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The T cell immunoglobulin domain and mucin domain-containing molecule-3 (TIM-3), an inhibitory checkpoint receptor, has been identified as a crucial regulator of cellular immune responses. TIM-3 has been discovered as a receptor involved in the negative regulation of T cells. Recent studies have demonstrated that TIM-3 is expressed on innate immune cells, including dendritic cells (DCs), even at a higher level than T cells. In the tumor microenvironment, the majority of DCs have a monocytic origin. Models for studying such DCs in vitro are DC cultures generated from monocytes in the presence of growth factors. The present study aimed to investigate the expression of TIM-3 in IFNα-induced monocyte-derived DCs (IFN-DCs) and the impact of DC activation on TIM-3 expression. DCs were obtained by culturing the adherent fraction of mononuclear cells from healthy donors for 4 days in the presence of GM-CSF and IFNα, followed by LPS addition for 24 hours. Human double-stranded DNA (dsDNA, 5 μg/mL) was added as an activation stimulus to intact IFN-DCs at the stage of maturation, along with LPS. Expression of the membrane TIM-3 molecule was determined by flow cytometry, and the level of expression of TIM-3 mRNA – by real-time RT-PCR with reverse transcription. Intact donor IFN-DCs expressed the membrane TIM-3 molecule at a high level (more than 70% of cells). The addition of LPS as a maturation stimulus almost halved the expression of TIM-3 (pW < 0.05) without affecting the expression of HAVCR2/TIM-3 mRNA. Exogenous dsDNA (along with LPS) increased the expression of HAVCR2/TIM-3 mRNA by more than three times (pW = 0.05) with a decrease in the number of TIM-3+DCs (pW = 0.003). Our findings indicate the presence of mechanisms that support expression of this inhibitory checkpoint receptor under conditions of DC activation. Further studies of the regulation of TIM-3 expression by monocyte-derived dendritic cells will expand the understanding of the biological significance of inhibitory receptors on DCs from the point of view of the immune response, as well as, in the future, increase the effectiveness of current approaches in cancer immunotherapy using IFN-DCs and inhibitors of checkpoint molecules.

Abstract Background Deoxyribonuclease 2 (DNase II) plays a key role in clearing cytoplasmic double-stranded DNA (dsDNA). Deficiency of DNase II leads to DNA accumulation in the cytoplasm. Persistent dsDNA in neurons is an early pathological hallmark of senescence and neurodegenerative diseases including Alzheimer’s disease (AD). However, it is not clear how DNase II and neuronal cytoplasmic dsDNA influence neuropathogenesis. Tau hyperphosphorylation is a key factor for the pathogenesis of AD. The effect of DNase II and neuronal cytoplasmic dsDNA on neuronal tau hyperphosphorylation remains unclarified. Methods The levels of neuronal DNase II and dsDNA in WT and Tau-P301S mice of different ages were measured by immunohistochemistry and immunolabeling, and the levels of DNase II in the plasma of AD patients were measured by ELISA. To investigate the impact of DNase II on tauopathy, the levels of phosphorylated tau, phosphokinase, phosphatase, synaptic proteins, gliosis and proinflammatory cytokines in the brains of neuronal DNase II-deficient WT mice, neuronal DNase II-deficient Tau-P301S mice and neuronal DNase II-overexpressing Tau-P301S mice were evaluated by immunolabeling, immunoblotting or ELISA. Cognitive performance was determined using the Morris water maze test, Y-maze test, novel object recognition test and open field test. Results The levels of DNase II were significantly decreased in the brains and the plasma of AD patients. DNase II also decreased age-dependently in the neurons of WT and Tau-P301S mice, along with increased dsDNA accumulation in the cytoplasm. The DNA accumulation induced by neuronal DNase II deficiency drove tau phosphorylation by upregulating cyclin-dependent-like kinase-5 (CDK5) and calcium/calmodulin activated protein kinase II (CaMKII) and downregulating phosphatase protein phosphatase 2A (PP2A). Moreover, DNase II knockdown induced and significantly exacerbated neuron loss, neuroinflammation and cognitive deficits in WT and Tau-P301S mice, respectively, while overexpression of neuronal DNase II exhibited therapeutic benefits. Conclusions DNase II deficiency and cytoplasmic dsDNA accumulation can initiate tau phosphorylation, suggesting DNase II as a potential therapeutic target for tau-associated disorders. Graphical Abstract Scheme depicting the possible mechanism by which DNase II deficiency induces cognitive impairment in mice. DNase II deficiency induces tau phosphorylation by regulating kinases CDK5 and CaMKII as well as phosphatase PP2A through accumulation of undigested damaged DNA in the cytoplasm of neurons. Then phosphorylated tau induces synaptic loss, neuroinflammation, and neuronal apoptosis, eventually rendering cognitive impairment in mice.

Background: Acute urticaria is a prevalent inflammatory dermatosis characterized by fulminant wheals, often accompanied by severe pruritis. It may also cause nausea, vomiting, and abdominal pain. Numerous studies have substantiated the pivotal involvement of double‐stranded DNA (dsDNA) in autoimmunity. However, the role of dsDNA in the pathogenesis of acute urticaria is unclear. Methods: We measured serum dsDNA levels in patients and controls. The relationship between dsDNA levels and environmental exposures (temperature, ultraviolet [UV] index, and season) was investigated by correlating disease onset dates with archived meteorological data. Finally, we used quantitative PCR to determine the expressions of genes encoding dsDNA receptors, single‐stranded RNA (ssRNA) receptors, exosome formation, and type I interferon in the peripheral blood of patients and controls. Results: Serum dsDNA levels were significantly higher in patients with acute urticaria compared with controls (mean values 1.38 and 0.94 ng/ml, respectively, P < 0.001). dsDNA levels were higher in patients exposed to higher environmental temperatures and UV indices and were higher during the summer months. We also found that the expressions of genes encoding dsDNA receptors, ssRNA receptors, absent in melanoma factor 2 (AIM2)‐related inflammatory factors, and interferon alpha were up‐regulated in patients. Conclusions: We demonstrated that serum dsDNA levels are elevated in acute urticaria and are influenced by climatic factors such as temperature, ultraviolet index, and season. We also found that elevated dsDNA promotes the expression of AIM2‐related factors and type I interferons. This study generates new hypotheses regarding the pathogenesis of acute urticaria and suggests novel therapeutic targets. [ABSTRACT FROM AUTHOR]

