Electrostatic and hydrophobic interactions involved in CNT biofunctionalization with short ss-DNA

Water-Dispersible Carbon Nano-Test Tubes as a Container for Concentrated DNA Molecules

Water-dispersible carbon nano-test tubes (CNTTs) with an inner and outer diameter of about 25 and 35 nm, respectively, were prepared by the template technique and then their inner carbon surface was selectively oxidized to introduce carboxy groups. The adsorption behavior of DNA molecules on the oxidized CNTTs (Ox-CNTTs) was examined in the presence of Ca2+ cations. Many DNA molecules are attracted to the inner space of Ox-CNTTs based on the Ca2+ -mediated electrostatic interaction between DNA phosphate groups and carboxylate anions on the inner carbon surface. Moreover, the total net charge of the DNA adsorbed was found to be equal to the total charge of the carboxylate anions. This selective adsorption into the interior of Ox-CNTTs can be explained from the fact that the electrostatic interaction onto the inner concave surface is much stronger than that on the outer convex surface. On the other hand, the desorption of DNA easily occurs whenever Ca2+ cations are removed by washing with deionized water. Thus, each of Ox-CNTTs works well as a nano-container for a large amount of DNA molecules, thereby resulting in the occurrence of DNA enrichment in the nanospace.

Effects of Complex DNA and MVs with GTF Extracted from Streptococcus mutans on the Oral Biofilm

Streptococcus mutans is one of the principal pathogens for the development of dental caries. Oral biofilms formed by S. mutans are constructed of insoluble glucan formation induced by the principal enzymes, GTF-I and GTF-SI, in sucrose-containing conditions. However, as another means of biofilm formation, extracellular DNA (eDNA) and membrane vesicles (MVs) are also contributors. To explore the roles of eDNA and MVs for biofilm formation, short and whole size pure DNAs, two types of sub-purified DNAs and MVs were extracted from S. mutans by beads destruction, treatment of proteinase K, and ultracentrifugation of culture supernatant, and applied into the biofilm formation assay using the S. mutans UA159 gtfBC mutant, which lost GTF-I and GTF-SI, on a human saliva-coated 96 well microtiter plate in sucrose-containing conditions. Sub-purified DNAs after cell lysis by beads destruction for total 90 and 180 s showed a complex form of short-size DNA with various proteins and MVs associated with GTF-I and GTF-SI, and induced significantly higher biofilm formation of the S. mutans UA159.gtfBC mutant than no sample (p < 0.05). Short-size pure DNA without proteins induced biofilm formation but whole-size pure DNA did not. Moreover, the complex form of MV associated with GTFs and short-size DNA showed significantly higher biofilm formation of initial colonizers on the human tooth surface such as Streptococcus mitis than no sample (p < 0.05). The short-size DNAs associated with MVs and GTFs are important contributors to the biofilm formation and may be one of additional targets for the prevention of oral biofilm-associated diseases.

Protein adsorption onto nanomaterials for the development of biosensors and analytical devices: a review

An important consideration for the development of biosensors is the adsorption of the biorecognition element to the surface of a substrate. As the first step in the immobilization process, adsorption affects most immobilization routes and much attention is given into the research of this process to maximize the overall activity of the biosensor. The use of nanomaterials, specifically nanoparticles and nanostructured films, offers advantageous properties that can be fine-tuned to maximize interactions with specific proteins to maximize activity, minimize structural changes, and enhance the catalytic step. In the biosensor field, protein-nanomaterial interactions are an emerging trend that span across many disciplines. This review addresses recent publications about the proteins most frequently used, their most relevant characteristics, and the conditions required to adsorb them to nanomaterials. When relevant and available, subsequent analytical figures of merits are discussed for selected biosensors. The general trend amongst the research papers allows concluding that the use of nanomaterials has already provided significant improvements in the analytical performance of many biosensors and that this research field will continue to grow.

Spectroscopic and electrochemical characterization of nanostructured optically transparent carbon electrodes

The present paper describes the results related to the optical and electrochemical characterization of thin carbon films fabricated by spin coating and pyrolysis of AZ P4330-RS photoresist. The goal of this paper is to provide comprehensive information allowing for the rational selection of the conditions to fabricate optically transparent carbon electrodes (OTCE) with specific electrooptical properties. According to our results, these electrodes could be appropriate choices as electrochemical transducers to monitor electrophoretic separations. At the core of this manuscript is the development and critical evaluation of a new optical model to calculate the thickness of the OTCE by variable angle spectroscopic ellipsometry. Such data were complemented with topography and roughness (obtained by atomic force microscopy), electrochemical properties (obtained by cyclic voltammetry), electrical properties (obtained by electrochemical impedance spectroscopy), and structural composition (obtained by Raman spectroscopy). Although the described OTCE were used as substrates to investigate the effect of electrode potential on the real-time adsorption of proteins by ellipsometry, these results could enable the development of other biosensors that can be then integrated into various CE platforms.

