Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes.

Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.

Electrical characterization of ZnO-coated nanospring ensemble by impedance spectroscopy: probing the effect of thermal annealing.

The effects of thermal annealing on the electrical properties of randomly oriented ZnO-coated nanospring ensembles were extensively investigated through AC impedance spectroscopy. Annealing the nanospring mats for an hour at 873 K in air showed significant change in ZnO morphology, reduced electrical conductivity due to the presence of grain boundaries, decreased apparent donor concentration, and faster decay of sub-band gap photocurrent. The role of the nanospring-nanospring junctions in the conduction of carriers in the ensemble was also examined, as well as evaluation of their responsiveness to thermal and optical stimulations. This work identifies the effects of heat treatment in the presence of air on the electrical properties of the nanospring ensembles, which are related to the mesoscopic morphology and interconnect within the ensemble and the properties of the ZnO coating.

Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA.

Much remains to be understood about the kinetics and thermodynamics of DNA helicase binding and activity. Here, we utilize probe-modified DNA monolayers on multiplexed gold electrodes as a sensitive recognition element and morphologically responsive transducer of helicase-DNA interactions. The electrochemical signals from these devices are highly sensitive to structural distortion of the DNA produced by the helicases. We used this DNA electrochemistry to distinguish the details of the DNA interactions of three distinct XPB helicases, which belong to the superfamily-2 of helicases. Clear changes in DNA melting temperature and duplex stability were observed upon helicase binding, shifts that could not be observed with conventional UV-visible absorption measurements. Binding dissociation constants were estimated in the range from 10 to 50 nM and correlated with observations of activity. ATP-stimulated DNA unwinding activity was also followed, revealing exponential time scales and distinct time constants associated with conventional and molecular wrench modes of operation further confirmed by crystal structures. These devices thus provide a sensitive measure of the structural thermodynamics and kinetics of helicase-DNA interactions.

Solvent Toolkit for Electrochemical Characterization of Hybrid Perovskite Films.

Organohalide lead (hybrid) perovskites have emerged as competitive semiconducting materials for photovoltaic devices due to their high performance and low cost. To further the understanding and optimization of these materials, solution-based methods for interrogating and modifying perovskite thin films are needed. In this work, we report a hydrofluoroether (HFE) solvent-based electrolyte for electrochemical processing and characterization of organic-inorganic trihalide lead perovskite thin films. Organic perovskite films are soluble in most of the polar organic solvents, and thus until now, they were not considered suitable for electrochemical processing. We have enabled electrochemical characterization and demonstrated a processing toolset for these materials utilizing highly fluorinated electrolytes based on a HFE solvent. Our results show that chemically orthogonal electrolytes based on HFE solvents do not dissolve organic perovskite films and thus allow electrochemical characterization of the electronic structure, investigation of charge transport properties, and potential electrochemical doping of the films with in situ diagnostic capabilities.

Discerning the Impact of a Lithium Salt Additive in Thin-Film Light-Emitting Electrochemical Cells with Electrochemical Impedance Spectroscopy.

Light-emitting electrochemical cells (LEECs) from small molecules, such as iridium complexes, have great potential as low-cost emissive devices. In these devices, ions rearrange during operation to facilitate carrier injection, bringing about efficient operation from simple, single-layer devices. Prior work has shown that the luminance, efficiency, and responsiveness of iridium LEECs is greatly enhanced by the inclusion of small fractions of lithium salts, but much remains to be understood about the origin of this enhancement. Recent work with planar devices demonstrates that lithium additives in iridium LEECs enhance double-layer formation. However, the quantitative influence of lithium salts on the underlying physics of conventional thin-film, sandwich structure LEECs, which beneficially operate at low voltages and generate higher luminance, has yet to be clarified. Here, we use electrochemical impedance spectroscopy to discern the impact of the lithium salt concentration on double-layer formation within the device and draw correlations with performance metrics, such as current, luminance, and external quantum efficiency.

The Electronic Influence of Abasic Sites in DNA.

Abasic sites in DNA are prevalent as both naturally forming defects and as synthetic inclusions for biosensing applications. The electronic impact of these defects in DNA sensor and device configurations has yet to be clarified. Here we report the effect of an abasic site on the rate and yield of charge transport through temperature-controlled analysis of DNA duplex monolayers on multiplexed devices. Transport yield through the abasic site monolayer strongly increases with temperature, but the yield relative to an undamaged monolayer decreases with temperature. This is opposite to the increasing relative yield with temperature from a mismatched base pair, and these effects are accounted for by the unique structural impact of each defect. Notably, the effect of the abasic site is nearly doubled when heated from room temperature to 37 °C. The rate of transport is largely unaffected by the abasic site, showing Arrhenius-type behavior with an activation energy of ∼300 meV. Detailed abasic site investigation elucidates the electrical impact of these biologically spontaneous defects and aids development of biological sensors.

