Enzymatic Recognition Research Articles

Innovating uric acid Biosensing: Development of a GSH@Cd-Mediated Dual-Signal fluorometric method

Uric acid (UA) is a crucial biomarker for various metabolic and renal disorders, making its accurate determination essential for clinical diagnostics and disease management. This study presents a novel fluorometric method for UA detection using a glutathione@cadmium/carbon dots/uricase system (GSH@Cd/CDs/uricase system), which offers enhanced sensitivity and selectivity compared to existing techniques. The method employs a cascade reaction mechanism initiated by uricase-catalyzed oxidation of UA to produce H2O2. This H2O2 subsequently oxidizes GSH to oxidized glutathione (GSSG), releasing cadmium ions from GSH complexes. The liberated Cd2+ ions interact with two types of carbon dots (CDs) in the system: blue-emitting CDs (BCDs) and red-emitting CDs (RCDs). This interaction triggers a dual fluorescence response, characterized by a decrease in fluorescence intensity at 400 nm (BCDs) and an increase at 610 nm (RCDs), enabling ratiometric detection of UA levels. Comprehensive characterization and mechanistic investigations were conducted using various optical and morphological techniques, including transmission electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, and fluorescence spectroscopy. The method exhibits outstanding analytical performance, characterized by strong linearity (R2 = 0.9932), a broad detection range (0.05–7.0 μM), and a low detection limit of 0.015 μM. The method demonstrated excellent selectivity against common interfering substances and was successfully applied to human serum and urine samples with high recovery values (97.65 % to 99.20 %), highlighting its potential for clinical applications. This innovative approach combines the specificity of enzymatic recognition with the sensitivity of dual-emission fluorescence, offering a promising tool for accurate UA quantification in complex biological matrices.

Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides.

The DNA building blocks 2'-deoxynucleotides are enantiomeric, with their natural β-D-configuration dictated by the sugar moiety. Their synthetic β-L-enantiomers (βLdNs) can be used to obtain L-DNA, which, when fully substituted, is resistant to nucleases and is finding use in many biosensing and nanotechnology applications. However, much less is known about the enzymatic recognition and processing of individual βLdNs embedded in D-DNA. Here, we address the template properties of βLdNs for several DNA polymerases and the ability of base excision repair enzymes to remove these modifications from DNA. The Klenow fragment was fully blocked by βLdNs, whereas DNA polymerase κ bypassed them in an error-free manner. Phage RB69 DNA polymerase and DNA polymerase β treated βLdNs as non-instructive but the latter enzyme shifted towards error-free incorporation on a gapped DNA substrate. DNA glycosylases and AP endonucleases did not process βLdNs. DNA glycosylases sensitive to the base opposite their cognate lesions also did not recognize βLdNs as a correct pairing partner. Nevertheless, when placed in a reporter plasmid, pyrimidine βLdNs were resistant to repair in human cells, whereas purine βLdNs appear to be partly repaired. Overall, βLdNs are unique modifications that are mostly non-instructive but have dual non-instructive/instructive properties in special cases.

Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin.

Enzymatic reactions that involve a luminescent substrate (luciferin) and enzyme (luciferase) from luminous organisms enable a luminescence detection of target proteins and cells with high specificity, albeit that conventional assay design requires a prelabeling of target molecules with luciferase. Here, we report a luciferase-independent luminescence assay in which the target protein directly catalyzes the oxidative luminescence reaction of luciferin. The SARS-CoV-2 antigen (spike) protein catalyzes the light emission of Cypridina luciferin, whereas no such catalytic function was observed for salivary proteins. This selective luminescence reaction is due to the enzymatic recognition of the 3-(1-guanidino)propyl group in luciferin at the interfaces between the units of the spike protein, allowing a specific detection of the spike protein in human saliva without sample pretreatment. This method offers a novel platform to detect virus antigens simply and rapidly without genetic manipulation or antibodies.

