/polymerase/deoxynucleotide triphosphate complexes was achieved in real time using finite state machine logic. This technique is applicable to numerous enzymes that bind or modify DNA or RNA including exonucleases, kinases and other polymerases.     

Recapturing and trapping single molecules with a solid-state nanopore

The development of solid-state nanopores, inspired by their biological counterparts, shows great potential for the study of single macromolecules. Applications such as DNA sequencing and the exploration of protein folding require control of the dynamics of the molecule's interaction with the pore, but DNA capture by a solid-state nanopore is not well understood. By recapturing individual molecules soon after they pass through a nanopore, we reveal the mechanism by which double-stranded DNA enters the pore. The observed recapture rates and times agree with solutions of a drift-diffusion model. Electric forces draw DNA to the pore over micrometer-scale distances, and upon arrival at the pore, molecules begin translocation almost immediately. Repeated translocation of the same molecule improves measurement accuracy, offers a way to probe the chemical transformations and internal dynamics of macromolecules on sub-millisecond time and sub-micrometre length scales, and demonstrates the ability to trap, study and manipulate individual macromolecules in solution.     

Label-free DNA detection with a nanogap embedded complementary metal oxide semiconductor

A nanogap embedded complementary metal oxide semiconductor (NeCMOS) is demonstrated as a proof-of-concept for label-free detection of DNA sequence. When a partially carved nanogap between a gate and a silicon channel is filled with charged biomolecules, the gate dielectric constant and charges are changed. When the gate oxide thickness reduces, the threshold voltage is significantly affected by a change of the charges, whereas it is scarcely influenced by a change of the dielectric constant. In the case of DNA, those two factors act on the threshold voltage oppositely in an n-channel NeCMOS but collaboratively in a p-channel NeCMOS because of the negative charges of DNA. Hence, a p-channel NeCMOS with a thin gate oxide is more attractive for DNA detection because it enhances the shift of threshold voltage; that is, it improves the sensitivity of DNA detection. In addition, the shift of threshold voltage according to the nanogap length is also investigated and the longer nanogap shows more shift of the threshold voltage.