Characterization of troponin T binding aptamers for an innovative enzyme-linked oligonucleotide assay (ELONA)

Antidote-controlled DNA aptamer modulates human factor IXa activity

Thrombosis leads to elevated mortality rates and substantial medical expenses worldwide. Human factor IXa (HFIXa) protease is pivotal in tissue factor (TF)-mediated thrombin generation, and represents a promising target for anticoagulant therapy. We herein isolated novel DNA aptamers that specifically bind to HFIXa through systematic evolution of ligands by exponential enrichment (SELEX) method. We identified two distinct aptamers, seq 5 and seq 11, which demonstrated high binding affinity to HFIXa (Kd = 74.07 ± 2.53 nM, and 4.93 ± 0.15 nM, respectively). Computer software was used for conformational simulation and kinetic analysis of DNA aptamers and HFIXa binding. These aptamers dose-dependently prolonged activated partial thromboplastin time (aPTT) in plasma. We further rationally optimized the aptamers by truncation and site-directed mutation, and generated the truncated forms (Seq 5-1t, Seq 11-1t) and truncated-mutated forms (Seq 5-2tm, Seq 11-2tm). They also showed good anticoagulant effects. The rationally and structurally designed antidotes (seq 5-2b and seq 11-2b) were competitively bound to the DNA aptamers and effectively reversed the anticoagulant effect. This strategy provides DNA aptamer drug-antidote pair with effective anticoagulation and rapid reversal, developing advanced therapies by safe, regulatable aptamer drug-antidote pair.

Surface plasmon resonance biosensors for early troponin detection

Acute myocardial infarction (AMI) is one of the life-threatening causes that decrease blood flow to the heart, leading to increased mortality and related complications. Recently, the measure of blood concentration of cardiac biomarkers has been suggested to overcome the limitations of electrocardiography (ECG) analyses for early diagnosis of this disease. Troponins, especially cardiac troponin I and cardiac troponin T, with high sensitivity and specificity, are considered the gold standards in myocardial diagnosis. Recently, the use of new biosensors such as surface plasmon resonance (SPR) for early detection of these biomarkers has been greatly appreciated. Due to the rapid, sensitive, real-time, and label-free detection of SPR-based biosensors, they can be applied for selective and nonspecific absorption that is intended to be used as an in situ cardiac biosensor. Here, we exclusively discussed the updated developments of these valuable predictors for the possible occurrence of AMI detected by SPR.

A DNA aptamer-based assay for the detection of soluble ST2, a prognostic biomarker for monitoring heart failure

Heart failure (HF) is emerging as a leading cause of death worldwide. Estimation of BNP levels is a routine diagnosis in these patients. However, in patients having high body-mass index (BMI), renal disease or in geriatric patients, BNP level is reported to be noisy and leads to incongruous conclusion. Thus, for better risk stratification among heart failure patients, it is imperative to look for a superior biomarker. In recent times, sST2 has shown promise as a biomarker. Identifying such biomarkers in peripheral blood of HF patients, need an affine and selective molecular recognition element. Thus, in the current study an aptamer (sS9_P) against sST2 was identified from an aptamer library. Systematic Evolution of Ligands through Exponential enrichment (SELEX) derived aptamer evinced role of its primer binding domains in maintaining its selectivity. This aptamer candidate demonstrated dissociation constant (Kd) in low nanomolar range, and the Limit of Detection (LOD) was ~4 ng. Circular dichroism confirms the formation of complex stem-loop like structure. The well characterized sS9_P aptamer was used in an Aptamer Linked Immobilized Sorbent Assay (ALISA) to detect sST2 level in patients' serum (n = 99). Aptamer sS9_P has shown significant discrimination to differentiate HF patients and healthy volunteers with a reasonable specificity (~83 %) with a modest sensitivity of ~64 %. While sST-2 antibody has shown poor specificity of ~44% but good sensitivity (~87%). The insight obtained from this study indicates that a combination of aptamer and antibody-based assay can be used to design a point-of-care assay for the rapid detection of HF patients in emergency settings.

