Characteristic differences in the X-ray photoelectron spectrum between B-DNA and M-DNA monolayers on gold

Electrochemical Sensor for the Detection and Accurate Early Diagnosis of Ovarian Cancer

Ovarian cancer (OC) has the highest mortality rate among malignant tumors, primarily because it is difficult to diagnose early. Exosomes, a type of extracellular vesicle rich in parental information, have garnered significant attention in the field of cancer diagnosis and treatment. They play an important regulatory role in the occurrence, development, and metastasis of OC. Consequently, exosomes have emerged as noninvasive biomarkers for early cancer detection. Therefore, identifying cancer-derived exosomes may offer a novel biomarker for the early detection of OC. In this study, we developed a metal-organic frameworks assembled "double hook"-type aptamer electrochemical sensor, which enables accurate early diagnosis of OC. Under optimal experimental conditions, electrochemical impedance spectroscopy technology demonstrated a good linear relationship within the concentration range of 31-3.1 × 106 particles per microliter, with a detection limit as low as 12 particles per microliter. The universal exosome detection platform is constructed, and this platform can not only differentiate between high-grade serous ovarian cancer (HGSOC) patients and healthy individuals but also distinguish between HGSOC patients and nonhigh-grade serous OC (non-HGSOC). Consequently, it provides a novel strategy for the early diagnosis of OC and holds great significance in clinical differential diagnosis.

Band gap, dielectric constant, and susceptibility of DNA layers as controlled by vanadium ion concentration

Deoxyribonucleic acid (DNA) doped with transition metal ions shows great versatility for molecular-based biosensors and bioelectronics. Methodologies for developing DNA lattices (formed by synthetic double-crossover tiles) and DNA layers (used by natural salmon) doped with vanadium ions (V3+), as well as an understanding of the physical characteristics of V3+-doped DNA nanostructures, are essential in practical applications in interdisciplinary research fields. Here, DNA lattices and layers doped with V3+ are constructed through substrate-assisted growth and drop-casting methods. In addition, enhanced physical characteristics such as the band gap energy, work function, dielectric constant, and susceptibility of V3+-doped DNA nanostructures with varying V3+ concentration ([V 3+ ]) are investigated. The critical concentration ([V 3+ ]C ) at a given amount of DNA was predicted based on an analysis of the phase transition of DNA lattices from crystalline to amorphous with specific [V 3+ ]. Generally, the [V 3+ ]C provided crucial information on the structural stability and extremum physical characteristics of V3+-doped DNA nanostructures due to the optimum incorporation of V3+ into DNA. We obtained the optical absorption spectra for energy band gap estimation; Raman spectra for identifying the preferential coordination sites of V3+ in DNA; x-ray photoelectron spectra to examine the chemical state, chemical composition, and functional groups; and ultraviolet photoelectron spectra to estimate the work function. In addition, we addressed the electrical properties (i.e. current, capacitance, dielectric constant, and storage energy) and magnetic properties (magnetic field-dependent and temperature-dependent magnetizations and susceptibility) of DNA layers in the presence of V3+. The development of biocompatible materials with specific optical, electrical, and magnetic properties is required for future applications because they must have designated functionality, high efficiency, and affordability.

DNA nanostructures doped with lanthanide ions for highly sensitive UV photodetectors

