Quantification Of Biomolecules Research Articles

All-Dielectric Metasurface-Based Terahertz Molecular Fingerprint Sensor for Trace Cinnamoylglycine Detection.

Terahertz (THZ) spectroscopy has emerged as a superior label-free sensing technology in the detection, identification, and quantification of biomolecules in various biological samples. However, the limitations in identification and discrimination sensitivity of current methods impede the wider adoption of this technology. In this article, a meticulously designed metasurface is proposed for molecular fingerprint enhancement, consisting of a periodic array of lithium tantalate triangular prism tetramers arranged in a square quartz lattice. The physical mechanism is explained by the finite-difference time-domain (FDTD) method. The metasurface achieves a high quality factor (Q-factor) of 231 and demonstrates excellent THz sensing capabilities with a figure of merit (FoM) of 609. By varying the incident angle of the THz wave, the molecular fingerprint signal is strengthened, enabling the highly sensitive detection of trace amounts of analyte. Consequently, cinnamoylglycine can be detected with a sensitivity limit as low as 1.23 μg·cm-2. This study offers critical insights into the advanced application of THz waves in biomedicine, particularly for the detection of urinary biomarkers in various diseases, including gestational diabetes mellitus (GDM).

Visualization of renal rotenone accumulation after oral administration and in situ detection of kidney injury biomarkers via MALDI mass spectrometry imaging.

The examination of drug accumulation within complex biological systems offers valuable insights into the molecular aspects of drug metabolism and toxicity. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is an innovative methodology that enables the spatial visualization and quantification of biomolecules as well as drug and its metabolites in complex biological system. Hence, this method provides valuable insights into the metabolic profile and any molecular changes that may occur as a result of drug treatment. The renal system is particularly vulnerable to adverse effects of drug-induced harm and toxicity. In this study, MALDI MSI was utilized to examine the spatial distribution of drug and renal metabolites within kidney tissues subsequent to a single oral dosage of the anticancer compound rotenone. The integration of ion mobility spectrometry with MALDI MSI enhanced the data acquisition and analysis, resulting to improved mass resolution. Subsequently, the MS/MS fragment ions of rotenone reference drug were detected and characterized using MALDI HDMS/MS imaging. Notably, drug accumulation was observed in the cortical region of the representative kidney tissue sections treated with rotenone. The histological examination of treated kidney tissues did not reveal any observable changes. Differential ion intensity of renal endogenous metabolites was observed between untreated and rotenone-treated tissues. In the context of treated kidney tissues, the ion intensity level of sphingomyelin (D18:1/16:0), a sphingolipid indicator of glomerular cell injury and renal damage, was found to be elevated significantly compared to untreated kidney tissues. Conversely, the ion intensities of choline, glycero-3-phosphocholine (GPC), inosine, and a lysophosphatidylcholine LysoPC(18:0) exhibited a significant decrease. The results of this study demonstrate the potential of MALDI MSI as a novel technique for investigating the in situ spatial distribution of drugs and renal endogenous molecules while preserving the anatomical integrity of the kidney tissue. This technique can be used to study drug-induced metabolism and toxicity in a dynamic manner.

Spectral-fluorescent study of substituted trimethine cyanine dyes in solutions and in complexes with DNA. Effects of aggregation, moderate heating, and decreasing pH

Trimethine cyanine dyes are widely used as probes for the detection, study and quantification of biomolecules. In particular, cationic trimethine cyanines noncovalently interact with DNA with growing fluorescence. However, their use is often limited by the tendency to self-association – to the formation of aggregates. Disubstituted trimethine cyanines with hydrophobic substituents are especially prone to aggregation. In this work, we studied the interaction of a number of substituted trimethine cyanines with DNA (in aqueous buffer solutions) and showed that their aggregation strongly interfered with their use as fluorescent probes for DNA. To eliminate this drawback, preliminary heating of dye solutions with DNA to 60–70 °C was used, followed by cooling to room temperature. Compared to the experiments without heating, an increase in the dye fluorescence intensity was observed due to the partial thermal decomposition of the aggregates and the interaction of the resulting monomers with DNA. To decompose aggregates, another method was also used – protonation of the dyes with amino substituents in buffer solutions with pH 5.0, which also led to growing the dye fluorescence intensity in the presence of DNA. Complexes of the dyes with DNA were modeled using molecular docking. Effective binding constants of the dyes to DNA and detection limits when using the dyes as probes for DNA (LOD and LOQ) were determined. It is shown that dye 3 with heating in neutral buffer and dye 1 in acidic buffer may be recommended as sensitive probes for DNA. It is concluded that the method of preliminary heating may be applied to dyes prone to aggregation, for improving their properties as biomolecular probes. Another possible means to reduce the interfering effects of dye aggregates is to use easily protonated dyes (with amino substituents) in slightly acidic media.