Temperature dependence of electrochemical DNA charge transport: influence of a mismatch.

Charge transfer through DNA is of interest as DNA is both the quintessential biomolecule of all living organisms and a self-organizing element in bioelectronic circuits and sensing applications. Here, we report the temperature-dependent properties of DNA charge transport in an electronically relevant arrangement of DNA monolayers on gold under biologically relevant conditions, and we track the effects of incorporating a CA single base pair mismatch. Charge transfer (CT) through double stranded, 17mer monolayers was monitored by following the yield of electrochemical reduction of a Nile blue redox probe conjugated to a modified thymine. Analysis with cyclic voltammetry and square wave voltammetry shows that DNA CT increases significantly with temperature, indicative of more DNA bridges becoming active for transport. The mismatch was found to attenuate DNA CT at lower temperatures, but the effect of the mismatch diminished as temperature was increased. Voltammograms were analyzed to extract the electron transfer rate k(0), the electron transfer coefficient α, and the redox-active surface coverage Γ*. Arrhenius behavior was observed, with activation energies of 100 meV for electron transfer through well-matched DNA. Single CA mismatches increased the activation energy by 60 meV. These results have clear implications for sensing applications and are evaluated with respect to the prominent models of DNA CT.

DNA as a molecular wire: distance and sequence dependence.

Functional nanowires and nanoelectronics are sought for their use in next generation integrated circuits, but several challenges limit the use of most nanoscale devices on large scales. DNA has great potential for use as a molecular wire due to high yield synthesis, near-unity purification, and nanoscale self-organization. Nonetheless, a thorough understanding of ground state DNA charge transport (CT) in electronic configurations under biologically relevant conditions, where the fully base-paired, double-helical structure is preserved, is lacking. Here, we explore the fundamentals of CT through double-stranded DNA monolayers on gold by assessing 17 base pair bridges at discrete points with a redox active probe conjugated to a modified thymine. This assessment is performed under temperature-controlled and biologically relevant conditions with cyclic and square wave voltammetry, and redox peaks are analyzed to assess transfer rate and yield. We demonstrate that the yield of transport is strongly tied to the stability of the duplex, linearly correlating with the melting temperature. Transfer rate is found to be temperature-activated and to follow an inverse distance dependence, consistent with a hopping mechanism of transport. These results establish the governing factors of charge transfer speed and throughput in DNA molecular wires for device configurations, guiding subsequent application for nanoscale electronics.

Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair.

DNA helicase activity is essential for the vital DNA metabolic processes of recombination, replication, transcription, translation, and repair. Recently, an unexpected, rapid exponential ATP-stimulated DNA unwinding rate was observed from an Archaeoglobus fulgidus helicase (AfXPB) as compared to the slower conventional helicases from Sulfolobus tokodaii, StXPB1 and StXPB2. This unusual rapid activity suggests a "molecular wrench" mechanism arising from the torque applied by AfXPB on the duplex structure in transitioning from open to closed conformations. However, much remains to be understood. Here, we investigate the concentration dependence of DNA helicase binding and ATP-stimulated kinetics of StXPB2 and AfXPB, as well as their binding and activity in Bax1 complexes, via an electrochemical assay with redox-active DNA monolayers. StXPB2 ATP-stimulated activity is concentration-independent from 8 to 200 nM. Unexpectedly, AfXPB activity is concentration-dependent in this range, with exponential rate constants varying from seconds at concentrations greater than 20 nM to thousands of seconds at lower concentrations. At 20 nM, rapid exponential signal decay ensues, linearly reverses, and resumes with a slower exponential decay. This change in AfXPB activity as a function of its concentration is rationalized as the crossover between the fast molecular wrench and slower conventional helicase modes. AfXPB-Bax1 inhibits rapid activity, whereas the StXPB2-Bax1 complex induces rapid kinetics at higher concentrations. This activity is rationalized with the crystal structures of these complexes. These findings illuminate the different physical models governing molecular wrench activity for improved biological insight into a key factor in DNA repair.

Stable and Bright Electroluminescent Devices utilizing Emissive 0D Perovskite Nanocrystals Incorporated in a 3D CsPbBr3 Matrix.