Background: Deoxyribonuclease 2 (DNase II) plays a key role in clearing cytoplasmic double-stranded DNA (dsDNA). Deficiency of DNase II leads to DNA accumulation in the cytoplasm. Persistent dsDNA in neurons is an early pathological hallmark of senescence and neurodegenerative diseases including Alzheimer's disease (AD). However, it is not clear how DNase II and neuronal cytoplasmic dsDNA influence neuropathogenesis. Tau hyperphosphorylation is a key factor for the pathogenesis of AD. The effect of DNase II and neuronal cytoplasmic dsDNA on neuronal tau hyperphosphorylation remains unclarified. Methods: The levels of neuronal DNase II and dsDNA in WT and Tau-P301S mice of different ages were measured by immunohistochemistry and immunolabeling, and the levels of DNase II in the plasma of AD patients were measured by ELISA. To investigate the impact of DNase II on tauopathy, the levels of phosphorylated tau, phosphokinase, phosphatase, synaptic proteins, gliosis and proinflammatory cytokines in the brains of neuronal DNase II-deficient WT mice, neuronal DNase II-deficient Tau-P301S mice and neuronal DNase II-overexpressing Tau-P301S mice were evaluated by immunolabeling, immunoblotting or ELISA. Cognitive performance was determined using the Morris water maze test, Y-maze test, novel object recognition test and open field test. Results: The levels of DNase II were significantly decreased in the brains and the plasma of AD patients. DNase II also decreased age-dependently in the neurons of WT and Tau-P301S mice, along with increased dsDNA accumulation in the cytoplasm. The DNA accumulation induced by neuronal DNase II deficiency drove tau phosphorylation by upregulating cyclin-dependent-like kinase-5 (CDK5) and calcium/calmodulin activated protein kinase II (CaMKII) and downregulating phosphatase protein phosphatase 2A (PP2A). Moreover, DNase II knockdown induced and significantly exacerbated neuron loss, neuroinflammation and cognitive deficits in WT and Tau-P301S mice, respectively, while overexpression of neuronal DNase II exhibited therapeutic benefits. Conclusions: DNase II deficiency and cytoplasmic dsDNA accumulation can initiate tau phosphorylation, suggesting DNase II as a potential therapeutic target for tau-associated disorders. Scheme depicting the possible mechanism by which DNase II deficiency induces cognitive impairment in mice. DNase II deficiency induces tau phosphorylation by regulating kinases CDK5 and CaMKII as well as phosphatase PP2A through accumulation of undigested damaged DNA in the cytoplasm of neurons. Then phosphorylated tau induces synaptic loss, neuroinflammation, and neuronal apoptosis, eventually rendering cognitive impairment in mice. [ABSTRACT FROM AUTHOR]

Objective To observe the changes in the expression of absent in melanoma 2(AIM2), inflammasome signal pathway-related factors, double-stranded DNA (dsDNA), interleukin (IL)-1β, IL-18 and gasdermin D (GSDMD) in peripheral blood mononuclear cells (PBMCs) of patients with acute gouty arthritis, to analyze the relationship between AIM2, GSDMD in mononuclear cells and the condition of patients with acute gouty arthritis [WBC, PLT, ESR, CRP, IL1β, IL-18, BMI, UA, BUN, serum creatinine (SCr), creatinine clearance rate (CCr), TG, TC], and to explore the role of AIM2 inflammasome signal pathway-mediated pyroptosis in the development and progression of acute gouty arthritis. Methods Thirty patients with acute gouty arthritis (observation group) and 30 healthy controls (control group) were included to compare the levels of AIM2, GSDMD in PBMCs, and IL-1β, IL-18, and dsDNA in serum. Spearman correlation analysis was used to investigate the relationships between AIM2 mRNA, GSDMD mRNA, and the related indicators of patients with acute gouty arthritis (IL-1β, IL-18, WBC, PLT, ESR, CRP, BMI, UA, BUN, SCr, CCr, TG, and TC). Results Compared with the control group, the expression levels of AIM2 and GSDMD mRNA in PBMCs of the observation group were higher (both P<0. 05), and the levels of serum dsDNA, IL-1β, IL-18 were higher (all P<0. 01). AIM2 mRNA in PBMCs was positively correlated with WBC, ESR, CRP, BMI, TC, TG, and SCr (all P<0. 05), and GSDMD mRNA was positively correlated with ESR, IL-1β, and SCr (all P<0. 05). Conclusion The levels of AIM2, GSDMD in PBMCs, and dsDNA, IL-1β, and IL-18 in the serum of patients with acute gouty arthritis increase, indicating that AIM2 inflammasome-mediated pyroptosis may be involved in the development and progression of acute gouty arthritis. [ABSTRACT FROM AUTHOR]

Abstract Background Small extracellular vesicles (sEVs) have great potential as new biomarkers in liquid biopsy. However, due to the limitations of sEVs extraction and component analysis procedures, further clinical applications of sEVs are hampered. Carcinoembryonic antigen (CEA) is a commonly used broad-spectrum tumor marker that is strongly expressed in a variety of malignancies. Results In this study, CEA+ sEVs were directly separated from serum using immunomagnetic beads, and the nucleic acid to protein ultraviolet absorption ratio (NPr) of CEA+ sEVs was determined. It was found that the NPr of CEA+ sEVs in tumor group was higher than that of healthy group. We further analyzed the sEV-derived nucleic acid components using fluorescent staining and found that the concentration ratio of double-stranded DNA to protein (dsDPr) in CEA+ sEVs was also significantly different between the two groups, with a sensitivity of 100% and a specificity of 41.67% for the diagnosis of pan-cancer. The AUC of dsDPr combined with NPr was 0.87 and the ACU of dsDPr combined with CA242 could reach 0.94, showing good diagnostic performance for pan-cancer. Conclusions This study demonstrates that the dsDPr of CEA+ sEVs can effectively distinguish sEVs derived from tumor patients and healthy individuals, which can be employed as a simple and cost-effective non-invasive screening technology to assist tumor diagnosis.

Immature hematopoietic progenitors are a constant source for renewal of hemocyte populations and the basic component of the tissue and cell repair apparatus. A unique property of these cells of internalizing extracellular double-stranded DNA has been previously shown. The leukostimulatory effect demonstrated in our pioneering studies was considered to be due to the feature of this cell. In the present research, we have analyzed the effects of DNA genome reconstructor preparation (DNAgr), DNAmix, and human recombinant angiogenin on both hematopoietic stem cells and multipotent progenitors. Treatment with bone marrow cells of experimental mice with these preparations stimulates colony formation by hematopoietic stem cells and proliferation of multipotent descendants. The main lineage responsible for this is the granulocyte-macrophage hematopoietic lineage. Using fluorescent microscopy as well as FACS assay, co-localization of primitive c-Kit- and Sca-1-positive progenitors and the TAMRA-labeled double-stranded DNA has been shown. Human recombinant angiogenin was used as a reference agent. Cells with specific markers were quantified in intact bone marrow and colonies grown in the presence of inducers. Quantitative analysis revealed that a total of 14,000 fragment copies of 500 bp, which is 0.2% of the haploid genome, can be delivered into early progenitors. Extracellular double-stranded DNA fragments stimulated the colony formation in early hematopoietic progenitors from the bone marrow, which assumed their effect on cells in G0. The observed number of Sca1+/c-Kit+ cells in colonies testifies to the possibility of both symmetrical and asymmetrical division of the initial hematopoietic stem cell and its progeny.

Objective: Elevated double-stranded DNA (dsDNA) antibody levels in blood serum are considered a disease-specific marker in systemic lupus erythematosus (SLE), correlate with disease activity and the incidence of lupus nephritis, and can be detected in up to 86% of all SLE cases. Despite the high clinical relevance, the variety of dsDNA antibody testing methods with heterogenous performance in clinical use remains challenging. This study is the first to prospectively investigate the performance of two of today's most commonly applied anti-dsDNA testing methods head-to-head under real-world conditions, as well as their correlation with other clinical and serological disease parameters in SLE patients. Methods: In this prospective study, all SLE patients undergoing treatment at the Department of Rheumatology at the University Hospital Bonn within a 13-months period (n=41) and control patients without connective-tissue disease (n=51) were consecutively enrolled and examined. For all study participants' serum samples both anti-dsDNA-NcX enzyme-linked immunoassay testing EUROIMMUN, Luebeck, Germany) and the fluorescence immunoassay ELiA dsDNA (Thermo Fisher Scientific, Waltham, USA) were performed. In addition, demographic data, further laboratory values and disease activity parameters were recorded. Clinical disease activity was assessed by SLEDAI-2K. Results: Both assays showed high specificity (anti-dsDNA-NcX ELISA: 0.9, ELiA dsDNA: 0.959), but there were notable differences in sensitivity (anti-dsDNA-NcX ELISA: 0.51, ELiA dsDNA: 0.38). Pearsons's correlation yielded a positive correlation between anti-dsDNA concentrations and CRP concentrations for the anti-dsDNA-NcX ELISA (R=0.22; p=0.038) and a mild-to-moderate inverse correlation between concentrations of anti-dsDNA and complement C4 for the ELiA dsDNA test (R=-0.22; p=0.045) when SLE and control patients were considered together. Other than, no significant correlation between anti-dsDNA concentrations and clinical or laboratory findings was found for either test procedure. Conclusion: Both anti-dsDNA antibody assays represent reliable examination methods with high specificity for the diagnosis of SLE that fulfill EULAR/ACR requirements. However, the anti-dsDNA-NcX ELISA showed superior sensitivity and significant correlation with disease activity (as measured by CRP concentrations). [ABSTRACT FROM AUTHOR]