An ultrasensitive biosensor with suppressed background signals for FEN1 detection in a homogeneous reaction via cascade primer exchange reaction and CRISPR/Cas12a system

Flap endonuclease 1 (FEN1) is a structure-specific enzyme which plays a crucial role in DNA replication and repair within mammalian cells. FEN1 is also known to be overexpressed in various cancer cells and has emerged as a potential biomarker for cancer diagnosis. However, there have been limited progress in development of sensitively analytical methods toward FEN1 detection. Herein, we have developed an ultrasensitive FEN1 sensing biosensor for FEN1 detection by combining primer exchange reaction (PER) with CRISPR/Cas12a signal amplification (PCSA). This innovative method achieves remarkable sensitivity for FEN1 detection, with a limit of detection (LOD) as low as 3.72 × 10−7 U/μL. Notably, PCSA effectively suppresses background signals, resulting in a high signal-to-noise ratio exceeding 31-fold due to three specific enzymatic recognition reactions. Consequently, PCSA demonstrates outstanding selectivity and robust anti-interference capabilities. The PCSA was employed to detect the FEN1 in complex serum samples, as well as in normal and tumor cells, achieving an LOD for FEN1 as low as in 10 cancer cells. Additionally, PCSA offers a simple operational process and yields a visually observable signal output, simplifying its use for the point-of-care testing (POCT) in some resource-limited regions. This straightforward approach holds significant promise for broad applications in FEN1 sensing and inhibitor screening.

Post-transcriptional capping generates coenzyme A-linked RNA

ABSTRACT NAD can be inserted co-transcriptionally via non-canonical initiation to form NAD-RNA. However, that mechanism is unlikely for CoA-linked RNAs due to low intracellular concentration of the required initiator nucleotide, 3’-dephospho-CoA (dpCoA). We report here that phosphopantetheine adenylyltransferase (PPAT), an enzyme of CoA biosynthetic pathway, accepts RNA transcripts as its acceptor substrate and transfers 4’-phosphopantetheine to yield CoA-RNA post-transcriptionally. Synthetic natural (RNAI) and small artificial RNAs were used to identify the features of RNA that are needed for it to serve as PPAT substrate. RNAs with 4–10 unpaired nucleotides at the 5’ terminus served as PPAT substrates, but RNAs having <4 unpaired nucleotides did not undergo capping. No capping was observed when the +1A was changed to G or when 5’ triphosphate was removed by RNA pyrophosphohydrolase (RppH), suggesting the enzyme recognizes pppA-RNA as an ATP analog. PPAT binding affinities were equivalent for transcripts with +1A, +1 G, or 5’OH (+1A), indicating that productive enzymatic recognition is driven more by local positioning effects than by overall binding affinity. Capping rates were independent of the number of unpaired nucleotides in the range of 4–10 nucleotides. Capping was strongly inhibited by ATP, reducing CoA-RNA production ~70% when equimolar ATP and substrate RNA were present. Dual bacterial expression of candidate RNAs with different 5’ structures followed by CoA-RNA CaptureSeq revealed 12-fold enrichment of the better PPAT substrate, consistent with in vivo CoA-capping of RNA transcripts by PPAT. These results suggest post-transcriptional RNA capping as a possible mechanism for the biogenesis of CoA-RNAs in bacteria.

Register-Shifted Structures in Base-Flipped Uracil-Damaged DNA.

We report the occurrence of register-shifted structures in simulations of uracil-containing dsDNA. These occur when the 3' base vicinal to uracil is thymine in U:A base-paired DNA. Upon base flipping of uracil, this 3' thymine hydrogen bonds with the adenine across the uracil instead of its complementary base. The register-shifted structure is persistent and sterically blocks re-entry of uracil into the helix stack. Register shifting might be important for DNA repair since the longer exposure of the lesion in register-shifted structures could facilitate enzymatic recognition and repair.

Quantification of Lactose in Lactose-Free and Low-Lactose Milk and Milk Products by BIOMILK 300/3000 Lac, Collaborative Study: Final Action 2020.09.

