Towards scalable plasmonic Fano-resonant metasurfaces for colorimetric sensing.

Transitioning plasmonic metasurfaces into practical, low-cost applications requires meta-atom designs that focus on ease of manufacturability and a robustness with respect to structural imperfections and nonideal substrates. It also requires the use of inexpensive, earth-abundant metals such as Al for plasmonic properties. In this study, we focus on combining two aspects of plasmonic metasurfaces-visible coloration and Fano resonances-in a morphology amenable to scalable manufacturing. The resulting plasmonic metasurface is a candidate for reflective colorimetric sensing. We examine the potential of this metasurface for reflective strain sensing, where the periodicity of the meta-atoms could ultimately be modified by a potential flexion, and for localized surface plasmon resonance refractive index sensing. This study evaluates the potential of streamlined meta-atom design combined with low-cost metallization for inexpensive sensor readout based on human optical perception.

Theoretical Development of DnaG Primase as a Novel Narrow-Spectrum Antibiotic Target.

The widespread use of antibiotics to treat infections is one of the reasons that global mortality rates have fallen over the past 80 years. However, antibiotic use is also responsible for the concomitant rise in antibiotic resistance because it results in dysbiosis in which commensal and pathogenic bacteria are both greatly reduced. Therefore, narrow-range antibiotics are a promising direction for reducing antibiotic resistance because they are more discriminate. As a step toward addressing this problem, the goal of this study was to identify sites on DnaG primase that are conserved within Gram-positive bacteria and different from the equivalent sites in Gram-negative bacteria. Based on sequence and structural analysis, the primase C-terminal helicase-binding domain (CTD) was identified as most promising. Although the primase CTD sequences are very poorly conserved, they have highly conserved protein folds, and Gram-positive bacterial primases fold into a compact state that creates a small molecule binding site adjacent to a groove. The small molecule would stabilize the protein in its compact state, which would interfere with the helicase binding. This is important because primase CTD must be in its open conformation to bind to its cognate helicase at the replication fork.

Towards the identification of the gold binding region within trypsin stabilized nanoclusters using microwave synthesis routes.

Elucidating the location of stabilized nanoclusters within their protein hosts is an existing challenge towards the optimized development of functional protein-nanoclusters. While nanoclusters of various metal compositions can be readily synthesized within a wide array of protein hosts and exhibit tailorable properties, the inability to identify the cluster stabilization region prevents controllable property manipulation of both metallic and protein components. Additionally, the ability to synthesize protein-nanoclusters in a consistent and high-throughput fashion is also highly desirable. In this effort, trypsin stabilized gold nanoclusters are synthesized through standard and microwave-enabled methodologies to determine the impact of processing parameters on the materials physical and functional properties. Density functional theory simulations are employed to localize high probability regions within the trypsin enzyme for Au25 cluster stabilization, which reveal that cluster location is likely within close proximity of the trypsin active region. Trypsin activity measurements support our findings from DFT, as trypsin enzymatic activity is eliminated following cluster growth and stabilization. Moreover, studies on the reactivity of Au NCs and synchrotron characterization measurements further reveal that clusters made by microwave-based techniques exhibit slight structural differences to those made via standard methodologies, indicating that microwave-based syntheses largely maintain the native structural attributes despite the faster synthetic conditions. Overall, this work illustrates the importance of understanding the connections between synthetic conditions, atomic-scale structure, and materials properties that can be potentially used to further tune the properties of metal cluster-protein materials for future applications.

A Supramolecular Coordination-Polymer-Derived Electrocatalyst for the Oxygen Evolution Reaction.

An iron oxide decorated nickel iron alloy nanoparticle/porous graphene hybrid exhibits high electrocatalytic activity and excellent durability toward oxygen evolution reaction (OER). It displays a low overpotential of 274 mV at 10 mA cm-2 , and low Tafel slope of 37 mV dec-1 , showing a superior performance to the state-of-the-art RuO2 OER electrocatalyst.

