Search Results (258)

Sotolon is a chiral furanone derivative featuring three distinct oxygen atoms at carbonyl, hydroxyl, and cyclic ether groups that can serve as hydrogen-bond acceptor sites, making it an ideal model system for probing water’s preferential interactions with competing functional groups. In this study, the rotational spectrum of sotolon and its microsolvated complexes, representing the early stages of hydration, was investigated using chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy. The conformational landscape of sotolon is dominated by a single conformer stabilized by an intramolecular O–H···O=C hydrogen bond. During hydration, water molecules disrupt this interaction by forming closed hydrogen-bonded cycles, resulting in mono- and dihydrated complexes. High-level theoretical calculations underscore the central role of electrostatic interactions in stabilizing these hydrated structures. Furthermore, A/E splittings observed in the rotational spectrum, arising from the internal rotation of one of sotolon’s methyl groups, provide insight into how hydration modulates the methyl internal rotation barrier. Full article

The crystal structure of the hydrated form of 7-chloro-4-(4-methyl-1-piperazinyl)quinoline (BPIP) was determined by single-crystal X-ray diffraction analysis. This study revealed a one-dimensional supramolecular network stabilized by hydrogen bonding interactions between BPIP and water molecules. This compound represents one-half of a piperaquine molecule, a member of the 4-aminoquinoline class of antimalarial treatments, currently employed as a partner agent in modern combination therapies. As a simplified structural analog, BPIP can serve as a critical model system for probing the intermolecular interactions, physicochemical properties, and structural behavior of the parent compound. As a result, conducting a thorough solid-state characterization of BPIP is critical for gaining insight into its physical properties and verifying the material’s identity and purity. Full article

Recent work has identified biomphalysin (BM) protein from the snail Biomphalaria glabrata as a cytolytic toxin against the Schistosoma mansoni parasite. Ex vivo interactome studies further evidenced BM’s ability to bind bacterial outer membrane proteins, but its specific antibacterial mechanisms and selectivity remain unclear. Accordingly, this study aims to elucidate the interaction between BM and two model bacteria with distinct cell surface architectures: Escherichia coli (Gram−) and Micrococcus luteus (Gram+). Employing a multiscale approach, we used in vivo single-molecule force spectroscopy (SMFS) to probe molecular interactions at the single cell level. Combined with cell aggregation assays, immunoblotting and Atomic Force Microscopy (AFM) imaging, SMFS results evidenced a selective interaction of BM from snail plasma with M. luteus but not E. coli. Exposure of M. luteus to BM compromised cell surface integrity and induced cell aggregation. These effects correlated with a patch-like distribution of BM on M. luteus reminiscent of pore-forming toxins, as revealed by the anti-BM antibody-functionalized AFM tip. Overall, this work highlights the utility of SMFS in dissecting host–pathogen molecular dialogs. It reveals BM’s selective action against M. luteus, potentially via surface clustering, and it shows spatially heterogeneous responses to the toxin within and between individual cells. Full article

Due to its unique molecular fingerprinting capability and multiplex detection advantages, surface-enhanced Raman scattering (SERS) has shown great application potential in the field of biological analysis. However, the weak signal intensity and large background interference significantly limited the application of SERS in biosensing and bioimaging. Loading a large amount of Raman molecules with signal in the silent region on the hotspots of the electromagnetic field of the SERS substrate can effectively avoid severe background noise signals and significantly improve the signal intensity, making the sensitivity and specificity of SERS detection remarkably improved. To achieve this goal, a new SERS signal-amplification strategy is herein reported for background-free detection of Cu²⁺ by using Raman-silent probes loaded on cabbage-like gold microparticles (AuMPs) with high enhancement capabilities and single-particle detection feasibility. In this work, carboxyl-modified AuMPs were used to enable Cu²⁺ adsorption via electrostatic interactions, followed by ferricyanide coordination with Cu²⁺ to introduce cyano groups, therefore generating a stable SERS signal with nearly zero background signals owing to the Raman-silent fingerprint of cyano at 2137 cm⁻¹. Based on the signal intensity of cyano groups correlated with Cu²⁺ concentration resulting from the specific coordination between Cu²⁺ and cyanide, a novel SERS method for Cu²⁺ detection with high sensitivity and selectivity is proposed. It is noted that benefiting from per ferricyanide possessing six cyano groups, the established method with the advantage of signal amplification can significantly enhance the sensing sensitivity beyond conventional approaches. Experimental results demonstrated this SERS sensor possesses significant merits towards the determination of Cu²⁺ in terms of high selectivity, broad linear range from 1 nM to 1 mM, and low limit of detection (0.1 nM) superior to other reported colorimetric, fluorescence, and electrochemical methods. Moreover, algorithm data processing for optimization of SERS original data was further used to improve the SERS signal reliability. As the proof-of-concept demonstrations, this work paves the way for improving SERS sensing capability through the silent-range fingerprint and signal amplification strategy, and reveals SERS as an effective tool for trace detection in complex biological and environmental matrices. Full article

