Search Results (141)

Modification of PLA with functional nanoparticles is a promising approach for imparting new properties to the material. In this work, titanium nanoparticles (Ti NPs) and titanium dioxide nanoparticles (TiO₂ NPs) were synthesized by laser ablation and characterized by dynamic light scattering, spectrophotometry, and transmission electron microscopy. The average hydrodynamic diameter of Ti NPs was 12 nm, while that of TiO₂ NPs was 24 nm; both dispersions possessed a positive zeta potential (23–27 mV) and spherical morphology. L-PLA composite films containing 0.1 wt.% Ti NPs or TiO₂ NPs were obtained by solution casting. Atomic force and modulation-interference microscopy confirmed the uniform distribution of nanoparticles within the polymer matrix, although partial aggregation was observed. The introduction of TiO₂ NPs increased the water contact angle. Mechanical testing revealed a significant reinforcing effect: the addition of 0.1 wt.% NPs increased the Young’s modulus by 62–68% and the ultimate tensile strength by 16–18% while maintaining a ductile fracture pattern with elongation at break up to ~8%. Both types of composites generated reactive oxygen species (ROS) in aqueous solutions: Ti NPs increased H₂O₂ production by 5.5 times and TiO₂ NPs by 4.9 times, and they also induced the formation of hydroxyl radicals. The accumulation of 8-oxoguanine in DNA and long-lived oxidized protein species confirmed the materials’ ability to cause oxidative damage to biomacromolecules. For E. coli, growth inhibition reached 40.5% (for composites with Ti NPs) and 71% (for composites with TiO₂ NPs). The effect was even more pronounced for S. aureus, where inhibition levels were approximately 70% and 80%, respectively; flow cytometry confirmed the strong bactericidal effect, showing that materials containing TiO₂ NPs increased the proportion of dead cells to 25% for E. coli and ~68% for S. aureus. Cytotoxicity assessment on human fibroblasts (HSF) demonstrated the high biocompatibility of neat L-PLA and composites with Ti NPs (viability > 95%) and with TiO₂ NPs (viability ~93%). The obtained results indicate that L-PLA-based composites with Ti NPs and TiO₂ NPs exhibit pronounced ROS-mediated antibacterial activity without additional UV irradiation. These findings position these materials as highly promising candidates for active biodegradable food packaging to extend shelf-life and for biomedical devices, such as wound dressings and implants, where reducing the risk of bacterial colonization is critical. Full article

We demonstrate that gold nanoparticles (AuNPs) are capable of unwinding double-stranded (ds) DNA. Upon unwinding, the exposed nucleobases of the separated strands adsorb onto the nanoparticle surface, resulting in the coating of the particles. The unwinding process was characterized by Atomic Force Microscopy (AFM) and absorption spectroscopy. Our results show that AuNPs initially bind to single-stranded overhangs at the duplex termini, forming dsDNA–nanoparticle dumbbells. This binding event subsequently initiates the separation of the DNA strands. As the unwinding proceeds, the nanoparticles become progressively wrapped by the unwound DNA strands, which leads to a gradual reduction in the interparticle distance within the dumbbells. This process is driven by the strong affinity of nucleobases for the gold surface. The efficiency of DNA unwinding was found to depend strongly on both nanoparticle size and temperature. These findings provide new insights into DNA-nanoparticle interactions and may facilitate the rational design of DNA–AuNP hybrid nanostructures such as dumbbell-shaped conjugates for applications in DNA-based nanoelectronics, biosensing, and self-assembled nanomaterials. Full article

The applicability of free and encapsulated DNA as tracers in surface water studies in Lithuanian climatic conditions was evaluated. Tracer DNA synthesis and analysis were performed using real-time polymerase chain reaction (RT-PCR). Alginate and chitosan were used to obtain the microcapsules with DNA, and their sizes were determined using an atomic force microscopy. The Murlė stream in the city of Vilnius was chosen for field experiments using the prepared tracers. It was found that both types of tracers may be applied to surface water studies, but the relative concentration recovery of encapsulated DNA tracers is 3–6 times higher than that of free DNA tracers. It was concluded that the alginate/chitosan capsules protect DNA from the sandy layer in Murlė stream, direct UV exposure and other environmental factors that could degrade DNA. To our knowledge, this is the first report about free and encapsulated DNA tracer application in surface water studies in Lithuania. Full article