Photoelectrochemical overall water splitting with textured CuBi2O4 as a photocathode.

Nanotextured CuBi2O4 photocathodes have been developed for applications toward solar water splitting. Tailoring the CuBi2O4 photocathodes to yield a high photocurrent and a positively large onset potential demonstrates their applicability in a photoelectrochemical tandem cell for entirely solar-driven overall water splitting.

Plasmonic gold nanostars as optical nano-additives for injection molded polymer composites.

Nanoscale engineering of noble metal particles has provided numerous material configurations to selectively confine and manipulate light across the electromagnetic spectrum. Transitioning these materials to a composite form while maintaining the desired resonance properties has proven challenging. In this work, the successful integration of plasmon-focusing gold nanostars (GNSs) into polymer nanocomposites (PNCs) is demonstrated. Tailored GNSs are produced with over a 90% yield and methods to control the branching structures are shown. A protective silica capping shell is employed on the nanomaterials to facilitate survivability in the high temperate/high shear processing parameters to create optically-tuned injection molded PNCs. The developed GNS PNCs possess dichroic scattering and absorption behavior, opening up potential applications in the fields of holographic imaging, optical filtering and photovoltaics.

Identification of a Ligand-Binding Site on the Staphylococcus aureus DnaG Primase C-Terminal Domain.

The interface between the DnaG primase C-terminal domain (CTD) and the N-terminal domain of DnaB helicase is essential for bacterial DNA replication because it allows coordinated priming of DNA synthesis at the replication fork while the DNA is being unwound. Because these two proteins are conserved in all bacteria and distinct from those in eukaryotes, their interface is an attractive antibiotic target. To learn more about this interface, we determined the solution structure and dynamics of the DnaG primase CTD from Staphylococcus aureus, a medically important bacterial species. Comparison with the known primase CTD structures shows there are two biologically relevant conformations, an open conformation that likely binds to DnaB helicase and a closed conformation that does not. The S. aureus primase CTD is in the closed conformation, but nuclear magnetic resonance (NMR) dynamic studies indicate there is considerable movement in the linker between the two subdomains and that N564 is the most dynamic residue within the linker. A high-throughput NMR ligand affinity screen identified potential binding compounds, among which were acycloguanosine and myricetin. Although the affinity for these compounds and adenosine was in the millimolar range, all three bind to a common pocket that is present only on the closed conformation of the CTD. This binding pocket is at the opposite end of helices 6 and 7 from N564, the key hinge residue. The identification of this binding pocket should allow the development of stronger-binding ligands that can prevent formation of the CTD open conformation that binds to DnaB helicase.

In situ Synthesis of Fluorescent Gold Nanoclusters by Nontumorigenic Microglial Cells.

To date, the directed in situ synthesis of fluorescent gold nanoclusters (AuNCs) has only been demonstrated in cancerous cells, with the theorized synthesis mechanism prohibiting AuNC formation in nontumorigenic cell lines. This limitation hinders potential biostabilized AuNC-based technology in healthy cells involving both chemical and mechanical analysis, such as the direct sensing of protein function and the elucidation of local mechanical environments. Thus, new synthesis strategies are required to expand the application space of AuNCs beyond cancer-focused cellular studies. In this contribution, we have developed the methodology and demonstrated the direct in situ synthesis of AuNCs in the nontumorigenic neuronal microglial line, C8B4. The as-synthesized AuNCs form in situ and are stabilized by cellular proteins. The clusters exhibit bright green fluorescence and demonstrate low (<10%) toxicity. Interestingly, elevated ROS levels were not required for the in situ formation of AuNCs, although intracellular reductants such as glutamate were required for the synthesis of AuNCs in C8B4 cells. To our knowledge, this is the first-ever demonstration of AuNC synthesis in nontumorigenic cells and, as such, it considerably expands the application space of biostabilized fluorescent AuNCs.

Enhanced Graphene Mechanical Properties through Ultrasmooth Copper Growth Substrates.

