Gating of single synthetic nanopores by proton-driven DNA molecular motors

A nanochannel array-based electrochemical device for quantitative label-free DNA analysis

A strategy for label-free oligonucleotide (DNA) analysis has been proposed by measuring the DNA-morpholino hybridization hindered diffusion flux of probe ions Fe(CN)(6)(3-) through nanochannels of a porous anodic alumina (PAA) membrane. The flux of Fe(CN)(6)(3-) passing through the PAA nanochannels is recorded using an Au film electrochemical detector sputtered at the end of the nanochannels. Hybridization of the end-tethered morpholino in the nanochannel with DNA forms a negatively charged DNA-morpholino complex, which hinders the diffusion of Fe(CN)(6)(3-) through the nanochannels and results in a decreased flux. This flux is strongly dependent on ionic strength, nanochannel aperture, and target DNA concentration, which indicates a synergetic effect of steric and electrostatic repulsion effects in the confined nanochannels. Further comparison of the probe flux with different charge passing through the nanochannels confirms that the electrostatic effect between the probe ions and DNA dominates the hindered diffusion process. Under optimal conditions, the present nanochannel array-based DNA biosensor gives a detection limit of 0.1 nM.

Biomimetic glass nanopores employing aptamer gates responsive to a small molecule

We report the preparation of 20 and 65 nm radii glass nanopores whose surface is modified with DNA aptamers controlling the molecular transport through the nanopores in response to small molecule binding.

Computational microscopy of the role of protonable surface residues in nanoprecipitation oscillations

A novel phenomenon has recently been reported in polymeric nanopores. This phenomenon, so-called nanoprecipitation, is characterized by the transient formation of precipitates in the nanopore lumen, producing a sequence of low and high conductance states in the ionic current through the pore. By means of all-atom molecular dynamics simulations, we studied nanoprecipitation for polyethylene terephthalate nanopore immersed in electrolytic solution containing calcium phosphate, covering a total simulation time of 1.24 micros. Our results suggest that protonable surface residues at the nanopore surface, namely carboxyl groups, trigger the formation of precipitates that strongly adhere to the surface, blocking the pore and producing the low conductance state. On the basis of the simulations, we propose a mechanism for the formation of the high conductance state; the mechanism involves detachment of the precipitate from the surface due to reprotonation of carboxyl groups and subsequent translocation of the precipitate out of the pore.

Functional nucleic acid nanostructures and DNA machines

The information encoded in the base sequence of DNA provides instructions for the structural and functional properties of this biopolymer. Structural information includes the formation of duplexes, supramolecular crossover tiles, G-quadruplexes, i-motifs, base-metal-ion complexes, and more. Functional information encoded in the DNA is reflected by specific binding (aptamers) or catalytic properties (DNAzymes). Recent advances in tailoring supramolecular DNA structures for DNA-based machinery and for amplified biosensing are reviewed. Different DNA machines that perform 'tweezer', 'walker' or 'metronome' functions are discussed, and the control of macroscopic surface properties or the motility of micro-objects by molecular DNA devices is introduced. Furthermore, the design of DNA machines for the ultrasensitive detection of DNA, low-molecular-weight substrates, and macromolecules is discussed. Supramolecular aptamer and DNAzyme structures are used as molecular tools for amplified sensing.

DNA-molecular-motor-controlled dendron association

In this letter, we described a new strategy to study the macromolecule interactions rationally controlled by the movements of a DNA molecular motor. Two amphiphilic dendrons are covalently attached to the 3' and 5' ends of a pH-driven DNA motor, a 21-mer single-stranded DNA containing four stretches of cytosine-rich sequences. The resulting DNA-dendron conjugates were purified by polyacrylamide gel electrophoresis (PAGE), and their molecular weights were confirmed by MALDI-TOF. The reversible association-dissociation of the two DNA-attached dendrons controlled by the opening and closing of the DNA motor following pH changes was verified by circular dichroism spectroscopy and DNA stability studies in aqueous solutions. The results suggest that the DNA molecular motor may serve as a new platform for studying nonspecific and specific macromolecular interactions on the molecular level.

Molecular control of ionic conduction in polymer nanopores

Polymeric nanopores show unique transport properties and have attracted a great deal of scientific interest as a test system to study ionic and molecular transport at the nanoscale. By means of all-atom molecular dynamics, we simulated the ion dynamics inside polymeric polyethylene terephthalate nanopores. For this purpose, we established a protocol to assemble atomic models of polymeric material into which we sculpted a nanopore model with the key features of experimental devices, namely a conical geometry and a negative surface charge density. Molecular dynamics simulations of ion currents through the pore show that the protonation state of the carboxyl group of exposed residues have a considerable effect on ion selectivity, by affecting ionic densities and electrostatic potentials inside the nanopores. The role of high concentrations of Ca2+ ions was investigated in detail.