In April 2020, the BIOMILK 300 LAC method for the quantification of lactose in lactose-free and low-lactose dairy products was adopted as First Action Official Method of AnalysisSM2020.09 by AOAC INTERNATIONAL. To test the reproducibility of the method, as the last step toward the Final Action status, a collaborative study was organized by BIOLAN Microbiosensores. Fifteen collaborators within the European Union took part in this study, where nine different samples were sent as duplicate blind test portions for lactose determination. The data obtained were used to determine method repeatability and reproducibility and also to validate the new version of the biosensor. The test method is based on the direct enzymatic recognition-electrochemical detection of trace levels of lactose over a wide range of dairy samples by means of the BIOMILK 300 biosensor, in less than 5 min, and without intricate sample pretreatments. All samples resulted in a repeatability relative standard deviation (RSDr) of <8.1% and a reproducibility relative standard deviation (RSDR) of 14% maximum, meeting requirements from Standard Method Performance Requirement (SMPR®) 2018.09. The method has proved to give reproducible results for the quantification of lactose in lactose-free and low-lactose dairy products. On the basis of these results, the enzymatic amperometric biosensor method developed by BIOLAN Microbiosensores was adopted as a Final Action Official Method in July 2022.

DNA-RNA Hybrid (R-Loop): From a Unified Picture of the Mammalian Telomere to the Genome-Wide Profile

Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular extract without antibody that allows their physical isolation and determination of their RNA nucleotide sequence. We then define in the normal mouse and human sperm genomes the notion of stable DNA associated RNA terminal R-loop complexes, including TERRA molecules synthesized from local promoters of every chromosome. Furthermore, the first strong evidence of all telomeric structures, applied additionally to the whole murine sperm genome compared to the testes, showed reproducible R-loop complexes of the whole genome and suggesting a defined profile in the sperm genome for the next generation.

Lanthanide DO3A-Complexes Bearing Peptide Substrates: The Effect of Peptidic Side Chains on Metal Coordination and Relaxivity.

Two DO3A-type ligands conjugated to substrates of urokinase (L3) and caspase-3 (L4) via a propyl-amide linker were synthesized and their lanthanide(III) (Ln3+) complexes studied. A model compound without peptide substrate (L2) and an amine derivative ligand mimicking the state after enzymatic cleavage (L1) were also prepared. Proton Nuclear Magnetic Relaxation Dispersion (NMRD) profiles recorded on the gadolinium(III) (Gd3+) complexes, complemented with the assessment of hydration numbers via luminescence lifetime measurements on the Eu3+ analogues, allowed us to characterize the lanthanide coordination sphere in the chelates. These data suggest that the potential donor groups of the peptide side chains (carboxylate, amine) interfere in metal coordination, leading to non-hydrated LnL3 and LnL4 complexes. Nevertheless, GdL3 and GdL4 retain a relatively high relaxivity due to an important second-sphere contribution generated by the strongly hydrophilic peptide chain. Weak PARACEST effects are detected for the amine-derivative EuL1 and NdL1 chelates. Unfortunately, the GdL3 and GdL4 complexes are not significantly converted by the enzymes. The lack of enzymatic recognition of these complexes can likely be explained by the participation of donor groups from the peptide side chain in metal coordination.

Three-Dimensional Microporous Hollow Fiber Membrane Microfluidic Device Integrated with Selective Separation and Capillary Self-Driven for Point-of-Care Testing.

