The i-motif is a biologically relevant non-canonical DNA structure formed by cytosine-rich sequences. Despite the importance of the factors affecting the formation/stability of such a structure, like pH, cation type and concentration, no systematic study that simultaneously analysed their effect on the i-motif in vitro has been carried out so far. Therefore, here we report a systematic study that aims to evaluate the effect of these factors, and their possible interaction, on the formation of an i-motif structure. Our results confirm that pH plays the main role in i-motif formation. However, we demonstrate that the effect of the cation concentration on the i-motif is strictly dependent on the pH, while no significant differences are observed among the investigated cation types.
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Exosomes are membrane-bound vesicles secreted by cells, and contain various important biological molecules, such as lipids, proteins, messenger RNAs, microRNAs, and noncoding RNAs. Emerging evidence demonstrates that proteomic analysis of exosomes is of great significance in studying metabolic diseases, tumor metastasis, immune regulation, and so forth. However, exosome proteomic analysis has high requirements with regard to the purity of collected exosomes. Here recent advances in the methods for isolating exosomes and their applications in proteomic analysis are summarized.
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We report a novel, fast, and automatic SPME-based method capable of extracting a small molecule-drug conjugate (SMDC) from biological matrices. Our method relies on the extraction of the drug conjugate followed by direct elution into an electrospray mass spectrometer (ESI-MS) source for qualitative and quantitative analysis. We designed a tool for extracting the targeting head of a recently synthesized SMDC, which includes acetazolamide (AAZ) as high-affinity ligand specific to carbonic anhydrase IX. Specificity of the extraction was achieved through systematic optimization. The design of the extraction tool is based on noncovalent and reversible interaction between AAZ and CAII that is immobilized on the SPME extraction phase. Using this approach, we showed a 330% rise in extracted AAZ signal intensity compared to a control, which was performed in the absence of CAII. A linear dynamic range from 1.2 to 25 μg/ml was found. The limits of detection (LOD) of extracted AAZ from phosphate-buffered saline (PBS) and human plasma were 0.4 and 1.2 μg/ml, respectively. This with a relative standard deviation of less than 14% (n = 40) covers the therapeutic range.
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Choosing an appropriate ion source is a crucial step in liquid chromatography mass spectrometry (LC/MS) method development. In this paper, we compare four ion sources for LC/MS analysis of 40 pesticides in tomato and garlic matrices. We compare electrospray ionisation (ESI) source, thermally focused/heated electrospray (HESI), atmospheric pressure photoionisation (APPI) source with and without dopant, and multimode source in ESI mode, atmospheric pressure chemical ionisation (APCI) mode, and combined mode using both ESI and APCI, i.e. altogether seven different ionisation modes. The lowest limits of detection (LoDs) were obtained by ESI and HESI. Widest linear ranges were observed with the conventional ESI source without heated nebuliser gas. In comparison to HESI, ESI source was significantly less affected by matrix effect. APPI ranked second (after ESI) by not being influenced by matrix effect; therefore, it would be a good alternative to ESI if low LoDs are not required.
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The rapid and simultaneous detection of DNA and protein biomarkers is necessary to detect the outbreak of a disease or to monitor a disease. For example, cardiovascular diseases are a major cause of adult mortality worldwide. We have developed a rapidly adaptable platform to assess biomarkers using a microfluidic technology. Our model mimics autoantibodies against three proteins, C-reactive protein (CRP), brain natriuretic peptide (BNP), and low-density lipoprotein (LDL). Cell-free mitochondrial DNA (cfmDNA) and DNA controls are detected via fluorescence probes. The biomarkers are covalently bound on the surface of size- (11–15 μm) and dual-color encoded microbeads and immobilized as planar layer in a microfluidic chip flow cell. Binding events of target molecules were analyzed by fluorescence measurements with a fully automatized fluorescence microscope (end-point and real-time) developed in house. The model system was optimized for buffers and immobilization strategies of the microbeads to enable the simultaneous detection of protein and DNA biomarkers. All prime target molecules (anti-CRP, anti-BNP, anti-LDL, cfmDNA) and the controls were successfully detected both in independent reactions and simultaneously. In addition, the biomarkers could also be detected in spiked human serum in a similar way as in the optimized buffer system. The detection limit specified by the manufacturer is reduced by at least a factor of five for each biomarker as a result of the antibody detection and kinetic experiments indicate that nearly 50 % of the fluorescence intensity is achieved within 7 min. For rapid data inspection, we have developed the open source software digilogger, which can be applied for data evaluation and visualization.