The growing global demand for phytochemicals as bioactive sources is prompting scientists to develop methods that link their sensory properties to their mechanisms of action in cancer treatment. Recent techniques for tracking the actions of small plant metabolites (SPMs) from single-cell plant sources to their molecular anticancer biomarkers could provide valuable insights in this field. Among the critical methods discussed in this review are the real-time tracking of cell components through stable isotope probing (Sis) and microspectroscopy, which has attracted the attention of biotechnologists. Additionally, the precise pathways required for studying new insights into functional materials are discussed, based on high-resolution and accurate technologies, which could aid their functional categorization. Notably, the molecules under study have recently garnered attention for their anticancer applications due to advancements in effective evaluation techniques that surpass traditional methods. In December 2020, the Food and Drug Administration (FDA) authorized 89 SPMs as safe anticancer natural molecules. In conclusion, by combining spatiotemporal techniques and SPMs’ mechanisms, they could facilitate the development of more exceptional, bio-efficient materials. Full article

Methylene blue (MB), a widely used industrial dye, is a persistent pollutant with documented toxicity to aquatic organisms and potential health risks to humans, even at ultra-trace levels. Conventional monitoring techniques such as UV–Vis spectroscopy and fluorescence emission suffer from limited sensitivity, typically failing to detect MB below ~10⁻⁷ M. In this study, we introduce a surface-enhanced Raman spectroscopy (SERS) platform based on silver nanowire (AgNW) substrates that enables MB detection over an unprecedented dynamic range—from 1.5 × 10⁻⁴ M down to 1.5 × 10⁻¹⁶ M. Raman mapping confirmed the presence of individual signal hot spots at the lowest concentration, consistent with the theoretical number of analyte molecules in the probed area, thereby demonstrating near-single-molecule detection capability. The calculated enhancement factors reached up to 1.90 × 10¹², among the highest reported for SERS-based detection platforms. A semi-quantitative calibration curve was established spanning twelve orders of magnitude, and this platform was successfully applied to monitor MB degradation during two advanced oxidation processes (AOPs): TiO₂ nanotube-mediated photocatalysis under UV irradiation and atmospheric-pressure dielectric barrier discharge (DBD) plasma treatment. While UV–Vis and fluorescence techniques rapidly lost sensitivity during the degradation process, the SERS platform continued to detect the characteristic MB Raman peak at ~1626 cm⁻¹ throughout the entire treatment duration. These persistent SERS signals revealed the presence of residual MB or partially degraded aromatic intermediates that remained undetectable by conventional optical methods. The results underscore the ability of AgNW-based SERS to provide ultra-sensitive, molecular-level insights into pollutant transformation pathways, enabling time-resolved tracking of degradation kinetics and validating treatment efficiency. This work highlights the importance of integrating SERS with AOPs as a powerful complementary strategy for advanced environmental monitoring and water purification technologies. By delivering an ultra-sensitive, low-cost sensor (<USD 0.16 per test) and promoting reagent-free treatment methods, this study directly advances SDG 6 (Clean Water and Sanitation) and SDG 12 (Responsible Consumption and Production). Full article

Pathogenic bacteria are one of the main causes of diseases and have become an important public health problem threatening human health and socio-economic development. Therefore, it is particularly important to develop an efficient and convenient detection method. Fluorescence detection has become a highly concerned analytical technology, which has gradually emerged in the aspect of pathogen detection, and is favored by researchers. In this review, we summarized a series of sensing strategies for pathogen detection based on fluorescence response signals in recent years, including single molecule fluorescent probes, biosensors, nanocomposite sensors and strategies for integrating different recognition elements with nanomaterials, along with the advantages and disadvantages of various design strategies. Based on the existing research reports, the existing problems and future research challenges of fluorescent sensor technology are proposed. Full article

