DNA sequencing with chain terminating inhibitors

DNA double-strand breaks (DSBs) are the most dangerous type of DNA damage because they can result in the loss of large chromosomal regions. In all mammalian cells, DSBs that occur throughout the cell cycle are repaired predominantly by the non-homologous DNA end joining (NHEJ) pathway. Defects in NHEJ result in sensitivity to ionizing radiation and the ablation of lymphocytes. The NHEJ pathway utilizes proteins that recognize, resect, polymerize and ligate the DNA ends in a flexible manner. This flexibility permits NHEJ to function on a wide range of DNA-end configurations, with the resulting repaired DNA junctions often containing mutations. In this Review, we discuss the most recent findings regarding the relative involvement of the different NHEJ proteins in the repair of various DNA-end configurations. We also discuss the shunting of DNA-end repair to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA) and the relevance of these different pathways to human disease.

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Non-homologous DNA end joining and alternative pathways to double-strand break repair.

Two-dimensional (2D) materials have attracted increasing research interest because of the abundant choice of materials with diverse and tunable electronic, optical, and chemical properties. Moreover, 2D material based heterostructures combining several individual 2D materials provide unique platforms to create an almost infinite number of materials and show exotic physical phenomena as well as new properties and applications. To achieve these high expectations, methods for the scalable preparation of 2D materials and 2D heterostructures of high quality and low cost must be developed. Chemical vapor deposition (CVD) is a powerful method which may meet the above requirements, and has been extensively used to grow 2D materials and their heterostructures in recent years, despite several challenges remaining. In this review of the challenges in the CVD growth of 2D materials, we highlight recent advances in the controlled growth of single crystal 2D materials, with an emphasis on semiconducting transition meta...

Chemical Vapor Deposition Growth and Applications of Two-Dimensional Materials and Their Heterostructures

The oxygen reduction reaction (ORR) is the cornerstone of various sustainable energy-conversion technologies. Metal-free nanocarbon electrocatalysts with competitive activity, enhanced durability, and satisfactory cost, have been proposed as the most promising substitute for precious-metal catalysts. However, their further development is still primarily based on trial-and-error approaches due to the controversial knowledge of critical active sites and mechanisms. Herein, the activity origins of nanocarbon-based ORR electro-catalysts are comprehensively reviewed and correlated, considering the dopants, edges, and defects. Analogously, they can effectively modify the charge/spin distribution on the sp2 -conjugated carbon matrix, leading to optimized intermediate chemisorption and facilitated electron transfer. Specific doping at defective edges is expected to render practical applications for metal-free nanocarbon electrocatalysts.

Nanocarbon for Oxygen Reduction Electrocatalysis: Dopants, Edges, and Defects.

The 2D transition metal carbides or nitrides, or MXenes, are emerging as a group of materials showing great promise in lithium ion batteries and supercapacitors. Until now, characterization and properties of single-layer MXenes have been scarcely reported. Here, using scanning transmission electron microscopy, we determined the atomic structure of freestanding monolayer Ti3C2Tx flakes prepared via the minimally intensive layer delamination method and characterized different point defects that are prevalent in the monolayer flakes. We determine that the Ti vacancy concentration can be controlled by the etchant concentration during preparation. Density function theory-based calculations confirm the defect structures and predict that the defects can influence the surface morphology and termination groups, but do not strongly influence the metallic conductivity. Using devices fabricated from single- and few-layer Ti3C2Tx MXene flakes, the effect of the number of layers in the flake on conductivity has been de...

Atomic Defects in Monolayer Titanium Carbide (Ti3C2Tx) MXene

Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

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Graphene nanodevices for DNA sequencing

Structural defects strongly impact the electrical transport properties of graphene nanostructures. In this Perspective, we give a brief overview of different types of defects in graphene and their effect on transport properties. We discuss recent experimental progress on graphene self-repair of defects, with a focus on in situ transmission electron microscopy studies. Finally, we present the outlook for graphene self-repair and in situ experiments.

http://pubs.acs.org/doi/pdf/10.1021/acsnano.5b01762

Controlling Defects in Graphene for Optimizing the Electrical Properties of Graphene Nanodevices

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.

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

Graphene nanopores are receiving great attention due to their atomically thin membranes and intrinsic electrical properties that appear greatly beneficial for biosensing and DNA sequencing. Here, we present an extensive study of the low-frequency 1/f noise in the ionic current through graphene nanopores and compare it to noise levels in silicon nitride pore currents. We find that the 1/f noise magnitude is very high for graphene nanopores: typically two orders of magnitude higher than for silicon nitride pores. This is a drawback as it significantly lowers the signal-to-noise ratio in DNA translocation experiments. We evaluate possible explanations for these exceptionally high noise levels in graphene pores. From examining the noise for pores of different diameters and at various salt concentrations, we find that in contrast to silicon nitride pores, the 1/f noise in graphene pores does not follow Hooge's relation. In addition, from studying the dependence on the buffer pH, we show that the increased noise cannot be explained by charge fluctuations of chemical groups on the pore rim. Finally, we compare single and bilayer graphene to few-layer and multi-layer graphene and boron nitride (h-BN), and we find that the noise reduces with layer thickness for both materials, which suggests that mechanical fluctuations may be the underlying cause of the high 1/f noise levels in monolayer graphene nanopore devices.

https://iopscience.iop.org/article/10.1088/0957-4484/26/7/074001/pdf

1/f noise in graphene nanopores

Many theoretical studies predict that DNA sequencing should be feasible by monitoring the transverse current through a graphene nanoribbon while a DNA molecule translocates through a nanopore in that ribbon. Such a readout would benefit from the special transport properties of graphene, provide ultimate spatial resolution because of the single-atom layer thickness of graphene, and facilitate high-bandwidth measurements. Previous experimental attempts to measure such transverse inplane signals were however dominated by a trivial capacitive response. Here, we explore the feasibility of the approach using a custom-made differential current amplifier that discriminates between the capacitive current signal and the resistive response in the graphene. We fabricate well-defined short and narrow (30 nm × 30 nm) nanoribbons with a 5 nm nanopore in graphene with a high-temperature scanning transmission electron microscope to retain the crystallinity and sensitivity of the graphene. We show that, indeed, resistive modulations can be observed in the graphene current due to DNA translocation through the nanopore, thus demonstrating that DNA sensing with inplane currents in graphene nanostructures is possible. The approach is however exceedingly challenging due to low yields in device fabrication connected to the complex multistep device layout.

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Stephanie J. Heerema

Papers

Graphene nanodevices for DNA sequencing

Controlling Defects in Graphene for Optimizing the Electrical Properties of Graphene Nanodevices

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

1/f noise in graphene nanopores

Probing DNA Translocations with Inplane Current Signals in a Graphene Nanoribbon with a Nanopore