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In this work, a straightforward analytical approach based on headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry was developed for the analysis of salivary volatile organic compounds without any prior derivatization step. With a sample volume of 500 μL, optimal conditions were achieved by allowing the sample to equilibrate for 10 min at 50 °C and then extracting the samples for 10 min at the same temperature, using a carboxen/polydimethylsiloxane fibre. The method allowed the simultaneous identification and quantification of 20 compounds in sample headspace, including short-chain fatty acids and their derivatives which are commonly analysed after analyte derivatization. The proof of applicability of the methodology was performed with a case study regarding the analysis of the dynamics of volatile metabolites in saliva of a single subject undergoing 5-day treatment with rifaximin antibiotic. Non-stimulated saliva samples were collected over 3 weeks from a nominally healthy volunteer before, during, and after antibiotic treatment. The variations of some metabolites, known to be produced by the microbiota and by bacteria that are susceptible to antibiotics, suggest that the study of the dynamics of salivary metabolites can be an excellent indirect method for analysing the gut microbiota. This approach is novel from an analytical standpoint, and it encourages further studies combining saliva metabolite profiles and gut microbiota dynamics.
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Graphite electrodes were modified with triangular (AuNTrs) or spherical (AuNPs) nanoparticles and further modified with fructose dehydrogenase (FDH). The present study reports the effect of the shape of these nanoparticles (NPs) on the catalytic current of immobilized FDH pointing out the different contributions on the mass transfer–limited and kinetically limited currents. The influence of the shape of the NPs on the mass transfer–limited and the kinetically limited current has been proved by using two different methods: a rotating disk electrode (RDE) and an electrode mounted in a wall jet flow-through electrochemical cell attached to a flow system. The advantages of using the wall jet flow system compared with the RDE system for kinetic investigations are as follows: no need to account for substrate consumption, especially in the case of desorption of enzyme, and studies of product-inhibited enzymes. The comparison reveals that virtually identical results can be obtained using either of the two techniques. The heterogeneous electron transfer (ET) rate constants (kS) were found to be 3.8 ± 0.3 s−1 and 0.9 ± 0.1 s−1, for triangular and spherical NPs, respectively. The improvement observed for the electrode modified with AuNTrs suggests a more effective enzyme-NP interaction, which can allocate a higher number of enzyme molecules on the electrode surface.
The shape of gold nanoparticles has a crucial effect on the catalytic current related to the oxidation of D-(-)-fructose to 5-keto-D-(-)-fructose occurring at the FDH-modified electrode surface. In particular, AuNTrs have a higher effect compared with the spherical one.
Folic acid (FA) is an essential vitamin in humans, and thus, rapid, accurate, and sensitive methods for its quantification in different biological samples are needed. This work describes a novel, simple, and effective dual-emission fluorescence nanoprobe for FA detection and quantification. The probe was covalently linked to amino-modified orange quantum dots (QDs) and carboxyl-modified blue graphene quantum dots (GQDs). The resulting material exhibited two emission peaks at 401 and 605 nm upon excitation at 310 nm. The probe had good selectivity and sensitivity toward FA with an exceptionally low detection limit (LOD = 0.09 nM). This probe was effectively used to quantify FA in animal serum samples. The method has potential utility for FA analysis in different types of biological samples.
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G-quadruplexes have been widely researched as new targets for cancer treatment owing to their non-canonical structure and crucial role in biological processes. Although attention has been paid to the development of selective G-quadruplex ligands, few studies have focused on the binding affinity of stereoisomers towards G-quadruplex, which will be conducive to support the optimal design of G-quadruplex ligands in future studies. Here, tetrandrine and isotetrandrine were used to study the binding affinity and difference of stereoisomers towards G-quadruplex structures. The results showed that tetrandrine had a high possibility of binding to the N-myc and Bcl-2 G-quadruplexes through hydrogen bonding, whereas the possibility of binding of isotetrandrine was low and it seemed to have no possibility of forming hydrogen bonds. Our study shows that optical isomerism of ligand molecules has an important effect on G-quadruplex recognition, which is helpful for the design of G-quadruplex ligands in future studies.