High spatial resolution surface plasmon resonance imaging using a plasmonic chip.

The surface plasmon resonance (SPR) technique has been widely applied to biosensing technologies for the rapid quantification of biomolecules without enzyme and fluorescent labeling. However, the conventional prism-coupling SPR method generally has a detection area of a few mm2, and the large contribution of the background signal forms a barrier to highly sensitive detection. Based on a highly spatially resolved SPR method, the present study constructed a scanning GC-SPR imaging instrument using an objective lens with a high numerical aperture and a plasmonic chip that could be used for grating-coupled SPR. Focusing light on the diffraction limit can suppress background signals and improve detection sensitivity. SPR imaging can also be performed by scanning a focal spot. Using this method, the refractive index of a mixture of water and dimethyl sulfoxide was measured with a detection accuracy of 2.43 × 10-3 RIU. Polydopamine films prepared with a thickness of <5nm were also measured, and each film thickness was evaluated with high sensitivity from the effective refractive index detected in a small area of <1 µm2.

Enzymatic Protein Immobilization for Nanobody Array.

Antibody arrays play a pivotal role in the detection and quantification of biomolecules, with their effectiveness largely dependent on efficient protein immobilization. Traditional methods often use heterobifunctional cross-linking reagents for attaching functional residues in proteins to corresponding chemical groups on the substrate surface. However, this method does not control the antibody's anchoring point and orientation, potentially leading to reduced binding efficiency and overall performance. Another method using anti-antibodies as intermediate molecules to control the orientation can be used but it demonstrates lower efficiency. Here, we demonstrate a site-specific protein immobilization strategy utilizing OaAEP1 (asparaginyl endopeptidase) for building a nanobody array. Moreover, we used a nanobody-targeting enhanced green fluorescent protein (eGFP) as the model system to validate the protein immobilization method for building a nanobody array. Finally, by rapidly enriching eGFP, this method further highlights its potential for rapid diagnostic applications. This approach, characterized by its simplicity, high efficiency, and specificity, offers an advancement in the development of surface-modified protein arrays. It promises to enhance the sensitivity and accuracy of biomolecule detection, paving the way for broader applications in various research and diagnostic fields.

Simple Rescue of Opaque Tissue Previously Cleared by iDISCO.

Recent advancements in tissue-clearing techniques and volumetric imaging have greatly facilitated visualization and quantification of biomolecules, organelles, and cells in intact organs or even entire organisms. Generally, there are two types of clearing methods: hydrophobic and hydrophilic (i.e., clearing with organic or aqueous solvents, respectively). The popular iDISCO approach and its modifications are hydrophobic methods that involve dehydration, delipidation, decolorization (optional), decalcification (optional), and refractive-index (RI) matching steps. Cleared samples are often stored for a relatively long period of time and imaged repeatedly. However, cleared tissues can become opaque over time, which prevents accurate reimaging. We reasoned that the resurgent haziness is likely due to rehydration, residual lipids, and uneven RI deep inside those tissue samples. For rescue, we have developed a simple procedure based on iDISCO. Beginning with a methanol dehydration, samples are delipidated using dichloromethane, followed by RI matching with dibenzyl ether (DBE). This simple method effectively re-clears mouse brains that have turned opaque during months of storage, allowing the user to effectively image immunolabeled samples over longer periods of time. Key features • This simple protocol rescues previously cleared tissue that has turned opaque. • The method does not cause detectable loss of immunofluorescence from previously stained samples. Graphical overview.

"Click Chemistry": An Emerging Tool for Developing a New Class of Structural Motifs against Various Neurodegenerative Disorders.