An electrochemically actuated reversible DNA switch

In this Letter, we have realized the electrical actuation of a DNA molecular device in a rapid and reliable manner with a microfabricated chip. The three-electrode chip containing Ir, IrO(2), and Ag electrodes deposited in designed shapes and positions on the SiO(2) surface was made by photolithography and magnetron reaction sputter deposition technology. In this design, the negative feedback property enabled the system to rapidly change and maintain the solution pH at arbitrary value by water electrolysis. As a proof-of-concept, we can drive a DNA switch based on the opening and close of an i-motif structure by switching the potential between the working and reference electrodes between -304 and -149 mV. We have demonstrated that DNA can be electrically switched within seconds, without obvious decay of the fluorescence amplitudes for at least 30 cycles, suggesting that this DNA switch is rapid in response and fairly robust. We have also demonstrated that this device could manipulate the DNA switch automatically by using chronoamperometry.

Bioinspired smart gating of nanochannels toward photoelectric-conversion systems

Learning from nature has inspired the creation of intelligent materials to better understand and imitate biology. Recent studies on bioinspired responsive surfaces that can switch between different states are shown, which open up new avenues for the development of smart materials in two dimensions. Based on this strategy, biomimetic nanochannel systems have been produced by introducing responsive molecules, which closely mimic the gating mechanism of biological nanochannels and show potential applications in many fields such as photoelectric-conversion systems demonstrated in this paper.

Learning from nature: building bio-inspired smart nanochannels

Learning from nature has inspired the fabrication of novel artificial materials that enable researchers to understand and to imitate biology. Bio-inspired research, in particular, owes much of its current development to advances in materials science and creative "smart" system design. The development and application of bio-inspired nanochannels is a burgeoning area in this field of research. Bio-inspired nanochannels enable many potential approaches to study various biomolecules in confined spaces and in real-time by current measurements. In this Perspective, we describe how these bio-inspired systems can be used to build novel, smart nanodevices with precisely controlled functions. Applications for these systems range from simulating the process of ion transport in living organisms by using biomimetic nanochannels to applying artificial nanochannel systems to investigate the chemistry, structure, size, and conformational states of biomolecules.

Surface modification of single track-etched nanopores with surfactant CTAB

In this letter, we report a method to modify the surface charge property of single track-etched nanopores with a cationic surfactant (CTAB). The dependence of surface charge density on the surfactant concentration was investigated by measuring the streaming current when the nanopore was immersed in 0.01 M KCl solution with different CTAB concentrations. The results showed that, when the concentration of CTAB was increased gradually, the surface charge of the nanopore was inverted from negative to positive. Our calculation indicated that the surface charge density changed from -9 to 8 mC/m2. We utilized this method to modify the surface property of single conical track-etched nanopores. Its current rectification properties (both the direction and magnitude) were successfully tuned by adjusting the CTAB concentration in the solutions.

Surface charge density of the track-etched nanopores in polyethylene terephthalate foils

Surface charge is one of the most important properties of nanopores, which determines the nanopore performance in many practical applications. We report the surface charge densities of track-etched nanopores, which were obtained by measuring the streaming current and pore conductance, respectively. Experimental results reveal that surface charge densities depend significantly on the salt concentrations. In addition the values obtained with the pore conductance were always several times higher than those calculated with the streaming current, and the gel-like surface layer on the nanopore was considered to be responsible for this discrepancy.

Biosensing and supramolecular bioconjugation in single conical polymer nanochannels. Facile incorporation of biorecognition elements into nanoconfined geometries

There is a growing quest for tailorable nanochannels or nanopores having dimensions comparable to the size of biological molecules and mimicking the function of biological ion channels. This interest is based on the use of nanochannels as extremely sensitive single molecule biosensors. The biosensing capabilities of these nanochannels depend sensitively on the surface characteristics of their inner walls to achieve the desired functionality of the biomimetic system. Nanoscale control over the surface properties of the nanochannel plays a crucial role in the biosensing performance due to the chemical groups incorporated on the inner channel walls that act as binding sites for different analytes and interact with molecules passing through the channel. Here we report a new approach to incorporate biosensing elements into polymer nanochannels by using electrostatic self-assembly. We describe a facile strategy based on the use of bifunctional macromolecular ligands to electrostatically assemble biorecongnition sites into the nanochannel wall, which can then be used as recognition elements for constructing a nanobiosensor. The experimental results demonstrate that the ligand-functionalized nanochannels are very stable and the biorecognition event (protein conjugation) does not promote the removal of the ligands from the channel surface. In addition, control experiments indicated that the electrostatically assembled nanochannel surface displays good biospecificity and nonfouling properties. Then, we demonstrate that this approach also enables the creation of supramolecular multilayered structures inside the nanopore that are stabilized by strong ligand-receptor interactions. We envision that the formation of multilayered supramolecular assemblies inside solid-state nanochannels will play a key role in the further expansion of the toolbox called "soft nanotechnology", as well as in the construction of new multifunctional biomimetic systems.

A pH-driven, reconfigurable DNA nanotriangle

A simple and robust DNA nanotriangle that can be conveniently reconfigured by environmental pH changes is demonstrated.