Measurements of the binding of a large protein using a substrate density-controlled DNA chip

A rapid and highly sensitive immunosorbent assay to monitor helicases unwinding diverse nucleic acid structures

Helicases are crucial enzymes in DNA and RNA metabolism and function by unwinding particular nucleic acid structures. However, most convenient and high-throughput helicase assays are limited to the typical duplex DNA. Herein, we developed an immunosorbent assay to monitor the Werner syndrome (WRN) helicase unwinding a wide range of DNA structures, such as a replication fork, a bubble, Holliday junction, G-quadruplex and hairpin. This assay could sensitively detect the unwinding of DNA structures with detection limits around 0.1 nM, and accurately monitor the substrate-specificity of WRN with a comparatively less time-consuming and high throughput process. Remarkably, we have established that this new assay was compatible in evaluating helicase inhibitors and revealed that the inhibitory effect was substrate-dependent, suggesting that diverse substrate structures other than duplex structures should be considered in discovering new inhibitors. Our study provided a foundational example for using this new assay as a powerful tool to study helicase functions and discover potent inhibitors.

Gallium plasmonic nanoparticles for label-free DNA and single nucleotide polymorphism sensing

A label-free DNA and single nucleotide polymorphism (SNP) sensing method is described. It is based on the use of the pseudodielectric function of gallium plasmonic nanoparticles (GaNPs) deposited on Si (100) substrates under reversal of the polarization handedness condition. Under this condition, the pseudodielectric function is extremely sensitive to changes in the surrounding medium of the nanoparticle surface providing an excellent sensing platform competitive to conventional surface plasmon resonance. DNA sensing has been carried out by immobilizing a thiolated capture probe sequence from Helicobacter pylori onto GaNP/Si substrates; complementary target sequences of Helicobacter pylori can be quantified over the range of 10 pM to 3.0 nM with a detection limit of 6.0 pM and a linear correlation coefficient of R(2) = 0.990. The selectivity of the device allows the detection of a single nucleotide polymorphism (SNP) in a specific sequence of Helicobacter pylori, without the need for a hybridization suppressor in solution such as formamide. Furthermore, it also allows the detection of this sequence in the presence of other pathogens, such as Escherichia coli in the sample. The broad applicability of the system was demonstrated by the detection of a specific gene mutation directly associated with cystic fibrosis in large genomic DNA isolated from blood cells.

DNA molecules site-specific immobilization and their applications

In addition to its role as a carrier of genetic information, DNA has been recognized as a construction material for the assembly of different objects and structural arrangements with nanoscale features. As a result of DNA’s self-recognition properties (based on the specific base-pairing of G-C and T-A), monolayer films of nucleic acids on solid supports have attracted an escalating attentions. Recently, numerous novel materials based on two-dimensional (2D) and three-dimensional (3D) DNA structures have been reported, which extends their utility to a large number of appliations. This review paper intends to be a new and comprehensive overview of recent strategies to site-specifically immobilized DNA on various materials, including carbonaceous substances, gold, and silica substrate, emphasizing the applications of site-specific DNA nanostructure-based devices for diagnostic, bioanalytical, food safety and environmental monitoring. Additionally, an up-to-date perspective is proposed at the end of this review.

Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds

Nucleic acids are useful for biomedical targeting and sensing applications in which the molecular environment is different from that of a dilute aqueous solution. In this study, the influence of various types of mixed solutions of water and water-soluble organic compounds on RNA was investigated by measuring the catalytic activity of the hammerhead ribozyme and the thermodynamic stability of an oligonucleotide duplex. The compounds with a net neutral charge, such as poly(ethylene glycol), small primary alcohols, amide compounds, and aprotic solvent molecules, added at high concentrations changed the ribozyme-catalyzed RNA cleavage rate, with the magnitude of the effect dependent on the NaCl concentration. These compounds also changed the thermodynamic stability of RNA base pairs of an oligonucleotide duplex and its dependence on the NaCl concentration. Specific interactions with RNA molecules and reduced water activity could account for the inhibiting effects on the ribozyme catalysis and destabilizing effects on the duplex stability. The salt concentration dependence data correlated with the dielectric constant, but not with water activity, viscosity, and the size of organic compounds. This observation suggests the significance of the dielectric constant effects on the RNA reactions under molecular crowding conditions created by organic compounds.