The novel 3D microfluidic concept of "lab-on-hollow fiber membrane (HFM)" was presented for multifunctional and rapid biological assays, integrating sample size sieving and colorimetric quantification in an HFM. Herein, microporous HFMs with a gradient pore size and high hydrophilic flux were used as microfluidic device substrates. The membrane pores selectively trapped macromolecules within the inner surface, while allowing free diffusion of smaller molecules, including glucose and protein. The microfluidic flow rate in HFM closely followed the Lucas-Washburn and Laplace's models, indicating that the microfluidics facilitated the upward flow of the fluid by microcapillary action without external pumping. Subsequently, for sensing of different biomolecules, a highly sensitive fluorescent or optical chromogenic reagent was immobilized in HFM by an electrostatic interaction. Pyronin G fluorescence reagent was quenched by blood glucose, and the quenching efficiency showed a good linear correlation with glucose concentration (1-22 mM, R2 = 0.997). Moreover, this sensing platform was then further applied for the analysis of urine protein or glucose in the visible spectrum, with a wide testing range. Compared to traditional 2D flat membrane devices, this 3D-HFM microfluidic device exhibited excellent sensing versatility and color rendering uniformity with enhanced sensitivity. Target molecules screening, conditioning, enzymatic recognition, and signal readout of biomolecules have all been implemented on this device, which has paved the way to highly sensitive assays on point-of-care testing (POCT).

A side-by-side evaluation of [18F]FDOPA enantiomers for non-invasive detection of neuroendocrine tumors by positron emission tomography

Neuroendocrine tumors (NETs) are an extremely heterogenous group of malignancies with variable clinical behavior. Molecular imaging of patients with NETs allows for effective patient stratification and treatment guidance and is crucial in selection of targeted therapies. Positron emission tomography (PET) with the radiotracer L-[18F]FDOPA is progressively being utilized for non-invasive in vivo visualization of NETs and pancreatic β-cell hyperplasia. While L-[18F]FDOPA-PET is a valuable tool for disease detection and management, it also exhibits significant diagnostic limitations owing to its inherent physiological uptake in off-target tissues. We hypothesized that the D-amino acid structural isomer of that clinical tracer, D-[18F]FDOPA, may exhibit superior clearance capabilities owing to a reduced in vivo enzymatic recognition and enzyme-mediated metabolism. Here, we report a side-by-side evaluation of D-[18F]FDOPA with its counterpart clinical tracer, L-[18F]FDOPA, for the non-invasive in vivo detection of NETs. In vitro evaluation in five NET cell lines, including invasive small intestinal neuroendocrine carcinomas (STC-1), insulinomas (TGP52 and TGP61), colorectal adenocarcinomas (COLO-320) and pheochromocytomas (PC12), generally indicated higher overall uptake levels of L-[18F]FDOPA, compared to D-[18F]FDOPA. While in vivo PET imaging and ex vivo biodistribution studies in PC12, STC-1 and COLO-320 mouse xenografts further supported our in vitro data, they also illustrated lower off-target retention and enhanced clearance of D-[18F]FDOPA from healthy tissues. Cumulatively our results indicate the potential diagnostic applications of D-[18F]FDOPA for malignancies where the utility of L-[18F]FDOPA-PET is limited by the physiological uptake of L-[18F]FDOPA, and suggest D-[18F]FDOPA as a viable PET imaging tracer for NETs.

Fluorescence Resonance Energy Transfer-Mediated Immunosensor Based on Design and Synthesis of the Substrate of Amp Cephalosporinase for Biosensing.

The traditional enzyme-linked immunosorbent assay (ELISA) has some disadvantages, such as insufficient sensitivity and low stability of the labeled enzyme, which limit its further applications. In this study, a more stable enzyme, Amp cephalosporinase (AmpC), was selected as the labeled enzyme, and its substrate was designed and synthesized. This substrate contained the cephalosporin ring core as the enzymatic recognition section and the structural motif of the 3-hydroxyflavone (3-HF) as the reporter molecule. AmpC can specifically catalyze the substrate and release 3-HF, which can enter the cavity of β-cyclodextrin (β-CD) on the surface of ZnS quantum dots and form a fluorescence resonance energy transfer (FRET) signal amplification system. An AmpC-catalyzed, FRET-mediated ultrasensitive immunosensor (ACF immunosensor) for procalcitonin (PCT) was developed by combining the signal amplification system of the polystyrene microspheres and effective immune-based magnetic separation. The ACF immunosensor has high sensitivity and specificity for the detection of PCT: its linear range is from 0.1 ng mL-1 to 70 ng mL-1, and the limit of detection can reach 0.03 ng mL-1. The spiking recoveries of PCT in human serum samples range from 98.3% to 107%, with relative standard deviations ranging from 2.14% to 12.0%. This approach was applied to detect PCT in real patient serum samples, and the results are consistent with those obtained with a commercial ELISA kit.