Deoxyribonucleic acid (DNA) and lanthanide ions (Ln³⁺) exhibit exceptional optical properties that are applicable to the development of nanoscale devices and sensors. Although DNA nanostructures and Ln³⁺ ions have been investigated for use in the current state of technology for more than a few decades, researchers have yet to develop DNA and Ln³⁺ based ultra-violet (UV) photodetectors. Here, we fabricate Ln³⁺ (such as holmium (Ho³⁺), praseodymium (Pr³⁺), and ytterbium (Yb³⁺))‒doped double crossover (DX)‒DNA lattices through substrate-assisted growth and salmon DNA (SDNA) thin films via a simple drop-casting method on oxygen (O₂) plasma-treated substrates for high performance UV photodetectors. Topological (AFM), optical (UV-vis absorption and FTIR), spectroscopic (XPS), and electrical (I‒V and photovoltage) measurements of the DX‒DNA and SDNA thin films doped with various concentrations of Ln³⁺ ([Ln³⁺]) are explored. From the AFM analysis, the optimum concentrations of various Ln³⁺ ([Ln³⁺]_O) are estimated (where the phase transition of Ln³⁺‒doped DX‒DNA lattices takes place from crystalline to amorphous) as 1.2 mM for Ho³⁺, 1.5 mM for Pr³⁺, and 1.5 mM for Yb³⁺. The binding modes and chemical states are evaluated through optical and spectroscopic analysis. From UV-vis absorption studies, we found that as the [Ln³⁺] was increased, the absorption intensity decreased up to [Ln³⁺]_O, and increased above [Ln³⁺]_O. The variation in FTIR peak intensities in the nucleobase and phosphate regions, and the changes in XPS peak intensities and peak positions detected in the N 1 s and P 2p core spectra of Ln³⁺‒doped SDNA thin films clearly indicate that the Ln³⁺ ions are properly bound between the bases (through chemical intercalation) and to the phosphate backbone (through electrostatic interactions) of the DNA molecules. Finally, the I‒V characteristics and time-dependent photovoltage of Ln³⁺‒doped SDNA thin films are measured both in the dark and under UV LED illuminations (λ_LED = 382 nm) at various illumination powers. The photocurrent and photovoltage of Ln³⁺‒doped SDNA thin films are enhanced up to the [Ln³⁺]_O compared to pristine SDNA due to the charge carriers generated from both SDNA and Ln³⁺ ions upon the absorption of light. From our observations, the photovoltages as function of illumination power suggest higher responsivities, and the photovoltages as function of time are almost constant which indicates the stability and retention characteristics of the Ln³⁺‒doped SDNA thin films. Hence, our method which provides an efficient doping of Ln³⁺ into the SDNA with a simple fabrication process might be useful in the development of high-performance optoelectronic devices and sensors.

Geometry-dependent DNA-TiO2 immobilization mechanism: A spectroscopic approach

DNA nucleotides are used as a molecular recognition system on electrodes modified to be applied in the detection of various diseases, but immobilization mechanisms, as well as, charge transfers are not satisfactorily described in the literature. An electrochemical and spectroscopic study was carried out to characterize the molecular groups involved in the direct immobilization of DNA structures on the surface of nanostructured TiO₂ with the aim of evaluating the influence of the geometrical aspects. X-ray photoelectron spectroscopy at O1s and P2p core levels indicate that immobilization of DNA samples occurs through covalent (POTi) bonds. X-ray absorption spectra at the Ti2p edge reinforce this conclusion. A new species at 138.5eV was reported from P2p XPS spectra analysis which plays an important role in DNA-TiO₂ immobilization. The POTi/OTi ratio showed that quantitatively the DNA immobilization mechanism is dependent on their geometry, becoming more efficient for plasmid ds-DNA structures than for PCR ds-DNA structures. The analysis of photoabsorption spectra at C1s edge revealed that the molecular groups that participate in the C1s→LUMO electronic transitions have different pathways in the charge transfer processes at the DNA-TiO₂ interface. Our results may contribute to additional studies of immobilization mechanisms understanding the influence of the geometry of different DNA molecules on nanostructured semiconductor and possible impact to the charge transfer processes with application in biosensors or aptamers.

Electromagnetic and optical characteristics of Nb5+-doped double-crossover and salmon DNA thin films