Nucleic Acid Aptamer-Based Biosensors: A Review

Aptamers, short strands of either DNA, RNA, or peptides, known for their exceptional specificity and high binding affinity to target molecules, are providing significant advancements in the field of health. When seamlessly integrated into biosensor platforms, aptamers give rise to aptasensors, unlocking a new dimension in point-of-care diagnostics with rapid response times and remarkable versatility. As such, this review aims to present an overview of the distinct advantages conferred by aptamers over traditional antibodies as the molecular recognition element in biosensors. Additionally, it delves into the realm of specific aptamers made for the detection of biomarkers associated with infectious diseases, cancer, cardiovascular diseases, and metabolomic and neurological disorders. The review further elucidates the varying binding assays and transducer techniques that support the development of aptasensors. Ultimately, this review discusses the current state of point-of-care diagnostics facilitated by aptasensors and underscores the immense potential of these technologies in advancing the landscape of healthcare delivery.

Progress in the Optical Sensing of Cardiac Biomarkers

Biomarkers play key roles in the diagnosis, risk assessment, treatment and supervision of cardiovascular diseases (CVD). Optical biosensors and assays are valuable analytical tools answering the need for fast and reliable measurements of biomarker levels. This review presents a survey of recent literature with a focus on the past 5 years. The data indicate continuing trends towards multiplexed, simpler, cheaper, faster and innovative sensing while newer tendencies concern minimizing the sample volume or using alternative sampling matrices such as saliva for less invasive assays. Utilizing the enzyme-mimicking activity of nanomaterials gained ground in comparison to their more traditional roles as signaling probes, immobilization supports for biomolecules and for signal amplification. The growing use of aptamers as replacements for antibodies prompted emerging applications of DNA amplification and editing techniques. Optical biosensors and assays were tested with larger sets of clinical samples and compared with the current standard methods. The ambitious goals on the horizon for CVD testing include the discovery and determination of relevant biomarkers with the help of artificial intelligence, more stable specific recognition elements for biomarkers and fast, cheap readers and disposable tests to facilitate rapid testing at home. As the field is progressing at an impressive pace, the opportunities for biosensors in the optical sensing of CVD biomarkers remain significant.

Advances and perspectives in the analytical technology for small peptide hormones analysis: A glimpse to gonadorelin

In the last twenty years, we have witnessed an important evolution of bioanalytical approaches moving from conventional lab bench instrumentation to simpler, easy-to-use techniques to deliver analytical responses on-site, with reduced analysis times and costs. In this frame, affinity reagents production has also jointly advanced from natural receptors to biomimetic, abiotic receptors, animal-free produced. Among biomimetic ones, aptamers, and molecular imprinted polymers (MIPs) play a leading role. Herein, our motivation is to provide insights into the evolution of conventional and innovative analytical approaches based on chromatography, immunochemistry, and affinity sensing referred to as peptide hormones. Indeed, the analysis of peptide hormones represents a current challenge for biomedical, pharmaceutical, and anti-doping analysis. Specifically, as a paradigmatic example, we report the case of gonadorelin, a neuropeptide that in recent years has drawn a lot of attention as a therapeutic drug misused in doping practices during sports competitions.

A Novel ssDNA Aptamer Targeting Carcinoembryonic Antigen: Selection and Characterization

One of the major causes of a drastically shorter life expectancy and one of the most prevalent diseases in the world today is cancer. Given the data on the rise in cancer cases throughout the world, it is obvious that, despite the diagnostic techniques currently being used, there is a pressing need to develop precise and sensitive techniques for early diagnosis of the disease. A high degree of affinity and specificity towards particular targets is maintained by the short nucleic acid molecules known as aptamers. Aptamers outperform antibodies due to their unique benefits, such as their simplicity in synthesis and modification, lack of toxicity, and long-term stability. Utilizing an accurate recognition element and a robust signal transduction mechanism, molecular diagnostics can be extremely sensitive and specific. In this study, development of new single-stranded DNA aptamers against CEA for use in cancer diagnostics was accomplished using SELEX and NGS methods. As a result of 12 iterative SELEX rounds, nine aptamer candidates against CEA were developed. NGS comparative analysis revealed that round twelve had an enriched number of aptamers that were specifically bound, as opposed to round eight. Among the selected nine sequences characterized by bioinformatics analysis and ELONA, an aptamer sequence with the highest specificity and affinity for the target protein was identified and further examined. Aptamer sequence (6) was screened in a concentration-dependent assay, specificity analysis was performed, and its potential secondary and tertiary structures were predicted, which enabled us to test one of the possible putative interactions with CEA. Finally, aptamer sequence (6) labelled with a Cy5 fluorescent tag was used in confocal microscopy to observe its binding towards the CEA expressed in HT-29 human colon adenocarcinoma cell line.