The electrochemical behavior of fish sperm double-strand deoxyribonucleic acid (dsDNA) in the presence of adriamycin (ADR) is based on the reduction of the guanine?s oxidation peak signal and examined using electrochemical techniques with pencil graphite electrodes (PGEs). A hallmark for identifying Adriamycin was the reduction in the peak height of the guanine oxidation signal, following the interaction of the drug with dsDNA. Differential pulse voltammetry (DPV), electrochemical impedance spectroscopy (EIS), and cyclic voltammetry (CV) were the characterizing methods used in the investigation. The parameters employed for the optimization experiments to ascertain the electrochemical behavior of Adriamycin were Scan rate and pH investigations. The results of the characterization and optimization investigations demonstrated that the ADR immobilized at various concentrations on the electrode surface interacted with the 100 µg/mL dsDNA. According to the EIS findings, as dsDNA and ADR concentration increase, charge transfer resistance (Rct) decreases. When the electrochemical behavior of ADR was examined using different pH values and scan rates, peak currents at pH 4.0 were observed to be the strongest, with the peak values changing to the negative with the peak current signal increasing. Limits of detection (LOD) and quantitation (LOQ) were determined to be 0.0014 µM and 0.004 µM, respectively. [ABSTRACT FROM AUTHOR]

Monkeypox virus (MPXV) was confirmed in May 2022 and designated a global health emergency by WHO in July 2022. MPX virions are big, enclosed, brick-shaped, and contain a linear, double-stranded DNA genome as well as enzymes. MPXV particles bind to the host cell membrane via a variety of viral-host protein interactions. As a result, the wrapped structure is a potential therapeutic target. DeepRepurpose, an artificial intelligence-based compound-viral proteins interaction framework, was used via a transfer learning setting to prioritize a set of FDA approved and investigational drugs which can potentially inhibit MPXV viral proteins. To filter and narrow down the lead compounds from curated collections of pharmaceutical compounds, we used a rigorous computational framework that included homology modeling, molecular docking, dynamic simulations, binding free energy calculations, and binding pose metadynamics. We identified Elvitegravir as a potential inhibitor of MPXV virus using our comprehensive pipeline.

ObjectiveElevated double-stranded DNA (dsDNA) antibody levels in blood serum are considered a disease-specific marker in systemic lupus erythematosus (SLE), correlate with disease activity and the incidence of lupus nephritis, and can be detected in up to 86% of all SLE cases. Despite the high clinical relevance, the variety of dsDNA antibody testing methods with heterogenous performance in clinical use remains challenging. This study is the first to prospectively investigate the performance of two of today’s most commonly applied anti-dsDNA testing methods head-to-head under real-world conditions, as well as their correlation with other clinical and serological disease parameters in SLE patients.MethodsIn this prospective study, all SLE patients undergoing treatment at the Department of Rheumatology at the University Hospital Bonn within a 13-months period (n=41) and control patients without connective-tissue disease (n=51) were consecutively enrolled and examined. For all study participants’ serum samples both anti-dsDNA-NcX enzyme-linked immunoassay testing EUROIMMUN, Luebeck, Germany) and the fluorescence immunoassay ELiA dsDNA (Thermo Fisher Scientific, Waltham, USA) were performed. In addition, demographic data, further laboratory values and disease activity parameters were recorded. Clinical disease activity was assessed by SLEDAI-2K.ResultsBoth assays showed high specificity (anti-dsDNA-NcX ELISA: 0.9, ELiA dsDNA: 0.959), but there were notable differences in sensitivity (anti-dsDNA-NcX ELISA: 0.51, ELiA dsDNA: 0.38). Pearsons’s correlation yielded a positive correlation between anti-dsDNA concentrations and CRP concentrations for the anti-dsDNA-NcX ELISA (R=0.22; p=0.038) and a mild-to-moderate inverse correlation between concentrations of anti-dsDNA and complement C4 for the ELiA dsDNA test (R=-0.22; p=0.045) when SLE and control patients were considered together. Other than, no significant correlation between anti-dsDNA concentrations and clinical or laboratory findings was found for either test procedure.ConclusionBoth anti-dsDNA antibody assays represent reliable examination methods with high specificity for the diagnosis of SLE that fulfill EULAR/ACR requirements. However, the anti-dsDNA-NcX ELISA showed superior sensitivity and significant correlation with disease activity (as measured by CRP concentrations).

Background: Small extracellular vesicles (sEVs) have great potential as new biomarkers in liquid biopsy. However, due to the limitations of sEVs extraction and component analysis procedures, further clinical applications of sEVs are hampered. Carcinoembryonic antigen (CEA) is a commonly used broad-spectrum tumor marker that is strongly expressed in a variety of malignancies. Results: In this study, CEA+ sEVs were directly separated from serum using immunomagnetic beads, and the nucleic acid to protein ultraviolet absorption ratio (NPr) of CEA+ sEVs was determined. It was found that the NPr of CEA+ sEVs in tumor group was higher than that of healthy group. We further analyzed the sEV-derived nucleic acid components using fluorescent staining and found that the concentration ratio of double-stranded DNA to protein (dsDPr) in CEA+ sEVs was also significantly different between the two groups, with a sensitivity of 100% and a specificity of 41.67% for the diagnosis of pan-cancer. The AUC of dsDPr combined with NPr was 0.87 and the ACU of dsDPr combined with CA242 could reach 0.94, showing good diagnostic performance for pan-cancer. Conclusions: This study demonstrates that the dsDPr of CEA+ sEVs can effectively distinguish sEVs derived from tumor patients and healthy individuals, which can be employed as a simple and cost-effective non-invasive screening technology to assist tumor diagnosis. [ABSTRACT FROM AUTHOR]