Click chemistry is a set of easy, atom-economical reactions that are often utilized to combine two desired chemical entities. Click chemistry accelerates lead identification and optimization, reduces the complexity of chemical synthesis, and delivers extremely high yields without undesirable byproducts. The most well-known click chemistry reaction is the 1,3-dipolar cycloaddition of azides and alkynes to form 1,2,3-triazoles. The resulting 1,2,3-triazoles can serve as both bioisosteres and linkers, leading to an increase in their use in the field of drug discovery. The current Review focuses on the use of click chemistry to identify new molecules for treating neurodegenerative diseases and in other areas such as peptide targeting and the quantification of biomolecules.

Urinary Metabolic Biomarker Profiling for Cancer Diagnosis by Terahertz Spectroscopy: Review and Perspective

In the last decade, terahertz (THz) technologies have been introduced to the detection, identification, and quantification of biomolecules in various biological samples. This review focuses on substances that represent important biomarkers in the urine associated with various cancers and their treatments. From a diagnostic point of view, urine liquid biopsy is particularly important because it allows the non-invasive and rapid collection of large volumes of samples. In this review, the THz spectral responses of substances considered metabolic biomarkers in urine and obtained in previous studies are collected. In addition, the findings from the relatively small number of prior studies that have already been carried out on urine samples are summarised. In this context, we also present the different THz methods used for urine analysis. Finally, a brief discussion is given, presenting perspectives for future research in this field, interpreted based on the results of previous studies. This work provides important information on the further application of THz techniques in biomedicine for detecting and monitoring urinary biomarkers for various diseases, including cancer.

DNA nanopores as artificial membrane channels for bioprotonics

Biological membrane channels mediate information exchange between cells and facilitate molecular recognition. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout, which results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces. Here we show that cholesterol modified DNA nanopores spontaneously and with remarkable affinity span the lipid bilayer formed over the planar bio-protonic electrode surface and mediate proton transport across the bilayer. Using the ability to easily modify DNA nanostructures, we illustrate that this bioprotonic device can be programmed for electronic recognition of biomolecular signals such as presence of Streptavidin and the cardiac biomarker B-type natriuretic peptide, without modifying the biomolecules. We anticipate this robust interface will allow facile electronic measurement and quantification of biomolecules in a multiplexed manner.

Quantile Index Biomarkers Based on Single-Cell Expression Data

Current histocytometry methods enable single-cell quantification of biomolecules in tumor tissue sections by multiple detection technologies, including multiplex fluorescence-based immunohistochemistry or in situ hybridization. Quantitative pathology platforms can provide distributions of cellular signal intensity (CSI) levels of biomolecules across the entire cell populations of interest within the sampled tumor tissue. However, the heterogeneity of CSI levels is usually ignored, and the simple mean signal intensity value is considered a cancer biomarker. Here we consider the entire distribution of CSI expression levels of a given biomolecule in the cancer cell population as a predictor of clinical outcome. The proposed quantile index (QI) biomarker is defined as the weighted average of CSI distribution quantiles in individual tumors. The weight for each quantile is determined by fitting a functional regression model for a clinical outcome. That is, the weights are optimized so that the resulting QI has the highest power to predict a relevant clinical outcome. The proposed QI biomarkers were derived for proteins expressed in cancer cells of malignant breast tumors and demonstrated improved prognostic value compared with the standard mean signal intensity predictors. The R package Qindex implementing QI biomarkers has been developed. The proposed approach is not limited to immunohistochemistry data and can be based on any cell-level expressions of proteins or nucleic acids.

Rapid and easy identification of genes associated with nanoparticles from plant protein structure database