The 0D cesium lead halide perovskite Cs4 PbBr6 has drawn remarkable interest due to its highly efficient robust green emission compared to its 3D CsPbBr3 counterpart. However, seizing the advantages of the superior photoluminescence properties for practical light-emitting devices remains elusive. To date, Cs4 PbBr6 has been employed only as a higher-bandgap nonluminescent matrix to passivate or provide quantum/dielectric confinement to CsPbBr3 in light-emitting devices and to enhance its photo-/thermal/environmental stability. To resolve this disparity, a novel solvent engineering method to incorporate highly luminescent 0D Cs4 PbBr6 nanocrystals (perovskite nanocrystals (PNCs)) into a 3D CsPbBr3 film, forming the active emissive layer in single-layer perovskite light-emitting electrochemical cells (PeLECs) is designed. A dramatic increase of the maximum external quantum efficiency and luminance from 2.7% and 6050 cd m-2 for a 3D-only PeLEC to 8.3% and 11 200 cd m-2 for a 3D-0D PNC device with only 7% by weight of 0D PNCs is observed. The majority of this increase is driven by the efficient inherent emission of the 0D PNCs, while the concomitant morphology improvement also contributes to reduced leakage current, reduced hysteresis, and enhanced operational lifetime (half-life of 129 h), making this one of the best-performing LECs reported to date.

Machine Learning for Estimating Electron Transfer Rates From Square Wave Voltammetry.

Electrochemistry of surface-bound molecules is of high importance for numerous electronic and sensor applications. Extracting the electron transfer rate is beneficial for understanding surface-bound processes, but it requires experimental or computational rigor. We evaluate methods to determine electron transfer rates from large voltammetry sets from experiments via machine learning using decision tree ensembles, neural networks, and gaussian process regression models. We applied these to reproduce computational measures of electron transfer rates modeled by first principles. The best machine learning models were a random forest with 80 decision trees and a neural network with Bayesian regularization, producing root mean squared errors of 0.37 and 0.49 s-1 , respectively, corresponding to mean percent errors of 0.38 % and 0.52 %, respectively. This work establishes machine learning methods for rapidly acquiring electron transfer rates across large datasets for widespread applications.

Detecting Attomolar DNA-Damaging Anticancer Drug Activity in Cell Lysates with Electrochemical DNA Devices.

Here, we utilize electrochemical DNA devices to quantify and understand the cancer-specific DNA-damaging activity of an emerging drug in cellular lysates at femtomolar and attomolar concentrations. Isobutyl-deoxynyboquinone (IB-DNQ), a potent and tumor-selective NAD(P)H quinone oxidoreductase 1 (NQO1) bioactivatable drug, was prepared and biochemically verified in cancer cells highly expressing NQO1 (NQO1+) and knockdowns with low NQO1 expression (NQO1-) by Western blot, NQO1 activity analysis, survival assays, oxygen consumption rate, extracellular acidification rate, and peroxide production. Lysates from these cells and the IB-DNQ drug were then introduced to a chip system bearing an array of DNA-modified electrodes, and their DNA-damaging activity was quantified by changes in DNA-mediated electrochemistry arising from base-excision repair. Device-level controls of NQO1 activity and kinetic analysis were used to verify and further understand the IB-DNQ activity. A 380 aM IB-DNQ limit of detection and a 1.3 fM midpoint of damage were observed in NQO1+ lysates, both metrics 2 orders of magnitude lower than NQO1- lysates, indicating the high IB-DNQ potency and selectivity for NQO1+ cancers. The device-level damage midpoint concentration in NQO1+ lysates was over 8 orders of magnitude lower than cell survival benchmarks, likely due to poor IB-DNQ cellular uptake, demonstrating that these devices can identify promising drugs requiring improved cell permeability. Ultimately, these results indicate the noteworthy potency and selectivity of IB-DNQ and the high sensitivity and precision of electrochemical DNA devices to analyze agents/drugs involved in DNA-damaging chemotherapies.

Multiplexed DNA-modified electrodes.

We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 microm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format.

Luminescent properties of a 3,5-diphenylpyrazole bridged Pt(ii) dimer.

