Humidity effects on the conductance of the assembly of DNA molecules

Low bias charge transport in DNA

The low-bias current-voltage technique was utilized to study charge transport in single-stranded DNA (ssDNA), assessing the method's effectiveness for future studies aimed at estimating the degree of mutation or DNA damage. In the paper, we showed that charge carrier transfer processes in ssDNA can be precisely monitored using low-bias currents. We used negative differential resistance and the Fowler-Nordheim model to differentiate the charge transport mechanisms observed in a device composed of gold electrode-thiol-ssDNA junctions. It was possible to distinguish the processes at the two junctions (Au/thiol and thiol/DNA) due to their distinct current-voltage characteristics. We observed positive charge carrier tunneling, which we attribute to oxidation and reduction processes in the nucleobases of the ssDNA. Our results suggest that even minor changes in DNA chains can be accurately detected using the described methodology.

Detection of nucleotides in hydrated ssDNA via 2D h-BN nanopore with ionic-liquid/salt-water interface

Accomplishing slow translocation speed with high sensitivity has been the most critical mission for solid-state nanopore (SSN) device to electrically detect nucleobases in ssDNA. In this study, a method to detect nucleobases of ssDNA using a 2D SSN is introduced by considerably reducing the translocation speed and effectively increasing its sensitivity. The ultra-thin titanium dioxide coated hexagonal boron nitride nanopore was fabricated, along with an ionic-liquid 1-butyl-3-methylimidazolium hexafluorophosphate/2.0 M KCl aqueous (cis/trans) interface, for increasing both the spatial and the temporal resolutions. As the ssDNA molecules entered the nanopore, a brief surge of electrical conductivity occurred, which was followed by multiple resistive pulses from nucleobases during the translocation of ssDNA and another brief current surge flagging the exit of the molecule. The continuous detection of nucleobases using a 2D SSN device is a novel achievement: the water molecules bound to ssDNA increased the molecular conductivity and amplified electrical signals during the translocation. Along with the experiment, computational simulations using COMSOL Multiphysics are presented to explain the pivotal role of water molecules bound to ssDNA to detect nucleobases using a 2D SSN.

Moving Electrons Purposefully through Single Molecules and Nanostructures: A Tribute to the Science of Professor Nongjian Tao (1963-2020)

Electrochemistry intersected nanoscience 25 years ago when it became possible to control the flow of electrons through single molecules and nanostructures. Many surprises and a wealth of understanding were generated by these experiments. Professor Nongjian Tao was among the pioneering scientists who created the methods and technologies for advancing this new frontier. Achieving a deeper understanding of charge transport in molecules and low-dimensional materials was the first priority of his experiments, but he also succeeded in discovering applications in chemical sensing and biosensing for these novel nanoscopic systems. In parallel with this work, the investigation of a range of phenomena using novel optical microscopic methods was a passion of his and his students. This article is a review and an appreciation of some of his many contributions with a view to the future.

SbSI Nanosensors: from Gel to Single Nanowire Devices

The gas-sensing properties of antimony sulfoiodide (SbSI) nanosensors have been tested for humidity and carbon dioxide in nitrogen. The presented low-power SbSI nanosensors have operated at relatively low temperature and have not required heating system for recovery. Functionality of sonochemically prepared SbSI nanosensors made of xerogel as well as single nanowires has been compared. In the latter case, small amount of SbSI nanowires has been aligned in electric field and bonded ultrasonically to Au microelectrodes. The current and photocurrent responses of SbSI nanosensors have been investigated as function of relative humidity. Mechanism of light-induced desorption of H₂O from SbSI nanowires' surface has been discussed. SbSI nanosensors have been tested for concentrations from 51 to 10⁶ ppm of CO₂ in N₂, exhibiting a low detection limit of 40(31) ppm. The current response sensitivity has shown a tendency to decrease with increasing CO₂ concentration. The experimental results have been explained taking into account proton-transfer process and Grotthuss' chain reaction, as well as electronic theory of adsorption and catalysis on semiconductors.