The study provides simple protocol for identifying unknown genes (DNA and RNA) and proteins present in the plants. The exact mechanism of nanoparticle synthesis from plant extracts is still unclear. Although functionalization of nanoparticle has been achieved by binding biomolecules and stabilizing through exchange of ligands and electrostatic interactions. This study will help in case of difficulty in extraction of proteins and DNA from nanoparticles due to less sample collection or degradation of active biomolecules. Plant extracts holds various biomolecules and can be used to presume the basic formulae of plant proteins by using software. The presence of DNA traces on silver nanoparticles confirmed and DNA sequence was extracted from NCBI gene bank. Homology modeling is an alternative method to predict 3D structure of proteins in the absence of experimental results. DNA gel electrophoresis and quantification of biomolecules and 3D protein structures have built from known sequences of conforming family members of protein using SWISS-MODEL. A major advantage of automated homology modeling is creating protein models that are easy to design the structure. Protein sequencing is continuously evolving nowadays. Experts are improving SWISS-MODEL to enhance the efficient transition. The study will help in easy and rapid identification of genes and proteins present on the surface of biological nanoparticles. Structural analysis of protein (proteomics) helps to identify novel functions that could facilitate designing of efficient biosensors.

Hydrogel Microneedle-Assisted Assay Integrating Aptamer Probes and Fluorescence Detection for Reagentless Biomarker Quantification.

Analyzing interstitial fluid (ISF) via microneedle (MN) devices enables patient health monitoring in a minimally invasive manner and in point-of-care settings. However, most MN-based diagnostic approaches require complicated fabrication processes and postprocessing of the extracted ISF or are limited to detection of electrochemically active biomarkers. Here, we show on-needle measurement of target analytes by integrating hydrogel microneedles with aptamer probes as the recognition elements. Fluorescently tagged aptamer probes are chemically attached to the hydrogel matrix using a simple and novel approach, while a cross-linked patch is formed. For reagentless detection, we employ a strand displacement strategy where fluorophore-conjugated aptamers are hybridized with a DNA competitor strand conjugated to a quencher molecule. The assay is utilized for rapid (2 min) measurement of glucose, adenosine triphosphate, l-tyrosinamide, and thrombin ex vivo. Furthermore, the system enables specific and sensitive quantification of rising and falling concentrations of glucose in an animal model of diabetes to track hypoglycemia, euglycemia, and hyperglycemia conditions. Our assay can be applied for rapid measurement of a diverse range of biomarkers, proteins, or small molecules, introducing a generalizable platform for biomolecule quantification, and has the potential to improve the quality of life of patients who are in need of close monitoring of biomarkers of health and disease.

Agarose-Droplet-Based Digital LAMP Assay for Counting Virus DNA in Single-Particle ICP-MS.

Inductively coupled plasma mass spectrometry (ICP-MS) has emerged as a promising analytical platform for the quantification of biomolecules using elemental tags; however, absolute quantification at extremely low concentrations by ICP-MS without a calibration curve remains challenging. Here, we developed a digital loop-mediated isothermal amplification (LAMP) assay for counting hepatitis B virus (HBV) DNA using single-particle (sp) ICP-MS. The sample and LAMP reagents were mixed and encapsulated in agarose droplets, which were generated by homemade centrifugal droplet generators. The agarose droplets were incubated at 65 °C for amplifying the virus DNA with LAMP primers and then cooled to 4 °C for generating "gel" particles during the temperature-dependent "sol-gel" transition. The LAMP amplicons were intercalated into the agarose particles using polyacrylamide-modified LAMP primers, enabling the labeling of dsDNA with [Ru(bpy)2dppz]2+ and the removal of excess reagents. Only those agarose particles, containing virus DNA, could be labeled with 101Ru and detected in spICP-MS. We also embedded the 153Eu-containing polystyrene microspheres into agarose droplets as the internal standard for counting the total number of agarose droplets. The copy number of virus DNA could be counted from the 101Ru/153Eu pulse numbers in spICP-MS. We achieved the lowest quantification of 25 copy μL-1 virus DNA in one analysis without the need for a calibration curve. The developed assay can be easily tuned for counting multiple types of nucleic acid targets and extended for new possibilities of the spICP-MS-based digital assay.

Computational simulation of 1 H NMR profiles of complex biofluid analyte mixtures at differential operating frequencies: Applications to low-field benchtop spectra.