The combination of extraordinary strength and stiffness in conjunction with exceptional electronic and thermal properties in lightweight two-dimensional materials has propelled graphene research toward a wide array of applications including flexible electronics and functional structural components. Tailoring graphene's properties toward a selected application requires precise control of the atomic layer growth process, transfer, and postprocessing procedures. To date, the mechanical properties of graphene are largely controlled through postprocess defect engineering techniques. In this work, we demonstrate the role of varied catalytic surface morphologies on the tailorability of subsequent graphene film quality and breaking strength, providing a mechanism to tailor the physical, electrical, and mechanical properties at the growth stage. A new surface planarization methodology that results in over a 99% reduction in Cu surface roughness allows for smoothness parameters beyond that reported to date in literature and clearly demonstrates the role of Cu smoothness toward a decrease in the formation of bilayer graphene defects, altered domain sizes, monolayer graphene sheet resistance values down to 120 Ω/□ and a 78% improvement in breaking strength. The combined electrical and mechanical enhancements achieved through this methodology allows for the direct growth of application quality flexible transparent conductive films with monolayer graphene.

Toward the Responsible Development and Commercialization of Sensor Nanotechnologies.

Nanotechnology-enabled sensors (or nanosensors) will play an important role in enabling the progression toward ubiquitous information systems as the Internet of Things (IoT) emerges. Nanosensors offer new, miniaturized solutions in physiochemical and biological sensing that enable increased sensitivity, specificity, and multiplexing capability, all with the compelling economic drivers of low cost and high-energy efficiency. In the United States, Federal agencies participating in the National Nanotechnology Initiative (NNI) "Nanotechnology for Sensors and Sensors for Nanotechnology: Improving and Protecting Health, Safety, and the Environment" Nanotechnology Signature Initiative (the Sensors NSI), address both the opportunity of using nanotechnology to advance sensor development and the challenges of developing sensors to keep pace with the increasingly widespread use of engineered nanomaterials. This perspective article will introduce and provide background on the NNI signature initiative on sensors. Recent efforts by the Sensors NSI aimed at promoting the successful development and commercialization of nanosensors will be reviewed and examples of sensor nanotechnologies will be highlighted. Future directions and critical challenges for sensor development will also be discussed.

Recent advances in the field of bionanotechnology: an insight into optoelectric bacteriorhodopsin, quantum dots, and noble metal nanoclusters.

Molecular sensors and molecular electronics are a major component of a recent research area known as bionanotechnology, which merges biology with nanotechnology. This new class of biosensors and bioelectronics has been a subject of intense research over the past decade and has found application in a wide variety of fields. The unique characteristics of these biomolecular transduction systems has been utilized in applications ranging from solar cells and single-electron transistors (SETs) to fluorescent sensors capable of sensitive and selective detection of a wide variety of targets, both organic and inorganic. This review will discuss three major systems in the area of molecular sensors and electronics and their application in unique technological innovations. Firstly, the synthesis of optoelectric bacteriorhodopsin (bR) and its application in the field of molecular sensors and electronics will be discussed. Next, this article will discuss recent advances in the synthesis and application of semiconductor quantum dots (QDs). Finally, this article will conclude with a review of the new and exciting field of noble metal nanoclusters and their application in the creation of a new class of fluorescent sensors.

DNase 1 retains endodeoxyribonuclease activity following gold nanocluster synthesis.

Here we present the synthesis of the enzyme DNase 1 stabilized gold nanoclusters (DNase 1:AuNCs) with core size consisting of either 8 or 25 atoms. The DNase 1:Au8NCs exhibit blue fluorescence whereas the DNase 1:Au25NCs are red emitting. In addition to the intense fluorescence emission, the synthesized DNase 1:AuNC hybrid retains the native functionality of the protein, allowing simultaneous detection and digestion of DNA with a detection limit of 2 µg/mL. The DNase 1:AuNCs could be conveniently employed as efficient and fast sensors to augment the current time-consuming DNA contamination analysis techniques.