Bioanalytical approaches for the detection of single nucleotide polymorphisms by Surface Plasmon Resonance biosensors

The mapping of specific single nucleotide polymorphisms (SNPs) in patients' genome is a main goal in theranostics, aiming to the development of therapies based on personalized medicine. In this review, Surface Plasmon Resonance (SPR) and Surface Plasmon Resonance imaging (SPRi) biosensors applied to the recognition of SNPs were reviewed, since these technologies are emerging in clinical diagnosis as powerful tools thanks to their analytical features, mainly the real-time and label-free monitoring based on array format for parallel analysis. Since the literature is heterogeneous, a critical classification and a systemic comparison of the analytical performances of published methods were here reviewed on the basis of the analytical strategy and the assay design. In particular, the use of helping agents (i.e. proteins, nanoparticles (NPs), intercalating agents) or artificial DNAs, often coupled to SPR to achieve allele discrimination and/or enhanced sensitivity, were here revised and classified. Finally, the real suitability of SPR biosensors to clinical diagnostics for SNPs detection was addressed by comparing their features and performances with those of other biosensors based on other techniques (e.g. electrochemical biosensors).

Assaying multiple restriction endonucleases functionalities and inhibitions on DNA microarray with multifunctional gold nanoparticle probes

Herein, a double-stranded (ds) DNA microarray-based resonance light scattering (RLS) assay with multifunctional gold nanoparticle (GNP) probes has been developed for studying restriction endonuclease functionality and inhibition. Because of decreasing significantly melting temperature, the enzyme-cleaved dsDNAs easily unwind to form single-stranded (ss) DNAs. The ssDNAs are hybridized with multiplex complementary ssDNAs functionalized GNP probes followed by silver enhancement and RLS detection. Three restriction endonucleases (EcoRI, BamHI and EcoRV) and three potential inhibitors (doxorubicin hydrochloride (DOX), ethidium bromide (EB) and an EcoRI-derived helical peptide (α4)) were selected to demonstrate capability of the assay. Enzyme activities of restriction endonucleases are detected simultaneously with high specificity down to the limits of 2.0 × 10(-2)U/mL for EcoRI, 1.1 × 10(-2)U/mL for BamHI and 1.6 × 10(-2)U/mL for EcoRV, respectively. More importantly, the inhibitory potencies of three inhibitors are showed quantitatively, indicating that our approach has great promise for high-throughput screening of restriction endonuclease inhibitors.

Surface plasmon resonance sensing of nucleic acids: a review

Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.

Towards a high-throughput label-free detection system combining localized-surface plasmon resonance and microfluidics

This work reports an integrated platform combining localized-surface plasmon resonance (LSPR) and microfluidic chips to carry out multiplexed and label-free protein analysis. We fabricated an optical bench to enable detection using only a laboratory UV-Vis spectrophotometer. This assay not only improves throughput, but also allows quantitative analysis.

Confocal micro-x-ray fluorescence spectrometer for light element analysis

An existing micro-x-ray fluorescence (micro-XRF) spectrometer designed for light element analysis (6 ≤ Z ≤ 14) has been extended to confocal geometry: a second polycapillary x-ray optic has been introduced in front of the energy dispersive x-ray detector. New piezo positioners for optimum alignment of both optics have been installed inside the vacuum chamber. The spectrometer offers now the possibility of true 3D elemental analysis in the micrometer regime. Depth resolution varies between 100 μm at 1 keV fluorescence energy (Na-Kα) and 30 μm for 17.5 keV (Mo). To further extend analytical capabilities a second x-ray tube with a Rh anode has been acquired to supplement to existing Mo anode tube. Lower limits of detection have been determined to be in the ppm region for confocal geometry. The spectrometer has been characterized and tested using different samples. Furthermore, results have been compared with SR micro-XRF to show the capabilities and limitations of this spectrometer.