We present a comprehensive vibrational spectroscopic analysis of vertical molecular junction devices constructed using single-layer graphene electrodes separated by an aryl alkane monolayer. In this work, inelastic electron tunneling spectroscopy (IETS) is employed to probe molecular vibrations within the junction, providing an in situ fingerprint of the molecules. Graphene has emerged as a promising electrode material for molecular electronics due to its atomically thin, mechanically robust nature and ability to form stable contacts. However, prior to this study, the vibrational spectra of molecules in graphene-based molecular junctions had not been fully explored. Here, we demonstrate that vertically stacked graphene electrodes can be used to form stable and reproducible molecular junctions that yield well-resolved IETS signatures. The observed IETS spectra exhibit distinct peaks corresponding to the vibrational modes of the sandwiched aryl alkane molecules, and all major features are assigned through density functional theory calculations of molecular vibrational modes. Furthermore, by analyzing the broadening of IETS peaks with temperature and AC modulation amplitude, we extract intrinsic vibrational linewidths, confirming that the spectral features originate from the molecular junction itself rather than extrinsic noise or instrumental artifacts. These findings conclusively verify the presence of the molecular layer between graphene electrodes as the charge transport pathway and highlight the potential of graphene–molecule–graphene junctions for fundamental studies in molecular electronics. Full article

Single-molecule fluorescence technology stands at the forefront of scientific research as a sophisticated tool, pushing the boundaries of our understanding. This review comprehensively summarizes the technological advancements in single-molecule fluorescence detection, highlighting the latest achievements in the development of single-molecule fluorescent probes, imaging systems, and biosensors. It delves into the applications of these cutting-edge tools in drug discovery and neuroscience research, encompassing the design and monitoring of complex drug delivery systems, the elucidation of pharmacological mechanisms and pharmacokinetics, the intricacies of neuronal signaling and synaptic function, and the molecular underpinnings of neurodegenerative diseases. The exceptional sensitivity demonstrated in these applications underscores the vast potential of single-molecule fluorescence technology in modern biomedical research, heralding its expansion into other scientific domains. Full article

Peptide nucleic acids (PNAs) are synthetic analogues of DNA/RNA characterized by the absence of negative phosphate groups, which confer a low sensitivity to ionic strength for hybridization with respect to the canonical counterpart. PNAs are a suitable probe for miRNAs, as well as endogenous molecules of single-strand non-coding RNA whose dysregulation is often linked to several diseases. The interaction forces between PNA and microRNA-155 (miR-155), a multifunctional microRNA overexpressed in a variety of tumors, were investigated by Atomic Force Spectroscopy (AFS) in fluid under different conditions. We found that the unbinding forces acquired at the ionic strength of 150 mM for a rather wide range of loading rates (ΔF/Δt) can be described using the Bell–Evans model. This allows us to extract information on the kinetics and thermodynamic properties of the miR-155/PNA duplex. Additionally, we probed the unbinding forces and the target recognition times between miR-155 and PNA in the 50–300 mM ionic strength range. Our results indicate that both of these parameters are practically independent from the ionic strength in the analyzed range. The results provide information that is useful for a wider use of PNA in biosensors for diagnostics and therapeutics, even in situ. Full article

The proteasome is an enzyme that sequentially degrades peptides into small fragments, so the ability to make electrical measurements of its conformational fluctuations could lead to an electronic readout of the sequence of single peptide molecules. Here, we report scanning tunneling microscope (STM) measurements of the conductance of the T. acidophilum 20S proteasome core particle (CP). The wild-type CP did not change conductance significantly as a 4 amino acid peptide substrate was added. Larger peptides were digested by a mutant, CP-Δ12, in which 12 residues were deleted from the N terminus of the alpha chains (opening the central pore). The conductance of this molecule decreased significantly in the presence of a denatured pleiotrophin substrate. Control experiments showed that strong bonding of the protein, both to the substrate electrode and the STM probe, was required for conductivity to be observed. It also appears that substantial penetration of the probe into the protein film is required, a problematic constraint on incorporating the CP into a fixed-gap device for technological applications. Full article