To address the current lack of validated molecular standards for analytical ultracentrifugation (AUC), we investigated the suitability of double-stranded DNA molecules. We compared the hydrodynamic properties of linear and circular DNA as a function of temperature. Negatively supercoiled, nicked, and linearized 333 and 339 bp minicircles were studied. We quantified the hydrodynamic properties of these DNAs at five different temperatures, ranging from 4 to 37 °C. To enhance the precision of our measurements, each sample was globally fitted over triplicates and five rotor speeds. The exceptional stability of DNA allowed each sample to be sedimented repeatedly over the course of several months without aggregation or degradation, and with excellent reproducibility. The sedimentation and diffusion coefficients of linearized and nicked minicircle DNA demonstrated a highly homogeneous sample, and increased with temperature, indicating a decrease in friction. The sedimentation of linearized DNA was the slowest; supercoiled DNA sedimented the fastest. With increasing temperature, the supercoiled samples shifted to slower sedimentation, but sedimented faster than nicked minicircles. These results suggest that negatively supercoiled DNA becomes less compact at higher temperatures. The supercoiled minicircles, as purified from bacteria, displayed heterogeneity. Therefore, supercoiled DNA isolated from bacteria is unsuitable as a molecular standard. Linear and nicked samples are well suited as a molecular standard for AUC and have exceptional colloidal stability in an AUC cell. Even after sixty experiments at different speeds and temperatures, measured over the course of 4 months, all topological states of DNA remained colloidal, and their concentrations remained essentially unchanged. [ABSTRACT FROM AUTHOR]

The dependences of the fluorescence intensity and anisotropy of molecular rotors SYBR Green (SG) and double-stranded DNA with 10, 20, and 100 base pairs on their relative concentrations in solutions and on the viscosity of the medium were studied. It was shown that an increase in the fluorescence intensity with an increase in the SG concentration and a subsequent leveling off at a constant value was associated with an initial increase in the number of SG molecules intercalated in DNA and further saturation with the formation of nonfluorescent states. A generalized model that takes into account both internal rotations and rotational diffusion of the molecular complex as a whole was developed to explain the sharp drop in fluorescence anisotropy due to Forster intramolecular energy transfer between DNA-bound SG molecules. The proposed model made it possible to calculate universally the obtained experimental dependences of the fluorescence anisotropy on the viscosity of the medium at various dye/DNA ratios and to estimate the Forster energy transfer rates. [ABSTRACT FROM AUTHOR]

Monkeypox virus (MPXV) was confirmed in May 2022 and designated a global health emergency by WHO in July 2022. MPX virions are big, enclosed, brick-shaped, and contain a linear, double-stranded DNA genome as well as enzymes. MPXV particles bind to the host cell membrane via a variety of viral-host protein interactions. As a result, the wrapped structure is a potential therapeutic target. DeepRepurpose, an artificial intelligence-based compound-viral proteins interaction framework, was used via a transfer learning setting to prioritize a set of FDA approved and investigational drugs which can potentially inhibit MPXV viral proteins. To filter and narrow down the lead compounds from curated collections of pharmaceutical compounds, we used a rigorous computational framework that included homology modeling, molecular docking, dynamic simulations, binding free energy calculations, and binding pose metadynamics. We identified Elvitegravir as a potential inhibitor of MPXV virus using our comprehensive pipeline. [ABSTRACT FROM AUTHOR]

Understanding and regulating DNA interactions with solvents and redox-active centers opens up new possibilities for improving electrochemical signals and developing adequate biosensors. This work reports the development of a modified indium tin oxide (ITO) electrode by chemical vapor deposition (CVD) of graphene for the detection of double-stranded DNA. The modified electrode shows a better electrical conductivity than ITO, as confirmed by electrochemical impedance spectroscopy (EIS), where a drastic decrease in the charge–transfer resistance, Rct, from ~320 to ~60 Ω was observed. Sequences of double-stranded genomic DNA with a different number of base pairs are evaluated through differential pulse voltammetry (DPV), using ferri/ferrocyanide ([Fe(CN)6]3−/4−) as a mediator in the solution. Variations in the electrochemical response of the [Fe(CN)6]3−/4− probe are observed after introducing redox inactive double-stranded DNA ions. The redox-active [Fe(CN)6]3−/4− probe serves as a scaffold to bring DNA into the graphene-modified ITO electrode surface, provoking an increase in the current and a change in the potential when the number of base pairs increases. These results are confirmed by EIS, which shows a variation in the Rct. The calibration of DPV intensity and Rct vs. DNA base pairs (bps) number were linear in the 495–607 bps range. The proposed method could replace the nucleic acid gel electrophoresis technique to determine the presence of a DNA fragment and quantify its size. [ABSTRACT FROM AUTHOR]

Single molecule FRET (Forster resonance energy transfer) is very powerful method for studying biomolecular binding dynamics and conformational transitions. Only a few donor - acceptor dye pairs have been characterized for use in single-molecule FRET (smFRET) studies. Hence, introducing and characterizing additional FRET dye pairs is important in order to widen the scope of applications of single-molecule FRET in biomolecular studies. Here we characterize the properties of the Cy3.5 and Cy5.5 dye pair under FRET at the single-molecule level using naked double-stranded DNA (dsDNA) and the nucleosome. We show that this pair of dyes is photostable for ~ 5 min under continuous illumination. We also report Cy3.5-Cy5.5 FRET proximity dependence and stability in the presence of several biochemical buffers and photoprotective reagents in the context of double-stranded DNA. Finally, we demonstrate compatibility of the Cy3.5-Cy5.5 pair for smFRET in vitro studies of nucleosomes. [ABSTRACT FROM AUTHOR]

The discovery of the cisplatin drug attracted considerable research attention as scientists strove to understand the drug's mechanism in the human body that is responsible for destroying cancer cells, particularly the coordination between the cisplatin drug and deoxyribonucleic acid. Here, the binding energies of a cisplatin molecule relative to double-stranded deoxyribonucleic acid are obtained. The interactions of the system are determined by performing double integrals, and the analytical expressions are derived from the Lennard–Jones function and the continuum approximation; here, it is assumed that a discrete atomic structure might be replaced by surfaces with a constant average atomic density. The results observed that the cisplatin molecule is binding to the double-stranded deoxyribonucleic acid at either the minor or major grooves. By minimizing the interaction energies between the cisplatin molecule and the minor and major grooves, for arbitrary distances λ and arbitrary tilt angles φ from the axis of the helix of the double-stranded deoxyribonucleic acid, the binding energies are determined, and their values are ≈ − 6 and ≈ − 12.5 (kcal/mol), respectively. Thus, we may deduce that the major groove in double-stranded deoxyribonucleic acid is the most preferred groove for linking with the cisplatin molecule. The current analysis might help in the equivalent continuum modeling of deoxyribonucleic acids and nanocomposites. [ABSTRACT FROM AUTHOR]

Background: Double-stranded fragmented extracellular DNA is a participant, inducer, and indicator of various processes occurring in the organism. When investigating the properties of extracellular DNA, the question regarding the specificity of exposure to DNA from different sources has always been raised. The aim of this study was to perform comparative assessment of biological properties of double-stranded DNA obtained from the human placenta, porcine placenta and salmon sperm. Methods: The intensity of leukocyte-stimulating effect of different dsDNA was assessed in mice after cyclophosphamide-induced cytoreduction. The stimulatory effect of different dsDNA on maturation and functions of human dendritic cells and the intensity of cytokine production by human whole blood cells was analyzed ex vivo. The oxidation level of the dsDNA was also compared. Results: Human placental DNA exhibited the strongest leukocyte-stimulating effect. DNA extracted from human and porcine placenta exhibited similar stimulatory action on maturation of dendritic cells, allostimulatory capacity, and ability of dendritic cells to induce generation of cytotoxic CD8+CD107a+ T cells in the mixed leukocyte reaction. DNA extracted from salmon sperm stimulated the maturation of dendritic cells, while having no effect on their allostimulatory capacity. DNA extracted from human and porcine placenta was shown to exhibit a stimulatory effect on cytokine secretion by human whole blood cells. The observed differences between the DNA preparations can be caused by the total methylation level and are not related to differences in oxidation level of DNA molecules. Conclusions: Human placental DNA exhibited the maximum combination of all biological effects. [ABSTRACT FROM AUTHOR]

Bacteriophage T4 gene 32 protein (gp32) preferentially binds to single-stranded DNA (ssDNA) to facilitate DNA replication but shows weak binding to double-stranded DNA (dsDNA). Polyclonal and monoclonal antibodies against gp32 were raised, and an enzyme-linked immunosorbent assay was used to evaluate their reactivities against gp32. The reactivity of the monoclonal antibody MGP45 was diminished in the presence of 5 ng/ml dsDNA, suggesting a conformational change that reduces epitope availability. Notably, the same concentration of ssDNA had little effect; instead, 500 ng/ml ssDNA was required to elicit the same degree of inhibition. A decrease in MGP45 reactivity with gp32 was observed in the presence of NaCl at concentrations less than 100 mM under neutral conditions. These changes in antibody reactivity reflect differences the gp32 conformation, which may underlie its different affinities for ssDNA and dsDNA., (© The Author(s) 2025. Published by Oxford University Press on behalf of Japan Society for Bioscience, Biotechnology, and Agrochemistry.)