We report the synthesis, electrochemistry, photophysical properties and electroluminescence of a highly luminescent pyrazolate-bridged platinum(ii) complex. The complex has the general formula of [((N^C^N)Pt)2(µ-pz)][PF6] where N^C^N = 1,3-di(2-pyridyl)benzene and µ-pz = 3,5-diphenylpyrazolate. The X-ray structure shows that the bridging pyrazolate ligand causes a close Pt-Pt interaction of 3.05(7) Å. The emission profile of the complex was determined in solution, glassy 2-methyltetrahydrofurane at 77 K, and the solid state at both room temperature and 77 K. Each emission profile displayed a strong red metal-metal-to-ligand charge transfer while the solution and glassy 2-methyltetrahydrofurane emission profiles also displayed a ligand-centred transition. The absolute quantum yields of the complex in solution and the solid state at room temperate are 86% and 39%, respectively. Light-emitting electrochemical cells (LEECs) of [((N^C^N)Pt)2(µ-pz)][PF6] were fabricated which displayed appreciable electroluminescence, among the brightest and most efficient LEECs from dinuclear compounds to date.

Enhancement of the Electrical Properties of DNA Molecular Wires through Incorporation of Perylenediimide DNA Base Surrogates.

DNA has long been viewed as a promising material for nanoscale electronics, in part due to its well-ordered arrangement of stacked, pi-conjugated base pairs. Within this context, a number of studies have investigated how structural changes, backbone modifications, or artificial base substitutions affect the conductivity of DNA. Herein, we present a comparative study of the electrical properties of both well-matched and perylene-3,4,9,10-tetracarboxylic diimide (PTCDI)-containing DNA molecular wires that bridge nanoscale gold electrodes. By performing current-voltage measurements for such devices, we find that the incorporation of PTCDI DNA base surrogates within our macromolecular constructs leads to an approximately 6-fold enhancement in the observed current levels. Together, these findings suggest that PTCDI DNA base surrogates may enable the preparation of designer DNA-based nanoscale electronic components.

The Effect of the Dielectric Constant and Ion Mobility in Light-Emitting Electrochemical Cells.

Light-emitting electrochemical cells (LEECs) are a promising low-cost option for display and solid-state lighting. In these devices, the interplay of mobile ions, electrons, and holes makes for rich physics that can be leveraged for high performance. One example of this interplay is in the formation and radiative decay of excitons-bound electron and hole pairs. Considerations from exciton binding and Langevin recombination suggest that a low dielectric constant (ϵ) would enhance emission. However, emission is also enhanced by the product of the bulk hole and electron concentrations, which in LEECs are enhanced by the motion of small mobile ions yielding high dielectric constants. These competing effects make it difficult to predict whether active layers with low or high dielectric constants will optimize device performance. Here, the effect of varying the dielectric constant on the performance of LEEC devices from ionic transition-metal complexes was studied by systematically exchanging the negative counterions paired with an iridium complex emitter. Electrochemical impedance spectroscopy, constant voltage and constant current device studies, and drift-diffusion simulations were performed. The results clarify the competing effects of Langevin bimolecular recombination and ion-assisted injection processes occurring in LEECs.

Following anticancer drug activity in cell lysates with DNA devices.

There is a great need to track the selectivity of anticancer drug activity and to understand the mechanisms of associated biological activity. Here we focus our studies on the specific NQO1 bioactivatable drug, ß-lapachone, which is in several Phase I clinical trials to treat human non-small cell lung, pancreatic and breast cancers. Multi-electrode chips with electrochemically-active DNA monolayers are used to track anticancer drug activity in cellular lysates and correlate cell death activity with DNA damage. Cells were prepared from the triple-negative breast cancer (TNBC) cell line, MDA-MB-231 (231) to be proficient or deficient in expression of the NAD(P)H:quinone oxidoreductase 1 (NQO1) enzyme, which is overexpressed in most solid cancers and lacking in control healthy cells. Cells were lysed and added to chips, and the impact of ß-lapachone (ß-lap), an NQO1-dependent DNA-damaging drug, was tracked with DNA electrochemical signal changes arising from drug-induced DNA damage. Electrochemical DNA devices showed a 3.7-fold difference in the electrochemical responses in NQO1+ over NQO1- cell lysates, as well as 10-20-fold selectivity to catalase and dicoumarol controls that deactivate DNA damaging pathways. Concentration-dependence studies revealed that 1.4 µM ß-lap correlated with the onset of cell death from viability assays and the midpoint of DNA damage on the chip, and 2.5 µM ß-lap correlated with the midpoint of cell death and the saturation of DNA damage on the chip. Results indicate that these devices could inform therapeutic decisions for cancer treatment.

Ionic Organic Small Molecules as Hosts for Light-Emitting Electrochemical Cells.