Structural and Biological Investigations for a Series of N-5 Substituted Pyrrolo[3,2-d]pyrimidines as Potential Anti-Cancer Therapeutics.

Pyrrolo[3,2-d]pyrimidines have been studied for many years as potential lead compounds for the development of antiproliferative agents. Much of the focus has been on modifications to the pyrimidine ring, with enzymatic recognition often modulated by C2 and C4 substituents. In contrast, this work focuses on the N5 of the pyrrole ring by means of a series of novel N5-substituted pyrrolo[3,2-d]pyrimidines. The compounds were screened against the NCI-60 Human Tumor Cell Line panel, and the results were analyzed using the COMPARE algorithm to elucidate potential mechanisms of action. COMPARE analysis returned strong correlation to known DNA alkylators and groove binders, corroborating the hypothesis that these pyrrolo[3,2-d]pyrimidines act as DNA or RNA alkylators. In addition, N5 substitution reduced the EC50 against CCRF-CEM leukemia cells by up to 7-fold, indicating that this position is of interest in the development of antiproliferative lead compounds based on the pyrrolo[3,2-d]pyrimidine scaffold.

Enzyme‐conjugated nanosensors with tunable detection limits for small biomolecule determination

AbstractPolymeric nanosensors are more appealing than electrochemical sensors for advanced biological imaging applications, but more development is required before polymeric nanosensors can achieve widespread application. The detection of small biomolecules without a suitable ionophore, such as the detection of glucose, depends on enzymatic recognition by mixing oxidase enzymes with nanosensors. However, conjugation schemes and response control methods are needed to make polymeric nanosensors suitable for real‐world applications. In this work, we develop enzyme‐conjugated nanosensors based on the biotin/avidin interaction with two unique structures. The response of the first structure is controllable through changes to the concentrations of enzyme and avidin as well as surface biotinylation level during synthesis, while the second structure requires a simpler synthesis and has a controllable response through changes to the surface biotinylation level. We also report findings about optimal avidin concentration and separation of unbound enzyme from the enzyme‐nanosensor conjugates through a magnetic purification approach.

5',8-Cyclopurine Lesions in DNA Damage: Chemical, Analytical, Biological, and Diagnostic Significance.

Purine 5′,8-cyclo-2′-deoxynucleosides (cPu) are tandem-type lesions observed among the DNA purine modifications and identified in mammalian cellular DNA in vivo. These lesions can be present in two diasteroisomeric forms, 5′R and 5′S, for each 2′-deoxyadenosine and 2′-deoxyguanosine moiety. They are generated exclusively by hydroxyl radical attack to 2′-deoxyribose units generating C5′ radicals, followed by cyclization with the C8 position of the purine base. This review describes the main recent achievements in the preparation of the cPu molecular library for analytical and DNA synthesis applications for the studies of the enzymatic recognition and repair mechanisms, their impact on transcription and genetic instability, quantitative determination of the levels of lesions in various types of cells and animal model systems, and relationships between the levels of lesions and human health, disease, and aging, as well as the defining of the detection limits and quantification protocols.

Real time monitoring of glucose in whole blood by smartphone

A combined thread-paper microfluidic device (μTPAD) is presented for the determination of glucose in blood. The device is designed to include all the analytical operations needed: red blood cell separation, conditioning, enzymatic recognition, and colorimetric transduction. The signal is captured with a smartphone or tablet working in video mode and processed by custom Android-based software in real-time. The automatic detection of the region of interest on the thread allows for the use of either initial rate or equilibrium signal as analytical parameters. The time needed for analysis is 12 s using initial rate, and 100 s using the equilibrium measurement with a LOD of 48 μM and 12 μM, respectively, and a precision around 7%. The μTPAD allows a rapid determination of glucose in real samples using only 3 μL of whole blood.