Pseudomonas putida KT2440 is a metabolically versatile bacterium with considerable promise as a chassis strain for production and degradation of complex organic compounds. Unlike most bacteria, P. putida KT2440 encodes the Ku and LigD proteins involved in Non-Homologous End Joining (NHEJ). This pathway of repair of double-strand breaks (DSBs) in DNA has an intrinsic mutagenic potential that could be exploited in combination with currently available genome editing tools that generate programmable DSBs. Here, we investigated the effect of removal or overproduction of NHEJ-associated P. putida KT2440 enzymes on mutations generated upon repair of Cas9-mediated DSBs with the double purpose of characterizing the NHEJ pathway and investigating how it functionally interacts with the current gold standard tool for gene editing. The results of our work shed light on non-templated mechanisms of DSB repair in P. putida KT2440, an information that will serve as foundation to expand the gene engineering toolbox for this important microorganism. [ABSTRACT FROM AUTHOR]

Innate immune response acts as the first line of host defense against damage and is initiated following the recognition of pathogen-associated molecular patterns (PAMPs). For double-stranded DNA (dsDNA) sensing, interferon gene stimulator (STING) was discovered to be an integral sensor and could mediate the immune and inflammatory response. Selective STING antagonist C-176 was administered and pain behaviors were assessed following spared nerve injury (SNI)-induced neuropathic pain. The level of serum dsDNA following neuropathic pain was assessed using Elisa analysis. STING signaling pathway, microglia activation, and proinflammatory cytokines were assessed by qPCR, western blots, Elisa, and immunofluorescence staining. STING agonist DMXAA was introduced into BV-2 cells to assess the inflammatory response in microglial cells. dsDNA was significantly increased following SNI and STING/TANK-binding kinase 1 (TBK1)/nuclear factor-kappa B (NF-κB) pathway was activated in vivo and vitro. Early but not the late intrathecal injection of C-176 attenuated SNI-induced pain hypersensitivity, microglia activation, proinflammatory factors, and phosphorylated JAK2/STAT3 in the spinal cord dorsal horn, and the analgesic effect of C-176 was greatly abolished by recombinant IL-6 following SNI. We provided evidence clarifying dsDNA mediated activation of microglia STING signaling pathway, after which promoting expression of proinflammatory cytokines that are required for hyperalgesia initiation in the spinal cord dorsal horn of SNI model. Further analysis showed that microglial STING/TBK1/NF-κB may contribute to pain initiation via IL-6 signaling. Pharmacological blockade of STING may be a promising target in the treatment of initiation of neuropathic pain. [ABSTRACT FROM AUTHOR]

Persistence length is a significant criterion to characterize the semi-flexibility of DNA molecules. The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively characterizing the mechanical constraint effects due to their complex interactions with electrostatic repulsions and thermal fluctuations. In this work, the classical buckling theory of Euler beam and Manning's statistical theories of electrostatic force and thermal fluctuation force are combined for an isolated DNA fragment to formulate a quantitative model, which interprets the relationship between DNA persistence length and critical buckling length. Moreover, this relationship is further applied to identify the mechanical constraints in different DNA experiments by fitting the effective length factors of buckled fragments. Then, the mechanical constraint effects on DNA persistence lengths are explored. A good agreement among the results by theoretical models, previous experiments, and present molecular dynamics simulations demonstrates that the new superposition relationship including three constraint-dependent terms can effectively characterize changes in DNA persistence lengths with environmental conditions, and the strong constraint-environment coupling term dominates the significant changes of persistence lengths; via fitting effective length factors, the weakest mechanical constraints on DNAs in bulk experiments and stronger constraints on DNAs in single-molecule experiments are identified, respectively. Moreover, the consideration of DNA buckling provides a new perspective to examine the bendability of short-length DNA. [ABSTRACT FROM AUTHOR]

(1) Double-stranded DNA (dsDNA) and deoxyribonuclease (DNase) as surrogate parameters for accumulating inflammatory hazards are insufficiently studied in resuscitation research. (2) Blood samples of 76 individuals after CA were analyzed 24 and 96 h after ICU admission. Plasma levels of dsDNA, interleukin-8, and monocyte chemoattractant protein-1 and activity of DNase were assessed along with baseline characteristics, intensive care measures, and outcome data. DsDNA/DNase ratio was used as main prognostication parameter. After calculating an optimal empirical cut-off for outcome prediction (death or Cerebral Performance Category ≥3 at 6 months), multivariable logistic regression was applied. (3) Using receiver operating characteristic (ROC) analysis, an area under the curve (AUC) of 0.65 (95% CI 0.50–0.79) was found for dsDNA/DNase after 24 h versus 0.83 (95% CI 0.73–0.92) after 96 h (p = 0.03). The empirical cut-off for dsDNA/DNase ratio after 96 h was 149.97 (Youden). DsDNA/DNase ratio was associated with unfavorable outcome at six months (aOR 1.006, 95% CI 1.0017–1.0094, p = 0.005). In multivariable analysis, the association of dsDNA/DNase ratio independently predicted outcome as a continuous variable (aOR 1.004, 95% CI 1.0004–1.0079, p = 0.029) after adjusting for potential confounders. (4) DsDNA/DNase ratio at 96 h demonstrates good predictive performance for estimating outcome after CA. [ABSTRACT FROM AUTHOR]

• The serum dsDNA of normal control samples was affected by climatic factors. • The serum dsDNA of psoriasis patients is affected by climatic factors. • The serum dsDNA levels are associated with psoriasis. Psoriasis is a recurrent autoimmune disease characterized by seasonal and latitudinal variations. Double-stranded DNA (dsDNA) is a crucial component of nucleic acids and nucleosomes that provoke innate immune responses. Given the potential influence of climate on immunity and the development of autoimmune diseases, a comprehensive quantitative analysis of dsDNA levels in the population is warranted. In this case–control study conducted from 2016 to 2020, 10,110 psoriasis patients and matched controls from 12 regions in China were included. This study examined variations in serum dsDNA levels based on season and latitude. The results revealed significant associations between geographical location, climatic conditions, and season with serum dsDNA concentration. Individuals residing in Northern China exhibited significantly higher serum dsDNA levels compared to those in the South (1.00 vs. 0.96 ng/ml), and those in medium latitude regions had higher levels than their counterparts in areas with extreme latitudes (0.98 vs. 0.96 ng/ml). Furthermore, individuals in regions with low to medium ultraviolet exposure demonstrated higher serum dsDNA concentrations than those in areas with high ultraviolet levels (1.03 vs. 0.93 ng/ml), and individuals in winter showed higher levels than those in summer (1.03 vs. 0.92 ng/ml). Factors such as sex, UV index, humidity, and sunshine duration were inversely related to serum dsDNA levels, while age and daylight hours showed a positive association. These findings suggest that meteorological and climatic factors play a role in influencing serum dsDNA levels. [ABSTRACT FROM AUTHOR]

BackgroundGenetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets.ResultsHere we explore the role of recombination in both maintaining and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra- and inter- lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations.ConclusionsThese findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.