We present the creation of an alignment layer for liquid crystal molecules based on DNA from fish waste and a selected cationic surfactant. The implemented biodegradable DNA-based surface offers excellent optical and physical properties, cost-effectiveness, and environmental benefits compared to conventional polymers. Our findings demonstrate that the biopolymer DNA-DODA effectively induces homeotropic alignment of nematic liquid crystals, which was confirmed by topography visualization using atomic force microscopy, macroscopy, and polarizing optical microscopy observations. Anchoring energy and response time studies in the well-known electro-optical effect show that DNA-DODA exhibits molecular interaction strengths comparable to those of commercial polyimide. The successful implementation of DNA-DODA as an alignment layer highlights its promise for next-generation technologies, including flexible, sustainable, and biocompatible optical devices. Full article

Drug resistance is a serious problem for human health worldwide. Day by day this drug resistance is increasing and creating an anxious situation for the treatment of both cancer and infectious diseases caused by pathogenic microorganisms. Researchers are trying to solve this terrible situation to overcome drug resistance. Biosynthesized gold nanoparticles (AuNPs) could be a promising agent for controlling drug-resistant pathogenic microorganisms and cancer cells. AuNPs can be synthesized via chemical and physical approaches, carrying many threats to the ecosystem. Green synthesis of AuNPs using biological agents such as plants and microbes is the most fascinating and attractive alternative to physicochemical synthesis as it offers many advantages, such as simplicity, non-toxicity, cost-effectiveness, and eco-friendliness. Plant extracts contain numerous biomolecules, and microorganisms produce various metabolites that act as reducing, capping, and stabilizing agents during the synthesis of AuNPs. The characterization of green-synthesized AuNPs has been conducted using multiple instruments including UV–Vis spectrophotometry (UV–Vis), transmission electron microscopy (TEM), scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray diffraction (XRD), DLS, and Fourier transform infrared spectroscopy (FT-IR). AuNPs have detrimental effects on bacterial and cancer cells via the disruption of cell membranes, fragmentation of DNA, production of reactive oxygen species, and impairment of metabolism. The biocompatibility and biosafety of synthesized AuNPs must be investigated using a proper in vitro and in vivo screening model system. In this review, we have emphasized the green, facile, and eco-friendly synthesis of AuNPs using plants and microorganisms and their potential antimicrobial and anticancer applications and highlighted their antibacterial and anticancer mechanisms. This study demonstrates that green-synthesized AuNPs may potentially be used to control pathogenic bacteria as well as cancer cells. Full article

This work demonstrates the preliminary results of rapid and direct detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) using the quartz crystal microbalance (QCM) method. Coronavirus Disease 2019 (COVID-19)-specific RNA-dependent RNA polymerase (RdRP) gene-dependent probe DNA was used as a selective agent toward target DNA, the inactivated SARS-CoV-2 virus, and RNAs extracted from clinical samples. This study developed and utilised a unique dry-QCM approach with a mitigated experimental procedure. Contact angle measurements, Atomic Force Microscopy (AFM) and X-ray Photoelectron Spectroscopy (XPS) measurements were employed to investigate the surface during probe immobilisation and target hybridisation. This study also investigates the effect of temperature on probe immobilisation and target hybridisation. The estimated probe density was 0.51 × 10¹² probes/cm², which is below the critical limit. The estimated hybridisation efficiency was about 58.9%. The linear detection range with a Limit of Detection (LoD) was about ~1.22 nM with high selectivity toward SARS-CoV-2 target DNA. The sensor shelf-life was found to be extended to 25 days. The novelty of using a new dry-QCM approach for SARS-CoV-2 detection was proven with the results. Full article

Nanoparticles could improve the bioavailability of active agents of various natures to human, animal, and plant tissues. In this work, we compared two methods on the synthesis of calcium phosphate nanoparticles (CaPs), differed by the synthesis temperature, pH, and concentration of the stabilizing agent, and explored the possibilities of incorporation of a low-molecular-weight peptide analogue enalaprilat, the enzyme superoxide dismutase 1 (SOD1), as well as DNA and dsRNA into these particles, by coprecipitation and sorption. CaPs obtained with and without cooling demonstrated the highest inclusion efficiency for enalaprilat upon coprecipitation: 250 ± 10 μg/mg of CaPs and 340 ± 30 μg/mg of CaPs, respectively. Enalaprilat sorption on the preliminarily formed CaPs was much less effective. SOD1 was only able to coprecipitate with CaPs upon cooling, with SOD1 loading 6.6 ± 2 μg/mg of CaPs. For the incorporation of DNA, the superiority of the sorption method was demonstrated, allowing loading of up to 88 μg/mg of CaPs. The ability of CaPs to incorporate dsRNa by sorption was also demonstrated by electrophoresis and atomic force microscopy. These results could have important implications for the development of the roots for incorporating substances of different natures into CaPs for agricultural and medical applications. Full article