We report the fabrication and physical characteristics of niobium ion (Nb⁵⁺)-doped double-crossover DNA (DX-DNA) and salmon DNA (SDNA) thin films. Different concentrations of Nb⁵⁺ ([Nb⁵⁺]) are coordinated into the DNA molecules, and the thin films are fabricated via substrate-assisted growth (DX-DNA) and drop-casting (SDNA) on oxygen plasma treated substrates. We conducted atomic force microscopy to estimate the optimum concentration of Nb⁵⁺ ([Nb⁵⁺]_O = 0.08 mM) in Nb⁵⁺-doped DX-DNA thin films, up to which the DX-DNA lattices maintain their structures without deformation. X-ray photoelectron spectroscopy (XPS) was performed to probe the chemical nature of the intercalated Nb⁵⁺ in the SDNA thin films. The change in peak intensities and the shift in binding energy were witnessed in XPS spectra to explicate the binding and charge transfer mechanisms between Nb⁵⁺ and SDNA molecules. UV-visible, Raman, and photoluminescence (PL) spectra were measured to determine the optical properties and thus investigate the binding modes, Nb⁵⁺ coordination sites in Nb⁵⁺-doped SDNA thin films, and energy transfer mechanisms, respectively. As [Nb⁵⁺] increases, the absorbance peak intensities monotonically increase until ∼[Nb⁵⁺]_O and then decrease. However, from the Raman measurements, the peak intensities gradually decrease with an increase in [Nb⁵⁺] to reveal the binding mechanism and binding sites of metal ions in the SDNA molecules. From the PL, we observe the emission intensities to reduce them at up to ∼[Nb⁵⁺]_O and then increase after that, expecting the energy transfer between the Nb⁵⁺ and SDNA molecules. The current-voltage measurement shows a significant increase in the current observed as [Nb⁵⁺] increases in the SDNA thin films when compared to that of pristine SDNA thin films. Finally, we investigate the temperature dependent magnetization in which the Nb⁵⁺-doped SDNA thin films reveal weak ferromagnetism due to the existence of tiny magnetic dipoles in the Nb⁵⁺-doped SDNA complex.

Ironing Out Genes in the Environment: An Experimental Study of the DNA-Goethite Interface

DNA fate in soil plays an important role in the cycling of genetic information in the environment. Adsorption onto mineral surfaces has great impact on this function. This study probes the kinetics, equilibrium behavior and bonding mechanisms associated with adsorption of DNA onto goethite, a common soil mineral. Surface sensitive ATR-FTIR and XPS approaches are applied to directly characterize the DNA-goethite interface. Adsorption kinetics follow a pseudo-first-order model, suggesting adsorption rate is surface limited. Adsorption rate constants increase with DNA concentration, ranging from 3.29 × 10^-3 to 3.55 × 10^-1 min^-1. Equilibrium adsorption, as monitored by ATR-FTIR and XPS, follows the Langmuir model, with a high affinity of DNA for goethite observed (K = 1.25 × 10³ and 9.48 × 10² mL/mg for ATR-FTIR and XPS, respectively). ATR-FTIR and XPS characterization of the structure of surface adsorbed DNA demonstrates inner-sphere coordination between backbone phosphate groups of DNA and goethite. Furthermore, adsorbed DNA retains a B-form, suggesting the DNA helix adsorbs on goethite without degradation or alteration to helical structure, despite binding of backbone phosphate groups. This work advances our understanding of the environmental behavior of DNA by characterizing the mechanism of adsorption onto a prominent soil mineral.

An easy way to realize SPR aptasensor: A multimode plastic optical fiber platform for cancer biomarkers detection

The introduction of new compact systems for sensitive, fast and simplified analysis is currently playing a substantial role in the development of point-of-care solutions aimed to assist both prognosis and diagnosis. Here we report a simple and low cost biosensor based on Surface Plasmon Resonance (SPR) taking advantage of a plastic optical fiber (POF) for the detection of Vascular endothelial growth factor (VEGF), selected as a circulating protein potentially associated with cancer. Our system is based onto two crucial aspects. By one hand, the functional layer which allows the transduction signal is based on DNA aptamers, short oligonucleotide sequences that bind to non-nucleic acid targets with high affinity and specificity. By the other hand, the light guiding structure is based on a POF with a planar gold layer as the sensing region, which is particularly suitable for bioreceptors implementation. The sensor revealed to be really useful in the interface characterization. The developed system is relatively easy to realize and could well address the development of a rapid, portable and low cost diagnostic platform, with a sensitivity in the nanomolar range.