Colorimetric determination of carbidopa in anti-Parkinson drugs based on 4-hydroxy-3-methoxybenzaldazine formation by reaction with vanillin

In this paper is reported the selective colorimetric detection and quantification of carbidopa, an inhibitor of aromatic amino acid decarboxylase, in the co-presence of levodopa as dopamine precursor in pharmaceutical formulations for the treatment of Parkinson's disease. The method is based on the selective condensation reaction between the hydrazine group from carbidopa and the formyl functional group of vanillin, a natural flavoring agent, in acidified alcoholic solution. The yellow color development (λmax ~ 420 nm) due to the formation of 4-hydroxy-3-methoxybenzaldazine (HMOB) was observed for carbidopa only, whereas levodopa, lacking the hydrazine group, did not color the solution, as expected. The calibration curves for two tablet formulations of levodopa in combination with carbidopa (4:1) were superimposable with levodopa/carbidopa (4:1), as well as carbidopa alone, in standard solution, i.e., the excipients and additives did not interfere with carbidopa determination, corresponding to a mean recovery about 105%. The linear dynamic range was between 5.00 and 50.0 mg L-1 with very good reproducibility within this range (CVav% about 3-4%) and very good sensitivity, with limits of quantification of about 1 mg L-1. The colorimetric method developed here is very simple, inexpensive, and effective for drug estimation and quality control of pharmaceutical formulations.

Aptamer-Based Biosensors for the Colorimetric Detection of Blood Biomarkers: Paving the Way to Clinical Laboratory Testing

Clinical diagnostics for human diseases rely largely on enzyme immunoassays for the detection of blood biomarkers. Nevertheless, antibody-based test systems have a number of shortcomings that have stimulated a search for alternative diagnostic assays. Oligonucleotide aptamers are now considered as promising molecular recognizing elements for biosensors (aptasensors) due to their high affinity and specificity of target binding. At the moment, a huge variety of aptasensors have been engineered for the detection of various analytes, especially disease biomarkers. However, despite their great potential and excellent characteristics in model systems, only a few of these aptamer-based assays have been translated into practice as diagnostic kits. Here, we will review the current progress in the engineering of aptamer-based colorimetric assays as the most suitable format for clinical lab diagnostics. In particular, we will focus on aptasensors for the detection of blood biomarkers of cardiovascular, malignant, and neurodegenerative diseases along with common inflammation biomarkers. We will also analyze the main obstacles that have to be overcome before aptamer test systems can become tantamount to ELISA for clinical diagnosis purposes.

Aptamers Targeting Cardiac Biomarkers as an Analytical Tool for the Diagnostics of Cardiovascular Diseases: A Review

The detection of cardiac biomarkers is used for diagnostics, prognostics, and the risk assessment of cardiovascular diseases. The analysis of cardiac biomarkers is routinely performed with high-sensitivity immunological assays. Aptamers offer an attractive alternative to antibodies for analytical applications but, to date, are not widely practically implemented in diagnostics and medicinal research. This review summarizes the information on the most common cardiac biomarkers and the current state of aptamer research regarding these biomarkers. Aptamers as an analytical tool are well established for troponin I, troponin T, myoglobin, and C-reactive protein. For the rest of the considered cardiac biomarkers, the isolation of novel aptamers or more detailed characterization of the known aptamers are required. More attention should be addressed to the development of dual-aptamer sandwich detection assays and to the studies of aptamer sensing in alternative biological fluids. The universalization of aptamer-based biomarker detection platforms and the integration of aptamer-based sensing to clinical studies are demanded for the practical implementation of aptamers to routine diagnostics. Nevertheless, the wide usage of aptamers for the diagnostics of cardiovascular diseases is promising for the future, with respect to both point-of-care and laboratory testing.

Enzyme Sensing Using 2-Mercaptopyridine-Carbonitrile Reporters and Surface-Enhanced Raman Scattering

The high sensitivity and functional group selectivity of surface-enhanced Raman scattering (SERS) make it an attractive method for enzyme sensing, but there is currently a severe lack of enzyme substrates that release SERS reporter molecules with favorable detection properties. We find that 2-mercaptopyridine-3-carbonitrile ( o-MPN) and 2-mercaptopyridine-5-carbonitrile ( p-MPN) are highly effective as SERS reporter molecules that can be captured by silver or gold nanoparticles to give intense SERS spectra, each with a distinctive nitrile peak at 2230 cm^-1. p-MPN is a more sensitive reporter and can be detected at low nanomolar concentrations. An assay validation study synthesized two novel substrate molecules, Glc-o-MPN and Glc-p-MPN, and showed that they can be cleaved efficiently by β-glucosidase (K _m = 228 and 162 μM, respectively), an enzyme with broad industrial and biomedical utility. Moreover, SERS detection of the released reporters ( o-MPN or p-MPN) enabled sensing of β-glucosidase activity and β-glucosidase inhibition. Comparative experiments using a crude almond flour extract showed that the presence of β-glucosidase activity could be confirmed by SERS detection in a much shorter time period (>10 time shorter) than by UV-vis absorption detection. It is likely that a wide range of enzyme assays and diagnostic tests can be developed using 2-mercaptopyridine-carbonitriles as SERS reporter molecules.