Fused in sarcoma (FUS) is involved in the formation of nuclear biomolecular condensates associated with poly(ADP-ribose) [PAR] synthesis catalyzed by a DNA damage sensor such as PARP1. Here, we studied FUS microphase separation induced by poly(ADP-ribosyl)ated PARP1^WT [PAR-PARP1^WT] or its catalytic variants PARP1^Y986S and PARP1^Y986H, respectively, synthesizing (short PAR)-PARP1^Y986S or (short hyperbranched PAR)-PARP1^Y986H using dynamic light scattering, fluorescence microscopy, turbidity assays, and atomic force microscopy. We observed that biologically relevant cations such as Mg²⁺, Ca²⁺, or Mn²⁺ or polyamines (spermine⁴⁺ or spermidine³⁺) were essential for the assembly of FUS with PAR-PARP1^WT and FUS with PAR-PARP1^Y986S in vitro. We estimated the range of the FUS-to-PAR-PARP1 molar ratio and the cation concentration that are favorable for the stability of the protein’s microphase-separated state. We also found that FUS microphase separation induced by PAR-PARP1^Y986H (i.e., a PARP1 variant attaching short hyperbranched PAR to itself) can occur in the absence of cations. The dependence of PAR-PARP1-induced FUS microphase separation on cations and on the branching of the PAR structure points to a potential role of the latter in the regulation of the formation of FUS-related biological condensates and requires further investigation. Full article

Biological warfare agents are infectious microorganisms or toxins capable of harming or killing humans. Francisella tularensis is a potential bioterrorism agent that is highly infectious, even at very low doses. Biosensors for biological warfare agents are simple yet reliable point-of-care analytical tools. Developing highly sensitive, reliable, and cost-effective label-free DNA biosensors poses significant challenges, particularly when utilizing traditional techniques such as fluorescence, electrochemical methods, and others. These challenges arise primarily due to the need for labeling, enzymes, or complex modifications, which can complicate the design and implementation of biosensors. In this study, we fabricated Graphene Quantum dot (GQD)-functionalized biosensors for highly sensitive label-free DNA detection. GQDs were immobilized on the surface of screen-printed gold electrodes via mercaptoacetic acid with a thiol group. The single-stranded DNA (ssDNA) probe was also immobilized on GQDs through strong π−π interactions. The ssDNA probe can hybridize with the ssDNA target and form double-stranded DNA, leading to a decrease in the effect of GQD but a positive shift associated with the increase in DNA concentration. The specificity of the developed system was observed with different microorganism target DNAs and up to three-base mismatches in the target DNA, effectively distinguishing the target DNA. The response time for the target DNA molecule is approximately 1010 s (17 min). Experimental steps were monitored using UV/Vis spectroscopy, Atomic Force Microscopy (AFM), and electrochemical techniques to confirm the successful fabrication of the biosensor. The detection limit can reach 0.1 nM, which is two–five orders of magnitude lower than previously reported methods. The biosensor also exhibits a good linear range from 10⁵ to 0.01 nM and has good specificity. The biosensor’s detection limit (LOD) was evaluated as 0.1 nM from the standard calibration curve, with a correlation coefficient of R² = 0.9712, showing a good linear range and specificity. Here, we demonstrate a cost-effective, GQD-based SPGE/F. tularensis DNA test suitable for portable electrochemical devices. This application provides good perspectives for point-of-care portable electrochemical devices that integrate sample processing and detection into a single cartridge without requiring a PCR before detection. Based on these results, it can be concluded that this is the first enzyme-free electrochemical DNA biosensor developed for the rapid and sensitive detection of F. tularensis, leveraging the nanoenzyme and catalytic properties of GQDs. Full article

Penetrating deep into the cells of the human body in real time has become increasingly possible with the implementation of modern technologies in medicine. Atomic force microscopy (AFM) enables the effective live imaging of cellular and molecular structures of biological samples (such as cells surfaces, components of biological membranes, cell nuclei, actin networks, proteins, and DNA) and provides three-dimensional surface visualization (in X-, Y-, and Z-planes). Furthermore, the AFM technique enables the study of the mechanical, electrical, and magnetic properties of cells and cell organelles and the measurements of interaction forces between biomolecules. The technique has found wide application in cancer research. With the use of AFM, it is not only possible to differentiate between healthy and cancerous cells, but also to distinguish between the stages of cancerous conditions. For many years, AFM has been an important tool for the study of neurodegenerative diseases associated with the deposition of peptide amyloid plaques. In recent years, a significant amount of research has been conducted on the application of AFM in the evaluation of connective tissue cell mechanics. This review aims to provide the spectrum of the most important applications of the AFM technique in medicine to date. Full article

