Iddo Heller

Influence of Electrolyte Composition on Liquid-Gated Carbon Nanotube and Graphene Transistors

Field-effect transistors based on single-walled carbon nanotubes (SWNTs) and graphene can function as highly sensitive nanoscale (bio)sensors in solution. Here, we compare experimentally how SWNT and graphene transistors respond to changes in the composition of the aqueous electrolyte in which they are immersed. We show that the conductance of SWNTs and graphene is strongly affected by changes in the ionic strength, the pH, and the type of ions present, in a manner that can be qualitatively different for graphene and SWNT devices. We show that this sensitivity to electrolyte composition results from a combination of different mechanisms including electrostatic gating, Schottky-barrier modifications, and changes in gate capacitance. Interestingly, we find strong evidence that the sensor response to changes in electrolyte composition is affected by a high density of ionizable groups on both the underlying substrate and the carbon surfaces. We present a model based on the (regulated) surface charge associated with these ionizable groups that explains the majority of our data. Our findings have significant implications for interpreting and optimizing sensing experiments with nanocarbon transistors. This is particularly true for complex biological samples such as cell extracts, growth media, or bodily fluids, for which the complete composition of the solution needs to be considered.

Carbon nanotube biosensors: The critical role of the reference electrode

Carbon nanotube transistors show tremendous potential for electronic detection of biomolecules in solution. However, the nature and magnitude of the sensing signal upon molecular adsorption have so far remained controversial. Here, the authors show that the choice of the reference electrode is critical and resolves much of the previous controversy. The authors eliminate artifacts related to the reference electrode by using a well-defined reference electrode to accurately control the solution potential. Upon addition of bovine serum albumin proteins, the authors measure a transistor threshold shift of ?15?mV which can be unambiguously attributed to the adsorption of biomolecules in the vicinity of the nanotube.

STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA.

Dense coverage of DNA by proteins is a ubiquitous feature of cellular processes such as DNA organization, replication and repair. We present a single-molecule approach capable of visualizing individual DNA-binding proteins on densely covered DNA and in the presence of high protein concentrations. Our approach combines optical tweezers with multicolor confocal and stimulated emission depletion (STED) fluorescence microscopy. Proteins on DNA are visualized at a resolution of 50 nm, a sixfold resolution improvement over that of confocal microscopy. High temporal resolution (<50 ms) is ensured by fast one-dimensional beam scanning. Individual trajectories of proteins translocating on DNA can thus be distinguished and tracked with high precision. We demonstrate our multimodal approach by visualizing the assembly of dense nucleoprotein filaments with unprecedented spatial resolution in real time. Experimental access to the force-dependent kinetics and motility of DNA-associating proteins at biologically relevant protein densities is essential for linking idealized in vitro experiments with the in vivo situation.

Charge Noise in Graphene Transistors

We report an experimental study of 1/f noise in liquid-gated graphene transistors. We show that the gate dependence of the noise is well described by a charge-noise model, whereas Hooges empirical relation fails to describe the data. At low carrier density, the noise can be attributed to fluctuating charges in close proximity to the graphene, while at high carrier density it is consistent with noise due to scattering in the channel. The charge noise power scales inversely with the device area, and bilayer devices exhibit lower noise than single-layer devices. In air, the observed noise is also consistent with the charge-noise model.

Three‐dimensional and quantitative analysis of atherosclerotic plaque composition by automated differential echogenicity

To validate automated and quantitative three‐dimensional analysis of coronary plaque composition using intracoronary ultrasound (ICUS).

Optical tweezers analysis of DNA-protein complexes.

Optical tweezers have grown to be one of the most powerful and versatile single-molecule methods for analysis of DNA-protein complexes. The power of optical tweezers lies primarily in its extremely high sensitivity and bandwidth in combination with a wide and biologically relevant force range. To accurately apply and measure a force in an optical tweezers assay, the biological system, a DNA molecule, is tethered on two opposite ends. Most commonly used are the single-beam and dual-beam force measuring optical tweezers. Extreme refinement of optical tweezers sensitivity has led to unprecedented mechanistic insight into the single-base-pair stepping of RNA polymerases during DNA transcription. Experiments on DNA repair, which involves the orchestrated action of many proteins, each with different physical characteristics, have showcased the versatility of optical tweezers assays and also illustrated the large advantages of concurrent visualization by fluorescence microscopy.