Background: Epigenetic biomarkers, particularly CpG methylation, are increasingly employed in clinical and forensic settings. However, we still lack a cost-effective, sensitive, medium-scale method for the analysis of hundreds to thousands of user-defined CpGs suitable for minute DNA input amounts (<10 ng). In this study, motivated by promising results in the genetics field, we investigated single-molecule molecular inversion probes (smMIPs) for simultaneous analysis of hundreds of CpGs by using an example set of 514 age-associated CpGs (Zhang model). Methods: First, we developed a novel smMIP design tool to suit bisulfite-converted DNA (Locksmith). Then, to optimize the capture process, we performed single-probe capture for ten selected, representative smMIPs. Based on this pilot, the full smMIP panel was tested under varying capture conditions, including hybridization and elongation temperature, smMIP and template DNA amounts, dNTP concentration and elongation time. Results: Overall, we found that the capture efficiency was highly probe-(and hence, sequence-) dependent, with a heterogeneous coverage distribution across CpGs higher than the 1000-fold range. Considering CpGs with at least 20X coverage, we yielded robust methylation detection with levels comparable to those obtained from the gold standard EPIC microarray analysis (Pearsons’s r: 0.96). Conclusions: The observed low specificity and uniformity indicate that smMIPs in their current form are not compatible with the lowered complexity of bisulfite-converted DNA. Full article

Perfluorooctanoic acid (PFOA) is one of the most persistent and bioaccumulative water contaminants. Sensitive, rapid, and in-field analysis is needed to ensure safe water supplies. Here, we present a single step (one shot) and rapid sensor capable of measuring PFOA at the sub-quadrillion (ppq) level, 4.5 × 10⁻⁴ ppq, within 10 s. This innovative sensor employs a synergistic combination of a molecularly imprinted polymer (MIP)-modified gold interdigitated microelectrode chip and AC electrothermal effects (ACETs), which enhance detection sensitivity by facilitating the accelerated movement of PFOA molecules towards specific recognition sites on the sensing surface. The application of a predetermined AC signal induces microfluidic enrichment and results in concentration-dependent changes in interfacial capacitance during the binding process. This enables real-time, rapid quantification with exceptional sensitivity. We achieved a linear dynamic range spanning from 0.4 to 40 fg/L (4 × 10⁻⁷–4 × 10⁻⁵ ppt) and demonstrated good selectivity (~1:100) against other PFAS compounds, including perfluorooctanoic acid (PFOS), in PBS buffer. The sensor’s straightforward operation, cost-effectiveness, elimination of the need for external redox probes, compact design, and functionality in relatively resistant environmental matrices position it as an outstanding candidate for deployment in practical applications. Full article

Within the framework of rational drug design, this study introduces a novel approach to enhance the specificity of small molecules in targeting cancer cells. This approach starts from the use of dyads merging into a single entity, a naphthalene diimide (NDI) and core-extended NDI (ceNDI), both known as G-quadruplex (G4) ligands and fluorescent probes. The strategy aims to leverage the unique diagnostic strengths of the ceNDI moiety featuring red emission by improving its binding affinity and target selectivity through inclusion in dyads built with different linkers. The newly developed NDI-ceNDI dyads are promising probes, as they exhibit fluorescence turn-on upon DNA recognition and induced circular dichroism signals dependent on DNA conformation. Both dyads have an excellent affinity for hybrid G4, with two orders of magnitude higher binding constants than those for ds DNA. Their high cytotoxicity on cancer cell lines further demonstrates their potential as therapeutic agents, highlighting the role of the linker in target selectivity. Specifically, only the dyad with the rigid triazole linker exhibits selectively induced DNA damage in transformed cells, compared to normal cells primarily targeting telomeric regions. Our findings shed light on DIPAC’s potential as a promising theranostic agent, offering insights into future developments in precision medicine. Full article

This study investigates the design and optimization of a nanoparticle-based surface-enhanced Raman scattering (SERS) biosensing platform using COMSOL Multiphysics simulations. The primary goal is to enhance the sensitivity and specificity of SERS biosensors, which are crucial for the precise detection and quantification of biomolecules. The simulation study explores the use of gold and silver nanoparticles in various arrangements, including single, multiple, and periodic nanospheres. The effects of polarization and the phenomenon of local hotspot switching in trimer and tetramer nanosphere systems are analyzed. To validate the simulation results, a SERS biosensing platform is fabricated by self-assembling gold nanoparticles on a silicon substrate, with methylene blue used as the Raman probe molecule. The findings demonstrate the feasibility of optimizing SERS biochips through simulation, which can be extended to various nanostructures. This work contributes to the advancement of highly sensitive and specific SERS biosensors for diagnostic and analytical applications. Full article