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A high-precision exact-matching quadruple isotope dilution method (ID4MS) was employed for the quantitation of nitrate in an air-dried spinach powder Certified Reference Material (CRM). The analyte was extracted in hot water following addition of 15NO\({}_{3}^{-}\) internal standard. The blend was then treated with sulfamic acid to remove nitrite and with triethyloxonium tetrafluoroborate to promote aqueous conversion of nitrate into volatile EtONO2. The derivative was analyzed by headspace GC–MS with 3-min elution time. The method performance was validated with a series of tests which demonstrated adequate selectivity and ruggedness. This method supported the development of novel SPIN-1 CRM giving a modest contribution to its uncertainty (uchar = 0.85%). With respect to previous attempts, the SPIN-1 was proven stable, homogeneous (uhom = 0.44%), and suitable for spinach monitoring under EU regulations. On dried basis, the nitrate content of SPIN-1 was found to be 22.53 ± 0.43 mg/g (Uc = 1.9%, k = 2). The material was also used in an inter-laboratory study where four laboratories employed a total of ten measurement methods.
SPIN-1 Certified Reference Material for nitrate in spinach powder
We report on the successful application of carboxyl-rich plasma polymerized (PP) films as a matrix layer for bioreceptor immobilization in surface plasmon resonance (SPR) immunosensing. Composition and chemical properties of the carboxyl-rich PP films deposited from a mixture of maleic anhydride and acetylene were investigated. Changes in the films stored in air, water, and buffer were studied and the involved chemical changes were described. Performance in SPR immunosensing was evaluated on interactions of human serum albumin (HSA) with a specific monoclonal antibody. The comparison with the mixed self-assembled monolayer of mercaptoundecanoic acid and mercaptohexanol (MUA/MCH) and one of the most widely used surfaces for SPR, the 2D and 3D carboxymethylated dextran (CMD), was presented to show the efficacy of plasma polymerized matrix layers for biosensing. The PP film-based SPR immunosensor provided a similar detection limit of HSA (100 ng/mL) as MUA/MCH- (100 ng/mL) and 3D CMD (50 ng/mL)-based sensors. However, the response levels were about twice higher in case of the PP film-based immunosensor than in case of MUA/MCH-based alternative. The PP film surfaces had similar binding capacity towards antibody as the 3D CMD layers. The response of PP film-based sensor towards HSA was comparable to 3D CMD-based sensor up to 2.5 μg/mL. For the higher concentrations (> 10 μg/mL), the response of PP film-based immunosensor was lower due to inaccessibility of active sites of the immobilized antibody inside the flat PP film surface. We have demonstrated that due to its high stability and cost-effective straightforward preparation, the carboxyl-rich PP films represent an efficient alternative to self-assembled monolayers (SAM) and dextran-based layers in label-free immunosensing.
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Evaluation of post-translational modifications of protein molecules is important for both basic and applied biomedical research. Mass spectrometric quantitative studies of modifications, which do not change the mass of the protein, such as isomerization of aspartic acid, do not necessarily require the use of isotope-labelled standards. However, the accurate solution of this problem requires a deep understanding of the relationship between the mole fractions of the isomers and the peak intensities in the mass spectra. In previous studies on the isomerization of aspartic acid in short beta-amyloid fragments, it has been shown that calibration curves used for such quantitative studies often have a non-linear form. The reason for the deviation in the shape of the calibration curves from linearity has not yet been established. Here, we propose an explanation for this phenomenon based on a probabilistic model of the fragmentation process and present a general approach for the selection of fragments that can be used for quantitative studies of the degree of isomerization.