Light-emitting electrochemical cells (LEECs) from ionic transition-metal complexes (iTMCs) offer the potential for high-efficiency electroluminescence in a simple, single-layer device. However, LEECs typically rely on the use of rare metal complexes. This has limited their cost effectiveness and put constraints on their applicability. With a view to leveraging the efficient emission of these complexes while mitigating costs, we describe here a host/guest LEEC strategy that relies on the use of carbazole (Cz)-based organic small-molecule hosts and iTMC guests. Three cationic host molecules were prepared via the coupling of 1-(4-bromophenyl)-2-phenylbenzimidazole (PBI-Br) with Cz. This has allowed a comparison between the hosts bearing methoxy (PBI-CzOMe) and tert-butyl (PBI-Cz tBu) substituents, as well as an unsubstituted analogue (PBI-CzH). Cyclic voltammetry and UV-visible absorption revealed that all three host materials have wide band gaps characterized by reversible oxidation and irreversible reduction events. On the basis of electronic structure calculations, the host highest occupied molecular orbital (HOMO) resides primarily on the Cz moiety, whereas the lowest unoccupied molecular orbital (LUMO) is located primarily on the phenyl-benzimidazolium unit. Photoluminescence analysis of thin-film blends of PBI-CzH with iTMC guests confirmed that the emission was blue-shifted relative to pristine iTMC films, which is consistent with what was seen in dilute dichloromethane solution. LEEC devices were prepared based on thin films of the pristine hosts, pristine guests, and 90%/10% (w/w) host/guest blends. Among these host/guest blends, LEECs based on PBI-CzH displayed the best performance, particularly when an iridium complex was used as the guest. The system in question yielded a luminance maximum of 624 cd/m2 at an external quantum efficiency of 3.80%. This result stands in contrast to what is seen with typical organic light-emitting diode host studies, where tert-butyl substitution of the host generally leads to a better performance. To rationalize the present observations, the host materials were subject to single-crystal X-ray diffraction analysis. The resulting structures revealed clear head-to-tail interactions in the case of both PBI-CzH and PBI-CzOMe. No such interactions were evident in the case of PBI-Cz tBu. Furthermore, PBI-CzH showed a relatively smaller spacing between the successive HOMO and successive LUMO levels relative to PBI-CzOMe and PBI-Cz tBu, a finding consistent with more favorable charge transport and energy transfer. The results presented here can help inform the design and preparation of host materials suitable for use in single-layer iTMC LEECs.

Enhanced Luminance of Electrochemical Cells with a Rationally Designed Ionic Iridium Complex and an Ionic Additive.

Light-emitting electrochemical cells (LEECs) offer the potential for high efficiency operation from an inexpensive device. However, long turn-on times and low luminance under steady-state operation are longstanding LEEC issues. Here, we present a single-layer LEEC with a custom-designed iridium(III) complex and a lithium salt additive for enhanced device performance. These devices display reduced response times, modest lifetimes, and peak luminances as high as 5500 cd/m(2), 80% higher than a comparable device from an unoptimized complex and 50% higher than the salt-free device. Improved device efficiency suggests that salt addition balances space charge effects at the interfaces. Extrapolation suggests favorable half-lives of 120 ± 10 h at 1000 cd/m(2) and 3800 ± 400 h at 100 cd/m(2). Overall, complex design and device engineering produce competitive LEECs from simple, single-layer architectures.

Using DNA devices to track anticancer drug activity.

It is beneficial to develop systems that reproduce complex reactions of biological systems while maintaining control over specific factors involved in such processes. We demonstrated a DNA device for following the repair of DNA damage produced by a redox-cycling anticancer drug, beta-lapachone (ß-lap). These chips supported ß-lap-induced biological redox cycle and tracked subsequent DNA damage repair activity with redox-modified DNA monolayers on gold. We observed drug-specific changes in square wave voltammetry from these chips at therapeutic ß-lap concentrations of high statistical significance over drug-free control. We also demonstrated a high correlation of this change with the specific ß-lap-induced redox cycle using rational controls. The concentration dependence of ß-lap revealed significant signal changes at levels of high clinical significance as well as sensitivity to sub-lethal levels of ß-lap. Catalase, an enzyme decomposing peroxide, was found to suppress DNA damage at a NQO1/catalase ratio found in healthy cells, but was clearly overcome at a higher NQO1/catalase ratio consistent with cancer cells. We found that it was necessary to reproduce key features of the cellular environment to observe this activity. Thus, this chip-based platform enabled tracking of ß-lap-induced DNA damage repair when biological criteria were met, providing a unique synthetic platform for uncovering activity normally confined to inside cells.