Controlled loading of oligodeoxyribonucleotide monolayers onto unoxidized crystalline silicon; fluorescence-based determination of the surface coverage and of the hybridization efficiency; parallel imaging of the process by Atomic Force Microscopy

Graphene for the Building of Electroanalytical Enzyme-Based Biosensors. Application to the Inhibitory Detection of Emerging Pollutants

Graphene and its derivates offer a wide range of possibilities in the electroanalysis field, mainly owing to their biocompatibility, low-cost, and easy tuning. This work reports the development of an enzymatic biosensor using reduced graphene oxide (RGO) as a key nanomaterial for the detection of contaminants of emerging concern (CECs). RGO was obtained from the electrochemical reduction of graphene oxide (GO), an intermediate previously synthesized in the laboratory by a wet chemistry top-down approach. The extensive characterization of this material was carried out to evaluate its proper inclusion in the biosensor arrangement. The results demonstrated the presence of GO or RGO and their correct integration on the sensor surface. The detection of CECs was carried out by modifying the graphene platform with a laccase enzyme, turning the sensor into a more selective and sensitive device. Laccase was linked covalently to RGO using the remaining carboxylic groups of the reduction step and the carbodiimide reaction. After the calibration and characterization of the biosensor versus catechol, a standard laccase substrate, EDTA and benzoic acid were detected satisfactorily as inhibiting agents of the enzyme catalysis obtaining inhibition constants for EDTA and benzoic acid of 25 and 17 mmol·L⁻¹, respectively, and a maximum inhibition percentage of the 25% for the EDTA and 60% for the benzoic acid.

Detection of single DNA molecule hybridization on a surface by atomic force microscopy

Improving the detection of DNA hybridization is a critical issue for several challenging applications encountered in microarray and biosensor domains. Herein, it is demonstrated that hybridization between complementary single-stranded DNA (ssDNA) molecules loosely adsorbed on a mica surface can be achieved thanks to fine-tuning of the composition of the hybridization buffer. Single-molecule DNA hybridization occurs in only a few minutes upon encounters of freely diffusing complementary strands on the mica surface. Interestingly, the specific hybridization between complementary ssDNA is not altered in the presence of large amounts of nonrelated DNA. The detection of single-molecule DNA hybridization events is performed by measuring the contour length of DNA in atomic force microscopy images. Besides the advantage provided by facilitated diffusion, which promotes hybridization between probes and targets on mica, the present approach also allows the detection of single isolated DNA duplexes and thus requires a very low amount of both probe and target molecules.

High-resolution X-ray photoelectron spectroscopy of mixed silane monolayers for DNA attachment

The amine density of 3-aminopropyldimethylethoxysilane (APDMES) films on silica is controlled to determine its effect on DNA probe density and subsequent DNA hybridization. The amine density is tailored by controlling the surface reaction time of (1) APDMES, or (2) n-propyldimethylchlorosilane (PDMCS, which is not amine terminated) and then reacting it with APDMES to form a mixed monolayer. High-resolution X-ray photoelectron spectroscopy (XPS) is used to quantify silane surface coverage of both pure and mixed monolayers on silica; the XPS data demonstrate control of amine density in both pure APDMES and PDMCS/APDMES mixed monolayers. A linear correlation between the atomic concentration of N atoms from the amine and Si atoms from the APDMES in pure APDMES films allows us to calculate the PDMCS/APDMES ratio in the mixed monolayers. Fluorescence from attached DNA probes and from hybridized DNA decreases as the percentage of APDMES in the mixed monolayer is decreased by dilution with PDMCS.

Controlling oligonucleotide surface density in light-directed DNA array fabrication

Over the past two decades high-density DNA arrays have developed into a central technology for nucleic acid analyses. Important application areas include whole-genome gene expression studies, high throughput analyses of single nucleotide polymorphisms, and, most recently, the determination of binding site specificities for transcription factors and other critical elements involved in gene regulation. A key parameter in the performance of DNA arrays is the density of the surface-bound oligonucleotides, which strongly affects both thermodynamic and kinetic aspects of DNA hybridization. In this report, we describe an approach for the control of oligonucleotide density in photolithographically fabricated DNA arrays, based upon a controlled UV light deprotection procedure. Modulation of the UV exposure permits a desired degree of deprotection of surface synthesis sites; a subsequent capping reaction to inactivate the exposed sites leaves only a desired fraction of active sites remaining for synthesis, corresponding to a lower oligonucleotide density. It is shown that the procedure is reasonably general, in that it is readily transferable to alternative substrate materials with similar results.

Quantitation of ultraviolet-induced single-strand breaks using oligonucleotide chip

A simple, accurate and robust methodology was established for the direct quantification of ultraviolet (UV)-induced single-strand break (SSB) using oligonucleotide chip. Oligonucleotide chips were fabricated by covalently anchoring the fluorescent-labeled ssDNAs onto silicon dioxide chip surfaces. Assuming that the possibility of more than one UV-induced SSB to be generated in a small oligonucleotide is extremely low, SSB formation was investigated quantifying the endpoint probe density by fluorescence measurement upon UV irradiation. The SSB yields obtained based on the highly sensitive laser-induced fluorometric determination of fluorophore-labeled oligonucleotides were found to coincide well with that predicted from a theoretical extrapolation of the results obtained for plasmid DNAs using conventional agarose gel electrophoresis. The developed method has the potential to serve as a high throughput, sample-thrifty, and time saving tool to realize more realistic, and direct quantification of radiation and chemical-induced strand breaks. It will be especially useful for determining the frequency of SSBs or lesions convertible to SSBs by specific cleaving reagents or enzymes.