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The cyanate anion (CNO−), formed spontaneously within cells from urea and carbamoyl phosphate, usually functions as a biomarker of some diseases such as chronic kidney disease. Therefore, accurate determination of CNO− is highly demanded. Herein, a 3-amino-2-naphthoic acid-based “turn-on” fluorescence probe was developed for specific detection of CNO−. Upon the addition of sodium cyanate, the weak-fluorescent 3-amino-2-naphthoic acid could react with CNO−, which triggered intense emission of green fluorescence. And up to 9-fold fluorescence enhancement was observed. The fluorescence enhancement ratios displayed a good linear relationship with the concentrations of CNO− in the range of 0.5–200 μM. The high selectivity and sensitivity for CNO− detection were investigated with the detection limit as low as 260 nM. The probe was further successfully applied to determine CNO− in real samples such as tap water, human urine and serum samples, which offered a promising approach in practical applications.
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A multichannel chip containing 16 microchambers was developed for fast and sensitive immunoassays. In each chamber, antibody-functionalized nonmagnetic beads were applied as the solid phase to capture target antigens. Four types of IgGs (human, rabbit, chicken, and mouse) could be detected simultaneously by our combining this microchip with a sandwich immunoassay technique. A three-layer chip structure was investigated for integration of multiple processes, including washing, immune reaction, and detection, in one microchip. Moreover, the proposed chip design could improve batch-to-batch repeatability and avoid interferences between different channels without the preparation of complex microvalves. The total operation time of this system was less than 30 min, with a desirable detection limit of 0.2 pg/mL. The results indicate that the microfluidic platform is promising for the immunoassay of multiple clinical biomarkers.
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A new class of magnetic ionic liquids (MILs) with metal-containing cations was applied in in situ dispersive liquid–liquid microextraction (DLLME) for the extraction of long and short double-stranded DNA. For developing the method, MILs comprised of N-substituted imidazole ligands (with butyl-, benzyl-, or octyl-groups as substituents) coordinated to different metal centers (Ni2+, Mn2+, or Co2+) as cations, and chloride anions were investigated. These water-soluble MILs were reacted with the bis[(trifluoromethyl)sulfonyl]imide anion during the extraction to generate a water-immiscible MIL capable of preconcentrating DNA. The feasibility of combining the extraction methodology with anion-exchange high-performance liquid chromatography with diode array detection (HPLC-DAD) or fluorescence spectroscopy was studied. The method with the Ni2+- and Co2+-based MILs was easily combined with fluorescence spectroscopy and provided a faster and more sensitive method than HPLC-DAD for the determination of DNA. In addition, the method was compared to conventional DLLME using analogous water-immiscible MILs. The developed in situ MIL-DLLME method required only 3 min for DNA extraction and yielded 1.1–1.5 times higher extraction efficiency (EFs) than the conventional MIL-DLLME method. The in situ MIL-DLLME method was also compared to the trihexyl(tetradecyl)phosphonium tris(hexafluorocetylaceto)nickelate(II) MIL, which has been used in previous DNA extraction studies. EFs of 42–99% were obtained using the new generation of MILs, whereas EFs of only 20–38% were achieved with the phosphonium MIL. This new class of MILs is simple and inexpensive to prepare. In addition, the MILs present operational advantages such as easier manipulation in comparison to hydrophobic MILs, which can have high viscosities. These MILs are a promising new class of DNA extraction solvents that can be manipulated using an external magnetic field.
Magnetic ionic liquids with metal-containing cations are applied in in situ dispersive liquid–liquid microextraction for the extraction of long and short double-stranded DNA
The preparation and fractionation of oligomeric proanthocyanidins (OPCs) are particularly important for the application of tannins in the biomedical field. By use of two different methods—gel filtration chromatography (GFC) with Sephadex LH-20 and progressive solvent precipitation—the OPCs were prepared and fractionated from mangosteen pericarp. The fractions were compared by reversed-phase and normal-phase high-performance liquid chromatography–electrospray ionization mass spectrometry and gel permeation chromatography. GFC directly purified oligomers (monomer to pentamer) with polydispersity values close to 1 and generated fractions with a higher level of total phenols (800.59 mg gallic acid equivalents per gram) but a lower yield (7.72%). Progressive solvent precipitation rapidly prepared and fractionated OPCs with a lower level of total phenols (609.57 mg gallic acid equivalents per gram) but a higher yield (24.74%) and higher polydispersity. Additionally, we found pronounced structural and quantitative differences among different tannin-rich fractions, and fractions obtained by GFC better reflected the structural diversity and complexity of OPCs from mangosteen pericarp. This study presents different ways of preparing and fractionating OPCs in the biomedical field.