Growth of large single-crystalline two-dimensional boron nitride hexagons on electropolished copper.

Hexagonal-boron nitride (h-BN) or "white graphene" has many outstanding properties including high thermal conductivity, high mechanical strength, chemical inertness, and high electrical resistance, which open up a wide range of applications such as thermal interface material, protective coatings, and dielectric in nanoelectronics that easily exceed the current advertised benefits pertaining to the graphene-based applications. The development of h-BN films using chemical vapor deposition (CVD) has thus far led into nucleation of triangular or asymmetric diamond shapes on different metallic surfaces. Additionally, the average size of the triangular domains has remained relatively small (∼ 0.5 µm(2)) leading to a large number of grain boundaries and defects. While the morphology of Cu surfaces for CVD-grown graphene may have impacts on the nucleation density, domain sizes, thickness, and uniformity, the effects of the decreased roughness of Cu surface to develop h-BN films are unknown. Here, we report the growth and characterization of novel large area h-BN hexagons using highly electropolished Cu substrate under atmospheric pressure CVD conditions. We found that the nucleation density of h-BN is significantly reduced while domain sizes increase. In this study, the largest hexagonal-shape h-BN domain observed is 35 µm(2), which is an order of magnitude larger than a typical triangular domain. As the domains coalesce to form a continuous film, the larger grain size offers a more pristine and smoother film with lesser grain boundaries induced defects.

Real-time electrochemical monitoring of adenosine triphosphate in the picomolar to micromolar range using graphene-modified electrodes.

We report on a competitive electrochemical detection system that is free of wash steps and enables the real-time monitoring of adenosine triphosphate (ATP) in a quantitative manner over a five-log concentration range. The system utilizes a recognition surface based on ATP aptamer (ATPA) capture probes prebound to electroactive flavin adenine dinucleotide (FAD) molecules, and a signaling surface utilizing graphene (Gr) and gold nanoparticle (AuNP) modified carbon paste electrode (Gr-AuNP-CPE) that is optimized to enhance electron-transfer kinetics and signal sensitivity. Binding of ATP to ATPA at the recognition surface causes the release of an equivalent concentration of FAD that can be quantitatively monitored in real time at the signaling surface, thereby enabling a wide linear working range (1.14 × 10(-10) to 3.0 × 10(-5) M), a low detection limit (2.01 × 10(-11) M using graphene and AuNP modified glassy carbon), and fast target binding kinetics (steady-state signal within 12 min at detection limit). Unlike assays based on capture probe-immobilized electrodes, this double-surface competitive assay offers the ability to speed up target binding kinetics by increasing the capture probe concentration, with no limitations due to intermolecular Coulombic interactions and nonspecific binding. We utilize the real-time monitoring capability to compute kinetic parameters for target binding and to make quantitative distinctions on degree of base-pair mismatch through monitoring target binding kinetics over a wide concentration range. On the basis of the simplicity of the assay chemistry and the quantitative detection of ATP within fruit and serum media, as demonstrated by comparison of ATP levels against those determined using a standard high-performance liquid chromatography (HPLC)-UV absorbance method, we envision a versatile detection platform for applications requiring real-time monitoring over a wide target concentration range.

Förster Resonance Energy Transfer between Core/Shell Quantum Dots and Bacteriorhodopsin.

An energy transfer relationship between core-shell CdSe/ZnS quantum dots (QDs) and the optical protein bacteriorhodopsin (bR) is shown, demonstrating a distance-dependent energy transfer with 88.2% and 51.1% of the QD energy being transferred to the bR monomer at separation distances of 3.5 nm and 8.5 nm, respectively. Fluorescence lifetime measurements isolate nonradiative energy transfer, other than optical absorptive mechanisms, with the effective QD excited state lifetime reducing from 18.0 ns to 13.3 ns with bR integration, demonstrating the Förster resonance energy transfer contributes to 26.1% of the transferred QD energy at the 3.5 nm separation distance. The established direct energy transfer mechanism holds the potential to enhance the bR spectral range and sensitivity of energies that the protein can utilize, increasing its subsequent photocurrent generation, a significant potential expansion of the applicability of bR in solar cell, biosensing, biocomputing, optoelectronic, and imaging technologies.