It is essential to develop a simple method to assess food quality quantitatively. Available methods primarily rely on nanotechnology and offer high selectivity and sensitivity. In this study, we aimed to develop a sensitive nanoprobe, and, to this end, a double-stranded DNA-encased HiPco carbon nanotube (dsDNA-HiPco) hybrid was prepared and used to evaluate the antioxidant potential of a Chinese tea against hydrogen peroxide (H2O2) with a range of irradiation wavelengths. The morphology and dispersion of the hybrids were analysed using atomic force microscopy, which showed that dsDNA wrapped on the SWCNT surface well and homogeneous dispersion of the rod-shaped tubes while the concentration of dsDNA was 1 mg mL-1. The antioxidant effect of Chinese tea was evaluated by using near-infrared absorption and photoluminescence of the hybrid. Experimental results revealed that the tea exerted excellent antioxidant effects when the hybrid was pre-treated with 0.03% wt H2O2. Catechin present in the Chinese tea played a pivotal role in exerting the antioxidant effects. Therefore, a simple detection method proposed herein can be successfully applied in various fields, including biology, medicine, and the food industry.

Aims Extracellular chromatin and deoxyribonuclease (DNase) have been identified as important players of thrombosis, inflammation, and homeostasis in a murine model. We previously demonstrated that activated neutrophils release neutrophil extracellular traps (NETs) at the culprit site in ST-elevation myocardial infarction (STEMI), which significantly contribute to extracellular chromatin burden, and are associated with larger infarcts. To understand the correlation between neutrophil activation, extracellular chromatin, and infarct size (IS), we investigated these parameters in a porcine myocardial infarction model, and at different time points and sites in a prospective STEMI trial with cardiac magnetic resonance (CMR) endpoints. Methods and results In a prospective STEMI trial (NCT01777750), 101 STEMI patients were included and blood samples were obtained from first medical contact until 6 months after primary percutaneous coronary intervention (pPCI) including direct sampling from the culprit site. CMR was performed 4 ± 2 days and 6 months after pPCI. Neutrophil counts, markers of extracellular chromatin, and inflammation were measured. Double-stranded deoxyribonucleic acid (dsDNA), citrullinated histone 3, nucleosomes, myeloperoxidase, neutrophil elastase, and interleukin (IL)-6 were significantly increased, while DNase activity was significantly decreased at the culprit site in STEMI patients. High neutrophil counts and dsDNA levels at the culprit site correlated with high microvascular obstruction (MVO) and low ejection fraction (EF). High DNase activity at the culprit site correlated with low MVO and high EF. In correspondence, dsDNA correlated with IS in the porcine myocardial infarction model. In porcine infarcts, neutrophils and extracellular chromatin were detected in congested small arteries corresponding with MVO. Markers of neutrophil activation, extracellular chromatin, DNase activity and CMR measurements correlated with markers of systemic inflammation C-reactive protein and IL-6 in patients. Conclusions NETs and extracellular chromatin are important determinants of MVO in STEMI. Rapid degradation of extracellular chromatin by DNases appears to be crucial for microvascular patency and outcome. [ABSTRACT FROM AUTHOR]

A “signal off” fluorescent aptasensor based on graphene oxide (GO) nanosheet and double-stranded DNA structure was fabricated for OTA detection. In the absence of OTA, the aptamer and its complementary DNA (cDNA) formed double-stranded conjugates that could coexist with GO, presenting fluorescence responses. Then, the presented OTA was captured by the aptamers, causing the release of cDNA-FAM probes. The free probes were adsorbed by GO, leading to an OTA concentration-dependent fluorescence quenching through fluorescence resonance energy transfer. Under optimum conditions, the fluorescent aptasensor exhibited outstanding sensitivity with a LOD of 11 pg/mL and a wide dynamic range of 0.04–30 ng/mL. The selectivity of the aptasensor was confirmed against other four mycotoxins, and the feasibility and reliability were verified by determining OTA in the spiked malt samples with satisfactory recovery of 95.50%-112.05%. This aptasensing platform could be adapted to measure other mycotoxins by replacing the aptamer sequences for food safety.

In this work we report on observations of new twisted (cholesteric-like) structures in liquid-crystalline dispersion particles with a hexagonal packing of double-stranded (ds) DNA molecules. Heating up to 80 °C of the DNA dispersion formed in a aqueous-salt solution with a high osmotic pressure (concentration) of poly(ethylene glycol) induces the formation of a new, optically active, spirally twisted structure of these molecules ("re-entrant" cholesteric structure (rest-A structure)). Cooling of this dispersion up to 22 °C is accompanied by the formation of an additional "re-entrant" cholesteric structure (rest-B). Modification of particles of the ds DNA dispersion (with rest-B structure) by replacing Na+ cations by multi-charged Gd3+ cations results in the third " re-entrant" structure (rest-C) despite a high density packing of ds nucleic acid molecules. [ABSTRACT FROM AUTHOR]

We report on the room-temperature experimental measurement of THz absorption signatures in aqueous, double-stranded nucleic acid solutions confined to the submicron silica channels on fused quartz substrates using THz frequency-domain (photomixing) spectroscopy. Three sharp (i.e., strong and narrow) signatures, ~10–20 GHz FWHM, are observed in the shortest base pair sample—small interfering, double-stranded (ds) RNA—in the range of 800 GHz to 1.1 THz. Three similar signatures are also observed in a 50-bp dsDNA ladder sample. For a 1-kbp dsDNA ladder sample, the three are still evident, but are broadened and weakened. For a 48.5-kbp sample (λ-DNA), no prominent signatures are observed, but rather a quasi-sinusoidal transmittance spectrum consistent with a substrate etalon effect. The division between sharp signatures and no signatures is consistent with the molecular length being shorter or longer than the persistence length. [ABSTRACT FROM AUTHOR]

Efforts to elucidate protein–DNA interactions at the molecular level rely in part on accurate predictions of DNA-binding residues in protein sequences. While there are over a dozen computational predictors of the DNA-binding residues, they are DNA-type agnostic and significantly cross-predict residues that interact with other ligands as DNA binding. We leverage a custom-designed machine learning architecture to introduce DNAgenie, first-of-its-kind predictor of residues that interact with A-DNA, B-DNA and single-stranded DNA. DNAgenie uses a comprehensive physiochemical profile extracted from an input protein sequence and implements a two-step refinement process to provide accurate predictions and to minimize the cross-predictions. Comparative tests on an independent test dataset demonstrate that DNAgenie outperforms the current methods that we adapt to predict residue-level interactions with the three DNA types. Further analysis finds that the use of the second (refinement) step leads to a substantial reduction in the cross predictions. Empirical tests show that DNAgenie's outputs that are converted to coarse-grained protein-level predictions compare favorably against recent tools that predict which DNA-binding proteins interact with double-stranded versus single-stranded DNAs. Moreover, predictions from the sequences of the whole human proteome reveal that the results produced by DNAgenie substantially overlap with the known DNA-binding proteins while also including promising leads for several hundred previously unknown putative DNA binders. These results suggest that DNAgenie is a valuable tool for the sequence-based characterization of protein functions. The DNAgenie's webserver is available at http://biomine.cs.vcu.edu/servers/DNAgenie/. [ABSTRACT FROM AUTHOR]