The HIV-1 nucleocapsid protein (NC) is a multifunctional viral protein necessary for HIV-1 replication. Recent studies have demonstrated that reverse transcription (RT) completes in the intact viral capsid, and the timing of RT and uncoating are correlated. How the small viral core stably contains the ~10 kbp double stranded (ds) DNA product of RT, and the role of NC in this process, are not well understood. We showed previously that NC binds and saturates dsDNA in a non-specific electrostatic binding mode that triggers uniform DNA self-attraction, condensing dsDNA into a tight globule against extending forces up to 10 pN. In this study, we use optical tweezers and atomic force microscopy to characterize the role of NC’s basic residues in dsDNA condensation. Basic residue mutations of NC lead to defective interaction with the dsDNA substrate, with the constant force plateau condensation observed with wild-type (WT) NC missing or diminished. These results suggest that NC’s high positive charge is essential to its dsDNA condensing activity, and electrostatic interactions involving NC’s basic residues are responsible in large part for the conformation, size, and stability of the dsDNA-protein complex inside the viral core. We observe DNA re-solubilization and charge reversal in the presence of excess NC, consistent with the electrostatic nature of NC-induced DNA condensation. Previous studies of HIV-1 replication in the presence of the same cationic residue mutations in NC showed significant defects in both single- and multiple-round viral infectivity. Although NC participates in many stages of viral replication, our results are consistent with the hypothesis that cationic residue mutations inhibit genomic DNA condensation, resulting in increased premature capsid uncoating and contributing to viral replication defects. Full article

Coupling spectroscopic ellipsometry (SE), quartz crystal microbalance with dissipation (QCM-D), X-ray photoemission spectroscopy (XPS), and atomic force microscopy (AFM), we developed a multi-technique approach to characterize the surface immobilization of probe DNA strands, as a tool for the design of a DNA-based biosensor for the detection of disease-related oligonucleotide strands [...] Full article

Apurinic/apyrimidinic endonuclease 1 (APE1) is involved in DNA repair and transcriptional regulation mechanisms. This multifunctional activity of APE1 should be supported by specific structural properties of APE1 that have not yet been elucidated. Herein, we applied atomic force microscopy (AFM) to characterize the interactions of APE1 with DNA containing two well-separated G-rich segments. Complexes of APE1 with DNA containing G-rich segments were visualized, and analysis of the complexes revealed the affinity of APE1 to G-rich DNA sequences, and their yield was as high as 53%. Furthermore, APE1 is capable of binding two DNA segments leading to the formation of loops in the DNA–APE1 complexes. The analysis of looped APE1-DNA complexes revealed that APE1 can bridge G-rich segments of DNA. The yield of loops bridging two G-rich DNA segments was 41%. Analysis of protein size in various complexes was performed, and these data showed that loops are formed by APE1 monomer, suggesting that APE1 has two DNA binding sites. The data led us to a model for the interaction of APE1 with DNA and the search for the specific sites. The implication of these new APE1 properties in organizing DNA, by bringing two distant sites together, for facilitating the scanning for damage and coordinating repair and transcription is discussed. Full article

Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a “hairpin” fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA–silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics. Full article

Drug delivery vehicles composed of lipids and gemini surfactants (GS) are promising in gene therapy. Tuning the composition and properties of the delivery vehicle is important for the efficient load and delivery of DNA fragments (genes). In this paper, we studied novel gene delivery systems composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoyl-sn-3-phosphocholine (DPPC), and GS of the type N,N-bis(dimethylalkyl)-$\alpha ,\omega$-alkanediammonium dibromide at different ratios. The nanoscale properties of the mixed DOPC–DPPC–GS monolayers on the surface of the gene delivery system were studied using atomic force microscopy (AFM) and Kelvin probe force microscopy (KPFM). We demonstrate that lipid–GS mixed monolayers result in the formation of nanoscale domains that vary in size, height, and electrical surface potential. We show that the presence of GS can impart significant changes to the domain topography and electrical surface potential compared to monolayers composed of lipids alone. Full article