¹H, ¹³C, and ¹5N NMR assignments for the helicase interaction domain of Staphylococcus aureus DnaG primase.

The interaction between DnaG primase and DnaB helicase is essential for stimulating primer synthesis during bacterial DNA replication. The interaction occurs between the N-terminal domain of helicase and the C-terminal domain of primase. Here we present the (1)H, (13)C, and (15)N backbone and side-chain resonance assignments for the C-terminal helicase interaction domain of Staphylococcus aureus primase.

Bacterial protein structures reveal phylum dependent divergence.

Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against each other to establish their relatedness. As expected, the analysis demonstrates a sharp structural divergence between the bacterial phyla Firmicutes and Proteobacteria. Additionally, each COG had a distinct sequence/structure relationship, indicating that different evolutionary pressures affect the degree of structural divergence. However, our analysis also shows the relative drift rate between sequence identity and structure divergence remains constant.

Optical protein modulation via quantum dot coupling and use of a hybrid sensor protein.

Harnessing the energy transfer interactions between the optical protein bacteriorhodopsin (bR) and CdSe/ZnS quantum dots (QDs) could provide a novel bio-nano electronics substrate with a variety of applications. In the present study, a polydimethyldiallyammonium chloride based I-SAM technique has been utilized to produce bilayers, trilayers and multilayers of alternating monolayers of bR, PDAC and QD's on a conductive ITO substrate. The construction of multilayer systems was directly monitored by measuring the unique A570 nm absorbance of bR, as well as QD fluorescence emission. Both of these parameters displayed a linear relationship to the number of monolayers present on the ITO substrate. The photovoltaic response of bilayers of bR/PDAC was observed over a range of 3 to 12 bilayers and the ability to efficiently create an electrically active multilayered substrate composed of bR and QDs has been demonstrated for the first time. Evaluation of QD fluorescence emission in the multilayer system strongly suggests that FRET coupling is occurring and, since the I-SAM technique provide a means to control the bR/QD separation distance on the nanometer scale, this technique may prove highly valuable for optimizing the distance dependent energy transfer effects for maximum sensitivity to target molecule binding by a biosensor. Finally, preliminary studies on the production of a sensor protein/bR hybrid gene construct are presented. It is proposed that the energy associated with target molecule binding to a hybrid sensor protein would provide a means to directly modulate the electrical output from a sensor protein/bR biosensor platform.

Diode-like properties of as-grown chemical vapor deposited single-walled carbon nanotubes.

Current rectification property of as-grown single-walled carbon nanotubes (SWNTs) is investigated. The SWNTs are grown by chemical vapor deposition (CVD) process. The process allowed to grow long strands of SWNT bundles, which are then used to fabricate multiple arrays of switching devices with the channel length of 3, 5, 7 and 10 microm on a 15 mm x 15 mm SiO2 on Si substrate. Regardless of the channel length, a majority of the fabricated devices show current rectification characteristics, with high throughput of current (I) in the forward bias (V) giving the forward and reverse current ratio (Ifor/Irev) of approximately 10(6). Atomic force microscopic (AFM) analysis of the device structure and surface topology of SWNT suggest the observed rectification of current to possibly result from (a) cross-tube junctions, (b) a mixture of metallic and semiconducting tubes in the SWNT bundles, and/or (c) chirality change along a single tube. The exact mechanism underlying the observed rectification could not be conclusively established. However, the analyses of the experimental results strongly suggest the observed rectification to result from Schottky-type diode properties of SWNTs with mixed chirality along the tube.

PROFESS: a PROtein function, evolution, structure and sequence database.

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are approximately 1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein-protein interaction networks. Database URL: http://cse.unl.edu/~profess/