Optimizing the Signal-to-Noise Ratio for Biosensing with Carbon Nanotube Transistors

The signal-to-noise ratio (SNR) for real-time biosensing with liquid-gated carbon nanotube transistors is crucial for exploring the limits of their sensitivity, but has not been studied thus far. Although biosensing is often performed at high transconductance where the device displays the largest gate response, here we show that the maximum SNR is actually obtained when the device is operated in the subthreshold regime. In the ON-state, additional contributions to the noise can lead to a reduction of the SNR by up to a factor of 5. For devices with passivated contact regions, the SNR in ON-state is even further reduced than for bare devices. We show that when the conductivity of the contact regions can be increased using a conventional back gate, the SNR in the ON-state can be improved. The results presented here demonstrate that biosensing experiments are best performed in the subthreshold regime for optimal SNR.

Alba shapes the archaeal genome using a delicate balance of bridging and stiffening the DNA

Architectural proteins have an important role in shaping the genome and act as global regulators of gene expression. How these proteins jointly modulate genome plasticity is largely unknown. In archaea, one of the most abundant proteins, Alba, is considered to have a key role in organizing the genome. Here we characterize the multimodal architectural properties and interplay of the Alba1 and Alba2 proteins using single-molecule imaging and manipulation techniques. We demonstrate that the two paralogues can bridge and rigidify DNA and that the interplay between the two proteins influences the balance between these effects. Our data yield a structural model that explains the multimodal behaviour of Alba proteins and its impact on genome folding.

Sliding sleeves of XRCC4–XLF bridge DNA and connect fragments of broken DNA

Non-homologous end joining (NHEJ) is the primary pathway for repairing DNA double-strand breaks (DSBs) in mammalian cells. Such breaks are formed, for example, during gene-segment rearrangements in the adaptive immune system or by cancer therapeutic agents. Although the core components of the NHEJ machinery are known, it has remained difficult to assess the specific roles of these components and the dynamics of bringing and holding the fragments of broken DNA together. The structurally similar XRCC4 and XLF proteins are proposed to assemble as highly dynamic filaments at (or near) DSBs. Here we show, using dual- and quadruple-trap optical tweezers combined with fluorescence microscopy, how human XRCC4, XLF and XRCC4–XLF complexes interact with DNA in real time. We find that XLF stimulates the binding of XRCC4 to DNA, forming heteromeric complexes that diffuse swiftly along the DNA. Moreover, we find that XRCC4–XLF complexes robustly bridge two independent DNA molecules and that these bridges are able to slide along the DNA. These observations suggest that XRCC4–XLF complexes form mobile sleeve-like structures around DNA that can reconnect the broken ends very rapidly and hold them together. Understanding the dynamics and regulation of this mechanism will lead to clarification of how NHEJ proteins are involved in generating chromosomal translocations.

Monitoring in vivo absorption of a drug-eluting bioabsorbable stent with intravascular ultrasound-derived parameters a feasibility study.

OBJECTIVES The aim of this study was to investigate the feasibility of using quantitative differential echogenicity to monitor the in vivo absorption process of a drug-eluting poly-l-lactic-acid (PLLA) bioabsorbable stent (BVS, Abbott Vascular, Santa Clara, California). BACKGROUND A new bioabsorbable, balloon-expanded coronary stent was recently evaluated in a first-in-man study. Little is known about the absorption process in vivo in diseased human coronary arteries. METHODS In the ABSORB (Clinical Evaluation of the BVS everolimus eluting stent system) study, 30 patients underwent treatment with the BVS coronary stent system and were examined with intracoronary ultrasound (ICUS) after implantation, at 6 months and at 2-year follow-up. Quantitative ICUS was used to measure dimensional changes, and automated ICUS-based tissue composition software (differential echogenicity) was used to quantify plaque compositional changes over time in the treated regions. RESULTS The BVS struts appeared as bright hyperechogenic structures and showed a continuous decrease of their echogenicity over time, most likely due to the polymer degradation process. In 12 patients in whom pre-implantation ICUS was available, at 2 years the percentage-hyperechogenic tissue was close to pre-implantation values, indicating that the absorption process was either completed or the remaining material was no longer differentially echogenic from surrounding tissues. CONCLUSIONS Quantitative differential echogenicity is a useful plaque compositional measurement tool. Furthermore, it seems to be valuable for monitoring the absorption process of bioabsorbable coronary stents made of semi-crystalline polymers.