Estimations of accurate and reliable NMR chemical shift values, coupling patterns and constants within a reasonable timeframe remain significantly challenging, and the unavailability of reliable software strategies for the prediction of low-field (e.g., 60 MHz) spectra from those acquired at higher operating frequencies hampers their direct comparison. Hence, this study explored the applications of accessible software options for predicting these parameters in the 1 H NMR profiles of analytes as a function of magnetic field strength; this was performed for individual analytes and also for complex biofluid matrices featured in metabolomics investigations. For this purpose, results from the very first successful experimental acquisition and simulation of the 1 H NMR profiles of intact human salivary supernatant samples on a 60 MHz benchtop spectrometer were evaluated. Using salivary metabolite concentrations determined at 400 MHz, it was demonstrated that simulation of the low-field spectra of five biomolecules with the most prominent 1 H resonances detectable allowed multiple component fits to be applied to experimental spectra. Hence, these salivary 1 H NMR profiles could be successfully predicted throughout the 45-600 MHz operating frequency range. With the exception of propionate resonance multiplets, which revealed more complex coupling patterns at low field and required more astute computational and fitting options, valuable quantitative metabolomics data on salivary acetate, formate, methanol and glycine could be attained from low-field spectrometres. These studies are both timely and pertinent in view of the recent advancement of low-field benchtop NMR facilities for diagnostically significant biomarker tracking in biofluids. Experiments performed with added ammonium chloride to facilitate the release of salivary metabolites from biopolymer binding sites provided evidence that a small but nevertheless significant proportion of propionate, but not lactate, was bound to such sites, an observation of much relevance to biomolecule quantification in salivary metabolomics investigations.

Combinatorial synthesis of new fluorescent scaffolds using click chemistry

Azides and acetylenes are bio-orthogonal functional groups that can be readily coupled using copper(I)- or ruthenium(II)- catalyzed 1,3-dipolar cycloaddition reactions. Using non-fluorescent aromatic azides and aromatic acetylenes, covering a range of electron rich and poor building blocks, the Huisgen cycloaddition afford 1,4-disubstituted or 1,5-disubstituted 1,2,3-triazoles. Using a combinatorial approach by running reaction in parallel in polypropylene 96-well plates we discovered several new fluorescent 1,2,3-triazoles scaffolds. These compounds show diverse interactions with biomolecules that could find applications in biology in, for example, fluorescence microscopy or biomolecule quantification.

Seasonal characterization and quantification of biomolecules from sargassum collected from Mexican Caribbean coast – A preliminary study as a step forward to blue economy

Since 2014, Mexican Caribbean coasts have experienced an atypical massive arrival of pelagic Sargassum accumulated on the shores triggers economic losses, public health problems, and ecosystem damaging near the coastline. Mechanical harvesting has been implemented ending in landfills. Since Sargassum algae represent abundant biomass in tropical regions of the world, it has shown potential as a feedstock to supply bioprocesses focused on obtaining high-value compounds and bioproducts. Nevertheless, there is a lack of data on the biochemical composition of Sargassum biomass from Mexican Caribbean coasts to propose valorization pathways. This study conducted a biochemical and elemental characterization of Sargassum biomass and compared, through statistical analysis, the effect of the season (dry and wet), place of collection (from the beach and shallow water), and method of extraction (Microwave-Assisted Extraction and Enzyme Assisted Extraction) on biomass composition. The biomass composition, expressed in dry weight basis, revealed 5–7% moisture content, 24–31 % ash, 2.6–3.8 % lipids, 1.8–7.0 %, total carbohydrates, 3–11 % total proteins, 1.5–2.31 mgGAg−1 total phenolic compounds (TPC), 2.7–2.9 kcal g−1 calorific power, and metals such as As (30–146.3 ppm), Fe (16.5–45 ppm), P (197–472 ppm). The most influential factor on the compositional content of Sargassum biomass was the season of the year, followed by the extraction method and the place of collection of Sargassum. These results will elucidate information on the biotechnological potential of Sargassum biomass from the Mexican Caribbean, contributing to sustainability challenges of the region, minimizing waste, and making the most of resources.

Old commercialized magnetic particles new trick: Intrinsic internal standard

Magnetic particles (MPs) are the most widely used commercialized engineering particles, which gained great success in various biological applications. Inspired by their intrinsic Fe isotope composition, we discovered a commercialized MPs-internal standard's novel function to realize the accurate quantification of biomolecules. The bioassay of carcinoembryonic antigen (CEA) was chosen as a modal system. The Fe isotope in MPs and Au isotope in report probes were simultaneously and sensitively detected by the elemental mass spectrometry. 197Au/57Fe isotopic ratios and CEA concentrations showed good linearity in the range of 0.6–300 ng/mL, with a detection limit of 0.09 ng/mL (3σ). The accuracy and precision of the proposed MPs-based immunoassay were greatly improved, by eliminating potential MPs loss during magnetic separation and absolute intensity fluctuations. Considering the exceptional availability and universality of commercialized MPs, the proposed method might open a new avenue for MPs' biological applications.