Investigation Into the Effects of Nucleotide Content on the Electrical Characteristics of DNA Plasmid Molecular Wires

In this study, we investigate the effect of nucleotide content on the conductivity of plasmid length DNA molecular wires covalently bound to high aspect-ratio gold electrodes. The DNA wires were all between [Formula: see text] in length (>6000bp), and contained either 39%, 53%, or 64% GC base-pairs. We compared the current-voltage (I-V) and frequency-impedance characteristics of the DNA wires with varying GC content, and observed statistically significantly higher conductivity in DNA wires containing higher GC content in both AC and DC measurement methods. Additionally, we noted that the conductivity decreased as a function of time for all DNA wires, with the impedance at 100 Hz nearly doubling over a period of seven days. All readings were taken in humidity and temperature controlled environments on DNA wires suspended above an insulative substrate, thus minimizing the effect of experimental and environmental factors as well as potential for nonlinear alternate DNA confirmations. While other groups have studied the effect of GC content on the conductivity of nanoscale DNA molecules (<50bp), we were able to demonstrate that nucleotide content can affect the conductivity of micrometer length DNA wires at scales that may be required during the fabrication of DNA-based electronics. Furthermore, our results provide further evidence that many of the charge transfer theories developed from experiments using nanoscale DNA molecules may still be applicable for DNA wires at the micro scale.

Formation of Conductive DNA-Based Nanowires via Conjugation of dsDNA with Cationic Peptide

A novel conductive DNA-based nanomaterial, DNA-peptide wire, composed of a DNA core and a peripheral peptide layer, is presented. The electrical conductivity of the wire is found to be at least three orders in magnitude higher than that of native double-stranded DNA (dsDNA). High conductivity of the wires along with a better resistance to mechanical deformations caused by interactions between the substrate and electrode surface make them appealing for a wide variety of nanoelectronic and biosensor applications.

Humidity influenced capacitance and resistance of an Al/DNA/Al Schottky diode irradiated by alpha particles

Deoxyribonucleic acid or DNA based sensors, especially as humidity and alpha particle sensors have become quite popular in recent times due to flexible and highly optimizable nature of this fundamental biomaterial. Application of DNA electronics allow for more sensitive, accurate and effective sensors to be developed and fabricated. In this work, we examined the effect of different humidity conditions on the capacitive and resistive response of Aluminum (Al)/DNA/Al Schottky barrier structure when bombarded by time-dependent dosages of alpha particles. Based on current-voltage profiles, which demonstrated rectifying behaviours, Schottky diode parameters such as ideality factor, barrier height and series resistance was calculated. Results observed generally pointed towards a decrease in the resistance value from the pristine to the radiated structures. It was also demonstrated that under the effect of humidity, the capacitance of the DNA thin film increased from 0.05894 to 92.736 nF, with rising relative humidity level. We also observed the occurrence of the hypersensitivity phenomena after alpha irradiation between 2 to 4 min by observing a drop in the series resistance, crucial in the study of DNA damage and repair mechanisms. These observations may also suggest the exciting possibility of utilizing Al/DNA/Al Schottky diodes as potentially sensitive humidity sensors.

Sequence dependent proton conduction in self-assembled peptide nanostructures

The advancement of diverse electrochemistry technologies depends on the development of novel proton conducting polymers. Inspired by the efficacy of proton transport through proteins, we show in this work that self-assembling peptide nanostructures may be a promising alternative for such organic proton conducting materials. We demonstrate that aromatic amino acids, which participate in charge transport in nature, unprecedentedly promote proton conduction under both high and low relative humidity conditions for d,l α-cyclic peptide nanotubes. For dehydrated networks long-range order of the assemblies, induced by the aromatic side chains, is shown to be a dominating factor for promoting conductivity. However, for hydrated networks this order of effect is less significant and conductivity can be improved by the introduction of proton donating carboxylic acid peptide side chains in addition to the aromatic side chains despite the lower order of the assemblies. Based on these observations, a novel cyclic peptide that incorporates non-natural naphthyl side chains was designed. Self-assembled nanotubes of this peptide show greatly improved dehydrated conductivity, while maintaining high conductivity under hydrated conditions. We envision that the demonstrated modularity and versatility of these bio inspired nanostructures will make them extremely attractive building blocks for the fabrication of devices for energy conversion and storage applications, as well as other applications that involve proton transport, whether dry or wet conductivity is desired.