A biomimetic enzyme-linked immunosorbent assay (BELISA) for the analysis of gonadorelin by using molecularly imprinted polymer-coated microplates

An original biomimetic enzyme-linked immunoassay (BELISA) to target the small peptide hormone gonadorelin is presented. This peptide has been recently listed among the substances banned in sports by the World Antidoping Agency (WADA) since its misuse by male athletes triggers testosterone increase. Hence, in response to this emerging issue in anti-doping controls, we proposed BELISA which involves the growth of a polynorepinephrine (PNE)–based molecularly imprinted polymer (MIP) directly on microwells. PNE, a polydopamine (PDA) analog, has recently displayed impressive performances when it was exploited for MIP preparation, giving even better results than PDA. Gonadorelin quantification was accomplished via a colorimetric indirect competitive bioassay involving the competition between biotinylated gonadorelin linked to the signal reporter and the unlabeled analyte. These compete for the same MIP binding sites resulting in an inverse correlation between gonadorelin concentration and the output color signal (λ = 450 nm). A detection limit of 277 pmol L⁻¹ was achieved with very good reproducibility in standard solutions (_avCV% = 4.07%) and in urine samples (_avCV% = 5.24%). The selectivity of the assay resulted adequate for biological specimens and non-specific control peptides. In addition, the analytical figures of merit were successfully validated by mass spectrometry, the reference anti-doping benchtop platform for the analyte. BELISA was aimed to open real perspectives for PNE-based MIPs as alternatives to antibodies, especially when the target analyte is a poorly or non-immunogenic small molecule, such as gonadorelin.

Synthesis of fluorescence labelled aptamers for use as low-cost reagents in HIV/AIDS research and diagnostics

Aptamers are nucleic acids selected by systematic evolution of ligands by exponential enrichment. They have potential as alternatives to antibodies in medical research and diagnostics, with the advantages of being non-immunogenic and relatively inexpensive to produce. In the present study, gp120 aptamers conjugated with fluorescein isothiocyanate (FITC) were generated, which could interact with HIV-1 gp120. A previously isolated gp120 aptamer, CSIR 1.1, was conjugated with FITC by incubation with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and imidazole. The conjugation and binding to the glycoprotein were confirmed by flow cytometry. FITC conjugated aptamers showed an increase in fluorescence emission 24-fold higher than baseline, and this difference was statistically significant (P=0.0016). Compared with a commercially available biotinylated anti-gp120 antibody, detected using FITC conjugated streptavidin, the emission of fluorescence obtained from the FITC-conjugated aptamer was 8-fold higher, suggesting a stronger interaction with gp120. In addition, the FITC conjugated aptamer neutralized HIV-1 pseudoviruses with an average IC₅₀ of 21.3 nM, similar to the parent aptamer that had an IC₅₀ of 19.2 nM. However, the difference in inhibition between the two aptamers was not statistically significant (P=0.784). These results indicate that the FITC-conjugated aptamer generated in the present study could potentially be used as a low-cost reagent in HIV/AIDS research and diagnostics.

Advances in point-of-care testing for cardiovascular diseases

Point-of-care testing (POCT) is a specific format of diagnostic testing that is conducted without accompanying infrastructure or sophisticated instrumentation. Traditionally, such rapid sample-to-answer assays provide inferior analytical performances to their laboratory counterparts when measuring cardiac biomarkers. Hence, their potentially broad applicability is somewhat bound by their inability to detect clinically relevant concentrations of cardiac troponin (cTn) in the early stages of myocardial injury. However, the continuous refinement of biorecognition elements, the optimization of detection techniques, and the fabrication of tailored fluid handling systems to manage the sensing process has stimulated the production of commercial assays that can support accelerated diagnostic pathways. This review will present the latest commercial POC assays and examine their impact on clinical decision-making. The individual elements that constitute POC assays will be explored, with an emphasis on aspects that contribute to economically feasible and highly sensitive assays. Furthermore, the prospect of POCT imparting a greater influence on early interventions for medium to high-risk individuals and the potential to re-shape the paradigm of cardiovascular risk assessments will be discussed.