Topological properties of a double-stranded DNA (dsDNA) proximity-coupled by an s -wave superconductor are investigated, in which the energy spectra and the differential conductance are calculated within the framework of tight-binding approximation. Our results indicate that this dsDNA-superconductor system hosts Majorana zero modes (MZMs) when the Zeeman field is perpendicular to the helix axis, whereas no MZM could be observed when the Zeeman field is parallel to the helix axis, in sharp contrast to previous studies on nanowires including single-stranded DNA. In particular, two topological phase transitions could take place in the dsDNA-superconductor system by changing the Zeeman field, one from a topological trivial phase to a topological nontrivial phase with one pair of MZMs in small Zeeman field regime, and the other from a phase with one pair of MZMs to a phase with two pairs of MZMs by further increasing the Zeeman field. In the presence of a gate field normal to the helix axis, the topological nontrivial phase with two pairs of MZMs can transform into the phase with one pair of MZMs. The topological phase with one pair of MZMs is more stable and robust against Anderson disorder. [ABSTRACT FROM AUTHOR]

The anti-double-stranded (ds)DNA antibody test is an integral part of diagnosing systemic lupus erythematosus when the entry criterion is satisfied. We investigated the sensitivity of the BioPlex 2200 instrument compared with the serological gold standard and other tests and clinical information. The results showed an unacceptable sensitivity for this method. Laboratories should be cognizant of this shortcoming when selecting this platform for dsDNA antibody testing., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society for Clinical Pathology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Abstract Pheochromocytomas (PCCs) and paragangliomas (PGLs) are the most heritable endocrine tumors. Genetic testing for 12 driver susceptibility genes is recommended in all PCC and PGL cases. However, detection of somatic mutations in PCC and PGL remains unrealizable for genetic diagnosis and preoperative assessment. We compared the serum exosomal DNA and tumor tissue DNA from patients or mice with PCC or PGL and found double-stranded DNA (dsDNA) fragments in the circulating exosomes of patients with PCC or PGL. Exosomal dsDNA shared the same mutations in the susceptibility genes with that of the parent tumor cells. Moreover, our research showed that serum-derived exosomal dsDNA in PCC and PGL was highly consistent with the paired tumor genome. Our findings provide the first definitive evidence of the presence of exosomal dsDNA that can be used as a noninvasive genetic marker in one of the most effective somatic mutation screens for the diagnosis and preoperative assessment of PCCs and PGLs.

Phospholipase A 2 (PLA 2) may be a vital biomarker for the prediction and diagnosis of some diseases. Consequently, it is of great significance to quantitatively detect PLA 2 in biologic samples. Herein, on the basis of the principle of luminescence resonance energy transfer (LRET) between upconversion nanoparticles (UCNPs) and SYBR Green I (SG), we proposed a technology for the highly sensitive detection of PLA 2 amount. Therein, as an energy receptor, SG will be quantitatively loaded into liposomes firstly. Then, due to the hydrolysis of liposomes under the catalysis of PLA 2 , SG will be released and inserted into the double-stranded DNA (dsDNA) on the surface of UCNPs, which triggers the LRET because of the shortening of effective spatial distance between UCNPs and SG. Under exciting of NIR light, UCNPs emit luminescence at 476 nm, which makes SG emit fluorescence at 522 nm through LRET. Under optimal conditions, the emission intensity ratio (I 522 nm /I 476 nm) increased linearly with the PLA 2 amount in the range of 20 U/L to 400 U/L, and the limit of detection (LOD) reached 15 U/L. Here, after comparing with the clinical standard method, it is found that the biosensor is expected to provide a convenient and sensitive assay for the detection of PLA 2 in actual serum samples. Furthermore, such biosensor can also be used to test the inhibitor of PLA 2. A detection technology based on LRET between upconversion nanoparticles (UCNPs) donor and SYBR Green I (SG) acceptor for ratiometric fluorescence detection of phospholipase A 2 (PLA 2) in serum was proposed, which could also be used for testing PLA 2 inhibitor. Image 1 • A detection technology based on LRET from UCNPs to SG was designed. • UCNPs acted as the LRET donor can effectively eliminate the background interference from biological samples. • The biosensor effectively utilizes the recognition function of SG for dsDNA. • The ratio fluorescent approach for testing PLA 2 has high sensitivity and wide linearity range. [ABSTRACT FROM AUTHOR]

Some antibodies and autoreactive antibodies are associated with the severity of infectious diseases. The roles of humoral responses to lung inflammation in children with human adenovirus (HAdVs) pneumonia remain unknown. A retrospective study was done to compare plasma immunoglobulin E (IgE) levels between HAdVs pneumonia patients and healthy children by searching the electronic medical record system of Guangzhou Women and Children's Medical Center. Then, a prospective study was performed for children with HAdVs pneumonia who needed flexible bronchoscopy for examination and treatment purposes during July 2017 to July 2019. We examined the IgE and autoreactive IgE levels in plasma and bronchoalveolar lavage fluid (BALF) of these children to explore their role in HAdVs pneumonia. A significantly higher level of IgE was found in plasma from children hospitalized with HAdVs pneumonia compared with that from healthy children in the same age range. Furthermore, the levels of IgE, double-stranded DNA (dsDNA), and double-stranded DNA-specific immunoglobulin E (dsDNA-IgE) in BALF were increased compared to plasma in children with HAdVs pneumonia. The levels of IgE, dsDNA, and dsDNA-IgE in BALF were significantly higher in the severe group compared to the non-severe group. The ability of IgE in BALF to recognize dsDNA was verified by the ELISPOT test. Our findings indicate that IgE and dsDNA-IgE in BALF may contribute to lung injury caused by HAdVs, especially in severe cases. Elevated dsDNA-IgE may serve as an indicator of severity in children with HAdVs pneumonia. [ABSTRACT FROM AUTHOR]

Aim: Despite an increased rate of return of spontaneous circulation (ROSC) in out-of-hospital cardiac arrest (OHCA) patients, almost half of patients do not survive up to hospital discharge. Understanding pathophysiological mechanisms of post-cardiac arrest syndrome is essential for developing novel therapeutic strategies. During systemic inflammatory responses and concomitant cell death, double-stranded (ds) DNA is released into circulation, exerting pro-inflammatory effects. Deoxyribonuclease (DNase) degrades dsDNA. The role of DNase activity in OHCA survivors and impact on clinical outcome has not been analyzed yet.Methods: In a prospective, single-center study, dsDNA and DNase activity were determined at hospital admission (acute phase) and 24 h (subacute phase) after ROSC. The ratio between dsDNA levels and DNase activity was calculated to determine the extent of dsDNA release in relation to the patients' capacity of degradation. Thirty-day mortality was defined as study end point.Results: We enrolled 64 OHCA survivors, of whom 26.6% (n = 17) died within 30 days. A peak of circulating dsDNA was observed at admission which decreased within 24 h. DNase activity did not differ between acute and subacute phase, while dsDNA load per DNase activity significantly decreased. The ratio between dsDNA levels and DNase activity in the subacute phase was the strongest predictor of 30-day mortality with an adjusted HR per 1 SD of 3.59 (95% CI, 1.80-7.18, p < 0.001).Conclusion: Disproportionally increased dsDNA levels uncompensated by DNase activity are a strong predictor of mortality in OHCA survivors. This pilot study points to a potentially protective effect of DNase activity in patients undergoing cardiac arrest. [ABSTRACT FROM AUTHOR]