Aligned deposition and electrical measurements on single DNA molecules

A reliable method of deposition of aligned individual dsDNA molecules on mica, silicon, and micro/nanofabricated circuits is presented. Complexes of biotinylated double stranded poly(dG)-poly(dC) DNA with avidin were prepared and deposited on mica and silicon surfaces in the absence of Mg(2+) ions. Due to its positive charge, the avidin attached to one end of the DNA anchors the complex to negatively charged substrates. Subsequent drying with a directional gas flow yields DNA molecules perfectly aligned on the surface. In the avidin-DNA complex only the avidin moiety is strongly and irreversibly bound to the surface, while the DNA counterpart interacts with the substrates much more weakly and can be lifted from the surface and realigned in any direction. Using this technique, avidin-DNA complexes were deposited across platinum electrodes on a silicon substrate. Electrical measurements on the deposited DNA molecules revealed linear IV-characteristics and exponential dependence on relative humidity.

Charge transport in desolvated DNA

The conductivity of DNA in molecular junctions is often probed experimentally under dry conditions, but it is unclear how much of the solvent remains attached to the DNA and how this impacts its structure, electronic states, and conductivity. Classical MD simulations show that DNA is unstable if the solvent is removed completely, while a micro-hydrated system with few water molecules shows similar charge transport properties as fully solvated DNA does. This surprising effect is analyzed in detail by mapping the density functional theory-based electronic structure to a tight-binding Hamiltonian, allowing for an estimate of conductivity of various DNA sequences with snapshot-averaged Landauer's approach. The characteristics of DNA charge transport turn out to be determined by the nearest hydration shell(s), and the removal of bulk solvent has little effect on the transport.

DNA gold nanoparticle nanocomposite films for chemiresistive vapor sensing

Chemiresistive vapor sensors combining functionalized gold nanoparticles and single-stranded DNA oligomers are investigated to enhance specificity in chemical sensing. Sensors are made by depositing DNA-functionalized gold nanoparticles onto microfabricated electrodes using four distinct sequences. Sensor performance is evaluated for response to relative humidity and exposure to vapor analytes including ethanol, methanol, hexane, dimethyl methylphosphonate, and toluene under different relative humidity. It is found that sensors display a nonmonotonic resistance change toward increasing humidity due to the combined effects of hydration induced swelling and ionic conduction. Responses to vapor analytes show sequence-dependent patterns as well as a strong influence of humidity. Overall, the findings are encouraging for using DNA oligomers to enhance specificity in chemical sensing.

Transverse charge transport through DNA oligomers in large-area molecular junctions

We investigate the nature of charge transport in deoxyribonucleic acid (DNA) using self-assembled layers of DNA in large-area molecular junctions. A protocol was developed that yields dense monolayers where the DNA molecules are not standing upright, but are lying flat on the substrate. As a result the charge transport is measured not along the DNA molecules but in the transverse direction, across their diameter. The electrical transport data are consistent with the derived morphology. We demonstrate that the charge transport mechanism through DNA is identical to non-resonant tunneling through alkanethiols with identical length, classifying DNA as a dielectric.

Defined-size DNA triple crossover construct for molecular electronics: modification, positioning and conductance properties

We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.

Ionic conductivity on a wetting surface

Recent experiments measuring the electrical conductivity of DNA molecules highlight the need for a theoretical model of ion transport along a charged surface. Here we present a simple theory based on the idea of unbinding of ion pairs. The strong humidity dependence of conductivity is explained by the decrease in the electrostatic self-energy of a separated pair when a layer of water (with high dielectric constant) is adsorbed to the surface. We compare our prediction for conductivity to experiment and discuss the limits of its applicability.