DNA hairpin stabilization on a hydrophobic surface

DNA hybridization in the vicinity of surfaces is a fundamental process for self-assembled nanoarrays, nanocrystal superlattices, and biosensors. It is widely recognized that solid surfaces alter molecular forces governing hybridization relative to a bulk solution, and these effects can either favor or disfavor the hybridized state depending on the specific sequence and surface. Results presented here provide new insights into the dynamics of DNA hairpin-coil conformational transitions in the vicinity of hydrophilic oligo(ethylene glycol) (OEG) and hydrophobic trimethylsilane (TMS) surfaces. Single-molecule methods are used to observe the forward and reverse hybridization hairpin-coil transition of adsorbed species while simultaneously measuring molecular surface diffusion in order to gain insight into surface interactions with individual DNA bases. At least 35 000 individual molecular trajectories are observed on each type of surface. It is found that unfolding slows and the folding rate increases on TMS relative to OEG, despite stronger attractions between TMS and unpaired nucleobases. These rate differences lead to near-complete hairpin formation on hydrophobic TMS and significant unfolding on hydrophilic OEG, resulting in the surprising conclusion that hydrophobic surface coatings are preferable for nanotechnology applications that rely on DNA hybridization near surfaces.

Research Spotlight: The next big thing is actually small

Recent developments in materials, surface modifications, separation schemes, detection systems and associated instrumentation have allowed significant advances in the performance of lab-on-a-chip devices. These devices, also referred to as micro total analysis systems (µTAS), offer great versatility, high throughput, short analysis time, low cost and, more importantly, performance that is comparable to standard bench-top instrumentation. To date, µTAS have demonstrated advantages in a significant number of fields including biochemical, pharmaceutical, military and environmental. Perhaps most importantly, µTAS represent excellent platforms to introduce students to microfabrication and nanotechnology, bridging chemistry with other fields, such as engineering and biology, enabling the integration of various skills and curricular concepts. Considering the advantages of the technology and the potential impact to society, our research program aims to address the need for simpler, more affordable, faster and portable devices to measure biologically active compounds. Specifically, the program is focused on the development and characterization of a series of novel strategies towards the realization of integrated microanalytical devices. One key aspect of our research projects is that the developed analytical strategies must be compatible with each other; therefore, enabling their use in integrated devices. The program combines spectroscopy, surface chemistry, capillary electrophoresis, electrochemical detection and nanomaterials. This article discusses some of the most recent results obtained in two main areas of emphasis: capillary electrophoresis, microchip-capillary electrophoresis, electrochemical detection and interaction of proteins with nanomaterials.

Adsorption of Glucose Oxidase to 3-D Scaffolds of Carbon Nanotubes: Analytical Applications

This study is the first to focus on the potential use of carbon nanotube (CNT) scaffolds as enzyme immobilization substrates for analytical purposes. Besides all the well-known advantages of CNT, three-dimensional scaffolds can significantly increase the amount of enzymes adsorbed per unit area, preserve the catalytic activity of the adsorbed molecules, and allow effective exposure to substrates present in the adjacent medium. Additionally, our results indicate that the sensitivity of analytical probes based on enzyme-loaded CNT scaffolds is proportional to the thickness of the scaffold providing 3-fold sensitivity improvements with respect to the control surfaces.

Recent applications of carbon-based nanomaterials in analytical chemistry: critical review

The objective of this review is to provide a broad overview of the advantages and limitations of carbon-based nanomaterials with respect to analytical chemistry. Aiming to illustrate the impact of nanomaterials on the development of novel analytical applications, developments reported in the 2005-2010 period have been included and divided into sample preparation, separation, and detection. Within each section, fullerenes, carbon nanotubes, graphene, and composite materials will be addressed specifically. Although only briefly discussed, included is a section highlighting nanomaterials with interesting catalytic properties that can be used in the design of future devices for analytical chemistry.

Adsorption and desorption of DNA on graphene oxide studied by fluorescently labeled oligonucleotides

Being the newest member of the carbon materials family, graphene possesses many unique physical properties resulting is a wide range of applications. Recently, it was discovered that graphene oxide can effectively adsorb DNA, and at the same time, it can completely quench adsorbed fluorophores. These properties make it possible to prepare DNA-based optical sensors using graphene oxide. While practical analytical applications are being demonstrated, the fundamental understanding of binding between graphene oxide and DNA in solution received relatively less attention. In this work, we report that the adsorption of 12-, 18-, 24-, and 36-mer single-stranded DNA on graphene oxide is affected by several factors. For example, shorter DNAs are adsorbed more rapidly and bind more tightly to the surface of graphene. The adsorption is favored by a lower pH and a higher ionic strength. The presence of organic solvents such as ethanol can either increase or decrease adsorption depending on the ionic strength of the solution. By adding the cDNA, close to 100% desorption of the absorbed DNA on graphene can be achieved. On the other hand, if temperature is increased, only a small percentage of DNA is desorbed. Further, the adsorbed DNA can also be exchanged by free DNA in solution. These findings are important for further understanding of the interactions between DNA and graphene and for the optimization of DNA and graphene-based devices and sensors.