Recent Advances in the Use of Transition-Metal Porphyrin and Phthalocyanine Complexes as Electro-Catalyst Materials on Modified Electrodes for Electroanalytical Sensing Applications

Metalloporphyrins (MP) and metallophtalocyanines (MPc) are innovative materials with catalytic properties that have attracted attention for their application for diverse electrochemical purposes. The presence of metallic centers in their structure offers a redox-active behavior that is being applied in the design of solid electrodes for the quantification of biomolecules, water contaminants, and pharmaceuticals, among others. Herein, we collect the recent information about porphyrin and phthalocyanine complexes as modifiers of electrodes, and the important aspects of the design, characterization, and application of these electrodes.

Toward a Point-of-Need Bioluminescence-Based Immunoassay Utilizing a Complete Shelf-Stable Reagent.

Enzyme-linked immunosorbent assays (ELISAs) are used extensively for the detection and quantification of biomolecules in clinical diagnostics as well as in basic research. Although broadly used, the inherent complexities of ELISAs preclude their utility for straightforward point-of-need testing, where speed and simplicity are essential. With this in mind, we developed a bioluminescence-based immunoassay format that provides a sensitive and simple method for detecting biomolecules in clinical samples. We utilized a ternary, split-NanoLuc luciferase complementation reporter consisting of two small peptides (11mer, 13mer) and a 17 kDa polypeptide combined with a luminogenic substrate to create a complete, shelf-stable add-and-read assay detection reagent. Directed evolution was used to optimize reporter constituent sequences to impart chemical and thermal stability, as well as solubility, while formulation optimization was applied to stabilize an all-in-one reagent that can be reconstituted in aqueous buffers or sample matrices. The result of these efforts is a robust, first-generation bioluminescence-based homogenous immunoassay reporter platform where all assay components can be configured into a stable lyophilized cake, supporting homogeneous, rapid, and sensitive one-step biomolecule quantification in complex human samples. This technology represents a promising alternative immunoassay format with significant potential to bring critical diagnostic molecular detection testing closer to the point-of-need.

Assessment of the Potential and Limitations of Elemental Mass Spectrometry in Life Sciences for Absolute Quantification of Biomolecules Using Generic Standards.

Inductively coupled plasma-mass spectrometry (ICP-MS) has been widely used in Life Sciences for the absolute quantification of biomolecules without specific standards, assuming the same response for generic compounds including complex biomolecules. However, contradictory results have been published on this regard. We present the first critical statistical comparison of the ICP-MS response factors obtained for 14 different relevant S-containing biomolecules (three peptides, four proteins, one amino acid, two cofactors, three polyethylene glycol (PEG) derivatives, and sulfate standard), covering a wide range of hydrophobicities and molecular sizes. Two regular flow nebulizers and a total consumption nebulizer (TCN) were tested. ICP-MS response factors were determined though calibration curves, and isotope dilution analysis was used to normalize the results. No statistical differences have been found for low-molecular-weight biocompounds, PEGs, and nonhydrophobic peptides using any of the nebulizers tested. Interestingly, while statistical differences were still found negligible (96-104%) for the proteins and hydrophobic peptide using the TCN, significantly lower response factors (87-40%) were obtained using regular flow nebulizers. Such differential behavior seems to be related mostly to hydrophobicity and partially to the molecular weight. Findings were validated using IDA in intact and digested bovine serum albumin solutions using the TCN (98 and 100%, respectively) and the concentric nebulizer (73 and 97%, respectively). Additionally, in the case of a phosphoprotein, results were corroborated using the P trace in parallel to the S trace used along the manuscript. This work seems to suggest that ICP-MS operated with regular nebulizers can offer absolute quantification using generic standards for most biomolecules except proteins and hydrophobic peptides.