Wiring efficiency of a metallizable DNA linker for site-addressable nanobioelectronic assembly

We report the first demonstration of DNA oligonucleotide tags used to address the site-specific assembly of multiple redox enzymes onto spatially distinct regions of a nanoelectronic platform, establishing a direct electrical contact. The resulting system constitutes a multiplexed carbon nanotube-redox protein biosensor capable of detecting varying concentrations of several different substances in real time. The efficiency and robustness of the enzyme linking scheme is explored in detail, showing a high degree of preservation of enzymatic activity and an efficient electrical contact at the enzyme-nanoelectrode interface. While five proteins have been used as a demonstration in this study, there is virtually no limit to the number of enzymes that could be bound in parallel using this linking strategy, which is universally applicable to all proteins due to the simple conjugation chemistry involved. We further demonstrate metallization of the linker in the presence of a divalent metal cation, inducing elevated electron transfer efficiency relative to the native DNA link.

Role of Surface Dimer Dynamics in Creating Ordered Organic−Semiconductor Interfaces

Understanding the chemical reaction mechanisms governing how small organic molecules attach to semiconductor surfaces can lead to new strategies for creating specific surface patterns such as single adduct monolayers. In this study, room-temperature ab initio molecular dynamics simulations of one and two 1,3-cyclohexadiene (CHD) molecule(s) reacting with the Si(100)-2x1 surface reveal that adducts form via a carbocation-mediated two-step mechanism. Dimer flipping can either promote or prevent bond formation depending on how the CHD approaches. CHDs often travel past several Si dimers before finding the proper local environment. The resulting intermediate can persist for more than 4 ps, allowing the second bond to form with any adjacent Si dimer. The additional reactive site accounts for a large portion of the discrepancy between the predicted thermodynamic and observed experimental product distribution. Surface adducts protect a 5.6 A region, direct unbound CHD exploration, and can cause adjacent dimers to flip.

Cathodic Electrografting of Versatile Ligands on Si(100) as a Low-Impact Approach for Establishing a SiC Bond: A Surface-Coordination Study of Substituted 2,2′-Bipyridines with CuI Ions

Three distinct wet chemistry recipes were applied to hydrogen-terminated n- and p-Si(100) surfaces in a comparative study of the covalent grafting of two differently substituted 2,2'-bipyridines. The applied reactions require the use of heat, or visible light under a controlled atmosphere, or a suitable potential in an electrochemical cell. In this last case, hydrogen-terminated silicon is the working electrode in a cathodic electrografting (CEG) reaction, in which it is kept under reduction conditions. The resulting Si--C bound hybrids were characterized by a combination of AFM, dynamic contact-angle, and XPS analysis, with the help of theoretical calculations. The three distinct approaches were found to be suitable for obtaining ligand-functionalized Si surfaces. CEG resulted in the most satisfactory anchoring procedure, because of its better correlation between high coverage and preservation of the Si surface from both oxidation and contamination. The corresponding Si-bipyridine hybrid was reacted in a solution of CH3CN containing CuI ions coordinatively bound to the anchored ligands, as evidenced from the XPS binding-energy shift of the N atom donor functions. The reaction gave a 1:2 Cu-bipyridine surface complex, in which two ligands couple to a single CuI ion. The surface complex was characterized by the Cu Auger parameter and Cu/N XPS atomic-ratio values coincident with those for pure, unsupported CuI complex with the same 2,2'-bipyridine. Further support for such a specific metal-ligand interaction at the functionalized Si surface came from the distinct values of Cu2p binding energy and the Cu Auger parameter, which were obtained for the species resulting from CuI ion uptake on hydrogen-terminated Si(100).

Different membrane modifications revealed by atomic force/lateral force microscopy after doping of human pancreatic cells with Cd, Zn, or Pb

The interaction of the cytotoxic metals cadmium, zinc, and lead with pancreatic cells was studied by atomic force/lateral Force microscopy (AFM/LFM), an approach that provides both topographic (with nanometer scale lateral resolution) and chemical information on the membrane. Different morphological modifications of the overall cell shape and roughness took place as consequence of 100 muM metal-dependent treatment. Furthermore, after exposure to Cd(Cl(2)) and Zn(Cl(2)), but not Pb(Cl(2)), the LFM images revealed several areas of the cell's surface showing lateral friction contrasts that have been interpreted as marker of different alterations of the cell physiology induced by the metal loading. Thus, the coupling of LFM detection to topographic AFM characterization allows to distinguish, through a nondestructive and surface characterising approach, between different metal-induced cytotoxic effects on cells. In this framework, the role of the LFM as an important tool to discriminate between different alteration of a biological system has to be highlighted.

Surface Modification for DNA and Protein Microarrays

Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.