Metal-cluster-decorated TiO2 nanotube arrays: a composite heterostructure toward versatile photocatalytic and photoelectrochemical applications

Recent years have witnessed increasing interest in the solution-phase synthesis of atomically precise thiolate-protected gold clusters (Aux ); nonetheless, research on the photocatalytic properties of Aux -semiconductor nanocomposites is still in its infancy. In this work, recently developed glutathione-capped gold clusters and highly ordered nanoporous layer-covered TiO2 nanotube arrays (NP-TNTAs) are employed as nanobuilding blocks for the construction of a well-defined Aux /NP-TNTA heterostructure via a facile electrostatic self-assembly strategy. Versatile photocatalytic performances of the Aux /NP-TNTA heterostructure which acts as a model catalyst, including photocatalytic oxidation of organic pollutant, photocatalytic reduction of aromatic nitro compounds and photoelectrochemical (PEC) water splitting under simulated solar light irradiation, are systematically exploited. It is found that synergistic interaction stemming from monodisperse coverage of Aux clusters on NP-TNTAs in combination with hierarchical nanostructure of NP-TNTAs reinforce light absorption of Aux /NP-TNTA heterostructure especially within visible region, hence contributing to the significantly enhanced photocatalytic and PEC water splitting performances. Moreover, photocatalytic and PEC mechanisms over Aux /NP-TNTA heterostructure are elucidated and corresponding reaction models were presented. It is anticipated that this work could boost new insight for photocatalytic properties of metal-cluster-sensitized semiconductor nanocomposites.

Controlled synthesis of peony-shaped photocatalyst grains of Ag3PO4/Zn3(PO4)2 by coprecipitation and recrystallization technology

Peony-shaped grains of a Ag₃PO₄/Zn₃(PO₄)₂ composite have been synthesized through a coprecipitation and recrystallization technology.

Sensitive Marker of the Cisplatin-DNA Interaction: X-Ray Photoelectron Spectroscopy of CL

The development of cisplatin and Pt-based analogues anticancer agents requires knowledge concerning the molecular mechanisms of interaction between such drugs with DNA. However, the binding dynamics and kinetics of cisplatin reactions with DNA determined by traditional approaches are far from satisfactory. In this study, a typical 20-base oligonucleotide (CGTGACAGTTATTGCAGGCG), as a simplified model representing DNA, was mixed with cisplatin in different molar ratios and incubation time. High-resolution XPS spectra of the core elements C, N, O, P, and Cl were recorded to explore the interaction between cisplatin and DNA. From deconvoluted Cl spectra we could readily differentiate the covalently bound chlorine from ionic chloride species in the cisplatin-oligo complexes, which displayed distinct features at various reaction times and ratios. Monitoring the magnitude and energy of the photoelectron Cl 2p signal by XPS could act as a sensitive marker to probe the interaction dynamics of chemical bonds in the reaction of cisplatin with DNA. At 37°C, the optimum incubation time to obtain a stable cisplatin-oligo complex lies around 20 hrs. This novel analysis technique could have valuable implications to understand the fundamental mechanism of cisplatin cytotoxicity and determine the efficiency of the bonds in treated cancer cells.

Heterobifunctional modification of DNA for conjugation to solid surfaces

Many biosensors, DNA arrays, and next-generation DNA sequencing technologies need common methods for end modification of random DNA sequences generated from a sample of DNA. Surface immobilization of chemically modified DNA is often the first step in creating appropriate sensing platforms. We describe a simple technique for efficient heterobifunctional modification of arbitrary double-stranded DNA fragments with chosen chemical groups. The modification requires the use of short (10-20 base pairs) synthetic adaptors having desired terminal functional groups and installs known sequences, which can be used for hybridization of primers in the sequencing-by-synthesis approaches. The method, based on ligation under optimized conditions, is selective and provides high yields of the target heterobifunctional DNA product. An additional two-step procedure can be applied to select further for the desired bifunctionalized product using PCR amplification with a chemically modified primer. Both functional groups in the modified DNA are chemically active and can be used in surface immobilization of the DNA strands to create the surface of a biosensor or sequencing chip.