A novel SBA-15-based fluorescent sensor, SBA-PI: mesoporous SBA-15 structure modified with iminostilbene groups, was designed, synthesized, and characterized by Fourier transform-infrared spectroscopy (FT-IR), ultraviolet–visible spectroscopy, field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDS), thermogravimetric analysis (TGA), low-angle X-ray diffraction techniques (low-angle XRD), and N2 adsorption–desorption techniques. The SBA-PI as a sensor with a selective behavior for detection of Cu2+ comprises iminostilbene carbonyl as the fluorophore group. The SBA-PI sensor displays an excellent fluorescence response in aqueous solutions and the fluorescence intensity quenches remarkably upon addition of Cu2+. Other common interfering ions even at high concentration ratio showed either no or very small changes in the fluorescence intensity of SBA-PI in the absence of Cu2+. A limit of detection of 8.7 × 10−9 M for Cu2+ indicated that this fluorescence sensor has a high sensitivity and selectivity toward the target copper (II) ion. The fabricated Cu2+ sensor was successfully applied for the determination of the Cu2+ in human blood samples without any significant interference. With the selective analysis of Cu2+ ions down to 0.9 nM in blood, the sensor is a promising and a novel detection candidate for Cu2+ and can be applied in the clinical laboratory. A reversibility and accuracy in the fluorescence behavior of the sensor was found in the presence of I¯ that was described as a masking agent for Cu2+.
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A new electrochemical sensor, based on NdFeO3 nanoparticles as electrocatalytic material, was proposed here for the detection of dopamine (DA). NdFeO3 nanoparticles were first synthesized by a simple thermal treatment method and subsequent annealing at high temperature (700 °C). The prepared electrocatalytic material has been characterized in detail by SEM-EDX, XRD, and Raman techniques. Characterization results display its sheet-like morphology, constituted by a porous network of very small orthorhombic NdFeO3 nanoparticles. NdFeO3 electrocatalytic material was then used to modify the working electrode of screen-printed carbon electrodes (SPCEs). Electrochemical tests demonstrated that NdFeO3– modified screen-printed carbon electrode (NdFeO3/SPCE) exhibited a remarkable enhancement of the dopamine electrooxidation, compared to the bare SPCE one. The analytical performance of the developed sensor has been evaluated for the detection of this analyte by means of the square-wave voltammetry (SWV) technique. The modified electrode showed two linear concentration ranges, from 0.5 to 100 μM and 150 to 400 μM, respectively, a limit of detection (LOD) of 0.27 μM (at S/N = 3), and good reproducibility, stability, and selectivity. Additionally, we also report an attempt made to propose the modified sensor for the simultaneous detection of dopamine and uric acid (UA). The procedure was also applied for the determination of dopamine in spiked real samples. So, this paper reports for the first time the use of a modified NdFeO3 screen-printed electrode for developing an electrochemical sensor for the quantification of important biomolecules.
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A biomass nitrogen and sulfur codoped carbon dots (NS-Cdots) was prepared by a simple and clean hydrothermal method using leek, and was employed as efficient fluorescent probes for sensitive detection of organophosphorus pesticides (OPs). The leek-derived NS-Cdots emitted blue fluorescence, but was quenched by H2O2. Due to acetylcholinesterase/choline oxidase–based cascade enzymatic reaction that produces H2O2 and the inhibition effect of OPs on acetylcholinesterase activity, a NS-Cdots-based fluorescence “off-on” method to detect OPs-dichlorvos (DDVP) was developed. More sensitivity and wider linear detection range were achieved from 1.0 × 10−9 to 1.0 × 10−3 M (limit of detection = 5.0 × 10−10 M). This developed method was applied to the detection of DDVP in Chinese cabbage successfully. The average recoveries were in the range of 96.0~104.0% with a relative standard deviation of less than 3.3%. In addition, the NS-Cdots fluorescent probes were also employed successfully in multicolor imaging of living cells, manifesting that the NS-Cdots fluorescent probes have great application potential in agricultural and biomedical fields.
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