The timely activation of homologous recombination is essential for the maintenance of genome stability, in which the RAD51 recombinase plays a central role. Biochemically, human RAD51 polymerises faster on single‐stranded DNA (ssDNA) compared to double‐stranded DNA (dsDNA), raising a key conceptual question: how does it discriminate between them? In this study, we tackled this problem by systematically assessing RAD51 binding kinetics on ssDNA and dsDNA differing in length and flexibility using surface plasmon resonance. By directly fitting a mechanistic model to our experimental data, we demonstrate that the RAD51 polymerisation rate positively correlates with the flexibility of DNA. Once the RAD51‐DNA complex is formed, however, RAD51 remains stably bound independent of DNA flexibility, but rapidly dissociates from flexible DNA when RAD51 self‐association is perturbed. This model presents a new general framework suggesting that the flexibility of DNA, which may increase locally as a result of DNA damage, plays an important role in rapidly recruiting repair factors that multimerise at sites of DNA damage. Synopsis: Kinetic studies of human RAD51 binding to DNA combined with mathematical modelling reveal that RAD51 preferentially polymerises on flexible DNA, explaining how RAD51 is recruited favourably to broken DNA and why certain rigid genomic regions, such as poly(dA) stretches, are left unrepaired. RAD51 polymerisation on ssDNA and dsDNA requires a minimal nucleus of four and two molecules, respectively.RAD51 polymerises faster on flexible ssDNA compared to rigid ssDNA, such as poly(dA), and dsDNA.RAD51 polymers, once assembled on DNA, stably associate with DNA independently of its flexibility.RAD51 polymers dissociate rapidly from flexible DNA, but not from rigid DNA, when RAD51 protomer‐protomer interaction is perturbed. [ABSTRACT FROM AUTHOR]

Rapid and reliable identification of genetically modified (GM) and non-GM crops is in urgent demand and remains a significant challenge in food safety. Here, a new and reliable Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-mediated magnetic surface-enhanced resonance Raman scattering (SERRS) biosensing is reported to identify specific gene sequences of transgenic crops (CaMV 35 S promoter and Nos terminator). This assay mainly combines the gene-specific recognition ability of CRISPR, the ultra-high sensitivity due to the Raman resonance effect, and the simple separation property of magnetic nanomaterials. A multifunctional SERRS-active nanoprobe was designed by decorating a gold-coated magnetic bead with the G-triplet deoxyribonucleic acid (DNA) sequences that enable a high loading of Raman reporters (methylene blue) inserted in G-triplet DNAs. The assay is achieved by the recognition of the CRISPR/Cas12a protein for bound target DNAs and the activation of the unlimited trans-cleavage action on the G-triplet DNAs, which causes a release of methylene blue above the nanoprobes and a reduction of the SERRS signal. Gel electrophoresis experiments imply that the designed crRNAs have good recognition and cleavage function for target DNAs and verify the feasibility of the experimental scheme. This SERRS assay exhibits a linear response of 4.15 × 10−12 M to 4.15 × 10−9 M with a pM detection level. Tests of the GM and non-GM crops of actual crop samples have been realized, which implies that this CRISPR-mediated magnetic SERRS method is available for assessing natural samples and working for GM crop regulation. • A combination of CRISPR/Cas12a and SERS technology for double-stranded DNA detection. • A general and simple preparation method of FeAuG-MB nanoprobes. • Utilize the high sensitivity of SERS to achieve ultra-low concentration DNA detection. • A highly sensitive detection method using resonance effect of MB molecules with a 633 nm laser. • A simple nucleic acid detection method using magnetic bead enrichment. [ABSTRACT FROM AUTHOR]

[Display omitted] • Novel electrochemistry explores temperature's impact on dsDNA-curcumin binding. • The article combines techniques to study dsDNA and curcumin binding. • Determines dsDNA-curcumin binding constant, quantifying interaction strength. • Using 3 methods, predicts dsDNA-curcumin minor groove binding. • Higher temperatures yield stronger dsDNA-curcumin interactions. In this study, we investigated the binding mode between double-stranded deoxyribonucleic acid (dsDNA) and curcumin (CU) using differential pulse voltammetry (DPV), UV–Vis spectroscopy, and molecular docking. By employing these techniques, we predicted the binding within the minor groove region of dsDNA and CU. Significantly, we employed electrochemistry, specifically cyclic voltammetry (CV), to explore the temperature effect on the dsDNA and CU binding. To the best of our knowledge, this is the first study to utilize electrochemical methods for investigating the temperature-dependent behavior of this binding interaction. Our findings revealed temperature-dependent variations in the binding constants: 2.42 × 103 M−1 at 25 °C, 4.26 × 103 M−1 at 30 °C, 5.44 × 103 M−1 at 35 °C, 6.29 × 103 M−1 at 40 °C, and 7.52 × 103 M−1 at 45 °C. Notably, the binding constant exhibited an increasing trend with elevated temperatures, indicating a temperature-dependent enhancement of the binding interaction. [ABSTRACT FROM AUTHOR]

We report on the room-temperature experimental measurement of THz absorption signatures in aqueous, double-stranded nucleic acid solutions confined to the submicron silica channels on fused quartz substrates using THz frequency-domain (photomixing) spectroscopy. Three sharp (i.e., strong and narrow) signatures, ~10–20 GHz FWHM, are observed in the shortest base pair sample—small interfering, double-stranded (ds) RNA—in the range of 800 GHz to 1.1 THz. Three similar signatures are also observed in a 50-bp dsDNA ladder sample. For a 1-kbp dsDNA ladder sample, the three are still evident, but are broadened and weakened. For a 48.5-kbp sample (λ-DNA), no prominent signatures are observed, but rather a quasi-sinusoidal transmittance spectrum consistent with a substrate etalon effect. The division between sharp signatures and no signatures is consistent with the molecular length being shorter or longer than the persistence length.

One of the most important properties of extracellular double-stranded DNA related to the treatment of various diseases is its ability to activate effector cells of the immune system (anti-tumor and vaccinal immunity) through dendritic cells (DCs). The stimulatory effect of DNA on DCs is mediated by the TLR9 signaling pathway and/or through a system of cytosolic sensors and is manifested by increased expression of MHC class II antigens and costimulatory molecules and by increased synthesis of immunoregulatory cytokines. In this work, the expression of cytokines, differentiation antigens and transcription factor genes has been investigated in DCs activated by double-stranded human DNA (i) without any additional factors, (ii) using a lipophilic agent, and (iii) by blocking TLR9 with chloroquine. Evaluation of the DNA effect was carried out after the 6- and 24-hour exposure. It was found that the preparation of double-stranded DNA transfected by Lipofectamine 2000 boosts DCs at the same level as Poly(dA : dT), a synthetic equivalent of double-stranded DNA. It was discovered that combined application of DNA and chloroquine enhances expression of the IFN-α, IFN-β, IFN-γ, IL­8, МСР1, VEGF, CD25, and CD83 genes by hour 24 of incubation. It was for the first time shown that genomic “self” double-stranded DNA as a mono agent activates mRNA synthesis of cytokines IFN-α, IFN-β, IFN-γ, IL­8, IL­10, and VEGF in DCs at 6 hours of induction.