Immobilization of silanized DNA on glass: influence of the silane tether on the DNA hybridization

Trifunctional Silyl Groups as Anchoring Units in the Preparation of Luminescent Phosphole-Silica Hybrids

A synthetic strategy to β-silylphospholes with three methoxy, ethoxy, chloro, hydrido, or phenyl substituents at silicon has been developed, starting from trimethoxy, triethoxy, or triphenyl silyl substituted phenyl phosphanides and 1,4-diphenyl-1,3-butadiyne. These trifunctional silylphospholes were attached to the surface of uniform spheric silica particles (15 μm) and, for comparison, to a polyhedral silsesquioxane (POSS)-trisilanol as a molecular model to explore their luminescent properties in comparison with the free phospholes. Density functional theory calculations were performed to investigate any electronic perturbation of the phosphole system by the trifunctional silyl anchoring unit. For the immobilized phospholes, cross-polarization magic-angle-spinning NMR measurements (¹³C, ²⁹Si, and ³¹P) were carried out to explore the bonding situation to the silica surface. Thermogravimetric analysis and X-ray photoelectron spectroscopy measurements were performed to approximate the amount of phospholes covering the silica surface. Identity and purity of all novel phospholes have been established with standard techniques (multinuclear NMR, mass spectrometry, and elemental analysis) and X-ray diffraction for the POSS derivative.

Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

The complex physical and chemical reactions between the large number of low-energy (0-30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.

Atomic Force Microscopy Imaging Study of Aligning DNA by Dumbbell-like Au-Fe3O4 Magnetic Nanoparticles

Studies on nucleic acid structure and interactions between nucleic acid and its binding molecules are of great importance for understanding and controlling many important biological processes. Atomic force microscopy (AFM) imaging is one of the most efficient methods to disclose the DNA structure and binding modes between DNA and DNA-binding molecules. Long-chain DNA tends to form a random coiled structure, which prevents direct AFM imaging observation of the subtle structure formed by DNA itself or protein binding. Aligning DNA from the random coiled state into the extended state is not only important for applications in DNA nanotechnology but also for elucidating the interaction mechanism between DNA and other molecules. Here, we developed an efficient method based on the magnetic field to align long-chain DNA on a silicon surface. We used AFM imaging to study the alignment of DNA at the single-molecule level, showing that DNA can be stretched and highly aligned by the manipulation of magnetic nanoparticles tethered to one end of DNA and that the aligned DNA can be imaged clearly by AFM. In the absence of the magnetic field, the aligned DNA can relax back to a random coiled state upon rinsing. Such alignment and relaxation can be repeated many times, which provides an efficient method for the manipulation of individual DNA molecules and the investigation of DNA and DNA-binding molecule interactions.

Direct electron irradiation of DNA in a fully aqueous environment. Damage determination in combination with Monte Carlo simulations

We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si₃N₄ membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSBs) and double-strand breaks (DSBs), was determined by gel electrophoresis. The median lethal dose of D_1/2 = 1.7 ± 0.3 Gy was found to be much smaller as compared to partially or fully hydrated DNA irradiated under vacuum conditions. The ratio of the DSBs to SSBs was found to be 1 : 12 as compared to 1 : 88 found for hydrated DNA. Our method enables quantitative measurements of radiation damage to biomolecules (DNA, proteins) in solutions under varying conditions (pH, salinity, co-solutes) for an electron energy range which is difficult to probe by standard methods.

Label-free ITO-based immunosensor for the detection of very low concentrations of pathogenic bacteria

Here we describe the fabrication of a highly sensitive and label-free ITO-based impedimetric immunosensor for the detection of pathogenic bacteria Escherichia coli O157:H7. Anti-E. coli antibodies were immobilized onto ITO electrodes using a simple, robust and direct methodology. First, the covalent attachment of epoxysilane on the ITO surface was demonstrated by Atomic Force Microscopy and cyclic voltammetry. The immobilization of antibody on the epoxysilane layer was quantified by Optical Waveguide Lightmode Spectroscopy, obtaining a mass variation of 12 ng cm(− 2) (0.08 pmol cm(− 2)). Microcontact printing and fluorescence microscopy were used to demonstrate the specific binding of E. coli O157:H7 to the antibody-patterned surface. We achieved a ratio of 1:500 Salmonella typhimurium/E. coli O157:H7, thus confirming the selectivity of the antibodies and efficiency of the functionalization procedure. Finally, the detection capacity of the ITO-based immunosensor was evaluated by Electrochemical Impedance Spectroscopy. A very low limit of detection was obtained (1 CFU mL(− 1)) over a large linear working range (10–10(6) CFU mL(− 1)). The specificity of the impedimetric immunosensor was also examined. Less than 20% of non-specific bacteria (S. typhimurium and E. coli K12) was observed. Our results reveal the applicability of ITO for the development of highly sensitive and selective impedimetric immunosensors.

Straightforward Micropatterning of Oligonucleotides in Microfluidics by Novel Spin-On ZrO₂ Surfaces

DNA biochip assays often require immobilization of bioactive molecules on solid surfaces. A simple biofunctionalization protocol and precise spatial binding represent the two major challenges in order to obtain localized region specific biopatterns into lab-on-a-chip (LOC) systems. In this work, a simple strategy to anchor oligonucleotides on microstructured areas and integrate the biomolecules patterns within microfluidic channels is reported. A photosensitive ZrO2 system is proposed as an advanced platform and versatile interface for specific positioning and oriented immobilization of phosphorylated DNA. ZrO2 sol-gel structures were easily produced on fused silica by direct UV lithography, allowing a simple and fast patterning process with different geometries. A thermal treatment at 800 °C was performed to crystallize the structures and maximize the affinity of DNA to ZrO2. Fluorescent DNA strands were selectively immobilized on the crystalline patterns inside polydimethylsiloxane (PDMS) microchannels, allowing high specificity and rapid hybridization kinetics. Hybridization tests confirmed the correct probe anchoring and the bioactivity retention, while denaturation experiments demonstrated the possibility of regenerating the surface.

Surface modifications using a water-stable silanetriol in neutral aqueous media

Surface modifications of glass slides employing the sterically hindered tert-butyl substituted silanetriol are described. To the best of our knowledge, this is the first time that a stable silanetriol has been directly used for this purpose. So far unprecedented, this process runs under neutral aqueous conditions and in the absence of organic solvents, which makes coating protocols accessible to acid-sensitive substrates. The layer thickness and surface topography are investigated by the Sarfus technique, by X-ray reflectivity, and by atomic force microscopy (AFM). These techniques yield values of 0.8±0.1 (XRR) and 0.6±0.2 nm (Sarfus) for layer thickness and 0.33 nm for root mean square roughness (AFM). The modified surfaces have hydrophobic and oleophilic character and contact angles (CA) between 60° (formamide, CH2I2) and 90° (water) are obtained. The thin coatings allow a structuring by UV/ozone treatment in order to get hydrophilic and hydrophobic compartments on the surfaces. For all coatings, surface free energies are calculated using different models. To determine the isoelectric points (IEP) of the modified surfaces, we performed zeta-potential measurements. Correlations between zeta potentials and hydrophilicity of the surfaces are shown.