Effect of degree of deacetylation on solubility of low‐molecular‐weight chitosan produced via enzymatic breakdown of chitosan

AbstractChitosan has emerged as a unique biomaterial, possessing scope in diverse applications in the biomedical, food and chemical industries. However, its high molecular weight is a concern when handling the polymer. Various techniques have been explored for depolymerization of this polymer, wherein enzymes have emerged as the most economic method having minimum degrading effect on the polymer and resulting in formation of side products. Chitosan can be depolymerized using a broad range of enzymes. In this study, various enzymes like α‐amylase, papain, pepsin and bromelain were employed to depolymerize chitosan and convert it into its lower molecular weight counterpart. Further, attempts were made to elucidate the process of depolymerization of chitosan, primarily by determining the change in its viscosity and hence its molecular weight. The process of depolymerization was optimized using a one‐factor‐at‐a‐time approach. The molecular weight of the resultant chitosan was estimated using gel permeation chromatography and infrared spectroscopy. These studies revealed a considerable decrease in molecular weights of chitosan depolymerized by pepsin, papain, bromelain and α‐amylase, resulting in recovery of the low‐molecular‐weight chitosan of 76.09 ± 5, 74.18 ± 5, 55.75 ± 5 and 49.18 ± 5%, respectively. Maximum yield and depolymerization were obtained using pepsin and papain due to their enzymatic recognition pattern, which was also validated using studies involving molecular dynamics. © 2019 Society of Chemical Industry

Minimally Invasive Microelectrode Biosensors Based on Platinized Carbon Fibers for in Vivo Brain Monitoring.

The ability to monitor the chemical composition of brain interstitial fluid remains an important challenge in the field of bioanalytical chemistry. In particular, microelectrode biosensors are a promising resource for the detection of neurochemicals in interstitial fluid in both animals and humans. These biosensors can provide second-by-second temporal resolution and enzymatic recognition of virtually any redox or nonredox molecule. However, despite miniaturization of these sensors to 50–250 μm in diameter to avoid vascular and cellular injury, inflammation and foreign-body reactions still occur following their implantation. Here, we fabricated microelectrodes with platinized carbon fibers to create biosensors that have an external diameter that is less than 15 μm. Platinization was achieved with physical vapor deposition, and increased sensitivity to hydrogen peroxide and improved enzymatic detection were observed for these carbon fiber microelectrodes. When these devices were implanted in the brains of rats, no injuries to the parenchyma or brain blood vessels were detected. In addition, these microelectrodes provided different estimates of basal glucose, lactate, and oxygen concentrations compared to conventional biosensors. Induction of spreading depolarization in the cerebral cortex further demonstrated the greater sensitivity of our microelectrodes to dynamic neurochemical changes. Thus, these minimally invasive devices represent a major advance in our ability to analyze brain interstitial fluid.

Cover Feature: Total Synthesis, Stereochemical Assignment, and Divergent Enantioselective Enzymatic Recognition of Larreatricin (Chem. Eur. J. 59/2018)

Cover Feature: Total Synthesis, Stereochemical Assignment, and Divergent Enantioselective Enzymatic Recognition of Larreatricin (Chem. Eur. J. 59/2018)

Total Synthesis, Stereochemical Assignment, and Divergent Enantioselective Enzymatic Recognition of Larreatricin.

A concise and efficient total synthesis of the lignan natural product larreatricin as well as an unambiguous assignment of configuration of its enantiomers are reported, resolving a long‐held controversy. Enzyme kinetic studies revealed that different polyphenol oxidases show high and remarkably divergent enantioselective recognition of this secondary metabolite.