Water induced weakly bound electrons in DNA

We have studied the effect of humidity on the electronic properties of DNA base pairs. We found that the hydrogen links of the nucleobases with water molecules lead to a shift of the pi electron density from carbon atoms to nitrogen atoms and can change the symmetry of the wave function for some nucleobases. As a result, the orbital energies are shifted which leads to a decrease in the potential barrier for the hole transfer between the G-C and A-T pairs from 0.7 eV for the dehydrated case to 0.123 eV for the hydrated. More importantly, the pi electron density redistribution activated by hydration is enhanced by the intrastrand interactions. This leads to a modification of the nucleobase chemical structures from the covalent type to a resonance structure with separated charges, where some pi electrons are not locked up into the covalent bonds. Within the (G-C)(2) sequences, there is overlapping of the electronic clouds of such unlocked electrons belonging to the stacked guanines, that significantly increases the electron coupling between them to V(DA)=0.095 eV against the V(DA)=0.025 eV for the dehydrated case. Consequently, the charge transfer between two guanines within the (G-C)(2) sequences is increased by 250 times due to hydration. The presence of nonbonded electrons suppress the band gap up to approximately 3.0 eV, that allows us to consider DNA as a narrow band gap semiconductor.

The effect of environmental factors on the electrical conductivity of a single oligo-DNA molecule measured using single-walled carbon nanotube nanoelectrodes

We present an electrical conductivity study on a double-stranded DNA molecule bridging a single-walled carbon nanotube (SWNT) gap. The amine terminated DNA molecule was trapped between carboxyl functionalized SWNT electrodes by dielectrophoresis. The conductivity of DNA was measured while under the influence of various environmental factors, including salt concentration, counterion variation, pH and temperature. Typically, a current of tens of picoamperes at 1 V was observed at ambient conditions, with a decrease in conductance of about 33% in high vacuum conditions. The counterion variation was analyzed by changing the buffer from sodium acetate to tris(hydroxymethyl) aminomethane, which resulted in a two orders of magnitude increase in the conductivity of the DNA. A reversible shift in the current signal was observed for pH variation. An increase in conductivity of the DNA was also observed at high salt concentrations.

Towards single biomolecule handling and characterization by MEMS

Applications of microelectromechanical systems (MEMS) technology are widespread in both industrial and research fields providing miniaturized smart tools. In this review, we focus on MEMS applications aiming at manipulations and characterization of biomaterials at the single molecule level. Four topics are discussed in detail to show the advantages and impact of MEMS tools for biomolecular manipulations. They include the microthermodevice for rapid temperature alternation in real-time microscopic observation, a microchannel with microelectrodes for isolating and immobilizing a DNA molecule, and microtweezers to manipulate a bundle of DNA molecules directly for analyzing its conductivity. The feasibilities of each device have been shown by conducting specific biological experiments. Therefore, the development of MEMS devices for single molecule analysis holds promise to overcome the disadvantages of the conventional technique for biological experiments and acts as a powerful strategy in molecular biology.

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Multisegment nanowire sensors for the detection of DNA molecules

We describe a novel application for detecting specific single strand DNA sequences using multisegment nanowires via a straightforward surface functionalization method. Nanowires comprising CdTe-Au-CdTe segments are fabricated using electrochemical deposition, and electrical characterization indicates a p-type behavior for the multisegment nanostructures, in a back-to-back Schottky diode configuration. Such nanostructures modified with thiol-terminated probe DNA fragments could function as high fidelity sensors for biomolecules at very low concentration. The gold segment is utilized for functionalization and binding of single strand DNA (ssDNA) fragments while the CdTe segments at both ends serve to modulate the equilibrium Fermi level of the heterojunction device upon hybridization of the complementary DNA fragments (cDNA) to the ssDNA over the Au segment. Employing such multisegment nanowires could lead to the fabrication more sophisticated and high multispecificity biosensors via selective functionalization of individual segments for biowarfare sensing and medical diagnostics applications.

Humidity dependence of charge transport through DNA revealed by silicon-based nanotweezers manipulation

The study of the electrical properties of DNA has aroused increasing interest since the last decade. So far, controversial arguments have been put forward to explain the electrical charge transport through DNA. Our experiments on DNA bundles manipulated with silicon-based actuated tweezers demonstrate undoubtedly that humidity is the main factor affecting the electrical conduction in DNA. We explain the quasi-Ohmic behavior of DNA and the exponential dependence of its conductivity with relative humidity from the adsorption of water on the DNA backbone. We propose a quantitative model that is consistent with previous studies on DNA and other materials, like porous silicon, subjected to different humidity conditions.