Personalized immunoglobulin aptamers for detection of multiple myeloma minimal residual disease in serum

Multiple myeloma (MM) is a neoplasm of plasma cells that secrete patient specific monoclonal immunoglobulins. A recognized problem in MM treatment is the early recognition of minimal residual disease (MRD), the major cause of relapse. Current MRD detection methods (multiparameter flow cytometry and next generation sequencing) are based on the analysis of bone marrow plasma cells. Both methods cannot detect extramedullary disease and are unsuitable for serial measurements. We describe the methodology to generate high affinity DNA aptamers that are specific to a patient’s monoclonal Fab region. Such aptamers are 2000-fold more sensitive than immunofixation electrophoresis and enabled detection and quantification of MRD in serum when conventional MRD methods assessed complete remission. The aptamer isolation process that requires small volumes of serum is automatable, and Fab specific aptamers are adaptable to multiple diagnostic formats including point-of-care devices.

Tapia-Alveal, Olsen and Worgall develop a novel strategy for patient-specific multiple myeloma diagnostics platform using DNA aptamers. The high affinity DNA aptamers enabled detection of minimal residual disease (MRD) when conventional MRD methods assessed complete remission and are adaptable to multiple diagnostic formats including point-of-care devices.

Regulation of the Peroxidase-Like Activity of nGO, MoS2 and WS2 Nanozymes by Using Metal Cations

Two dimensional nanoparticles (2D-NPs) along with other nanoscale materials have been deemed to be the next generation of artificial enzymes (nanozymes). The low-cost bulk-scale production, ease of storage and modification of such nanomaterials have given nanozymes an advantage over traditional enzymes. Many studies have been aimed at developing methods to increase the performance of these nanozymes, and also identify interfering agents. To investigate the interference of a number of metal cations, we studied the effect of Ti²⁺ , Fe²⁺ , Ag⁺ , Hg²⁺ , Co²⁺ , Cu²⁺ , Ni²⁺ , Pb²⁺ , Ca²⁺ , Zn²⁺ and Mn²⁺ in a nanozyme assays of 2D-NPs using ABTS radical formation. Ti²⁺ , Co²⁺ , Cu²⁺ , Ni²⁺ , Ca²⁺ , Zn²⁺ and Mn²⁺ ions did not display any notable effect on the peroxidase-like activity of nGO, MoS₂ and WS₂ 2D-NPs. However, Fe²⁺ , Ag⁺ , Hg²⁺ and Pb²⁺ ions' effects on the overall ABTS reaction were significant enough to be visualised by partial least square discriminant analysis (PLSDA). We report that, similar to that of many natural enzymes, the nanozyme activity of 2D-NPs is regulated by a number of metal cations allowing their identification and discrimination by using a statistical analysis tool.

Norepinephrine as new functional monomer for molecular imprinting: An applicative study for the optical sensing of cardiac biomarkers

The continuous research for alternatives to antibody-based detection drove, in the last decades, the development of numerous strategies. Molecularly imprinted polymers (MIPs) emerged thanks to the low-cost and long-term stability features, where the choice of natural functional monomer(s) represents the key step for efficient imprinting of biomolecules. The chemical structure of dopamine (DA), one of the most used natural functional monomers, provided the inspiration for this work. We wondered why norepinephrine (NE) that differs from dopamine only for an additional hydroxyl group was not investigated at all in biosensing applications. In fact, there is only one paper exploiting polynorepinephrine (PNE) in molecular recognition applications, taking advantage of molecular imprinting, but not for biosensing purposes. In contrast, hundreds of papers describe polydopamine-based sensors. Therefore, we firstly investigated how the additional hydroxyl group of NE could affect the properties of the resulting polymer, and how these properties could be exploited for biosensing applications. The results highlighted the reduced non-specific adsorption of proteins onto PNE with respect to dopamine polymer. Furthermore, as a case study, we successfully developed a PNE-based imprinted biosensor for the early detection of Troponin I, a crucial biomarker for heart failure, by coupling the MIP biosensor with surface plasmon resonance (SPR) detection. The results indicate the feasible use of imprinted PNE as synthetic receptor for biomolecules, opening new perspectives for this biopolymer, so far not considered, and encouraging further investigations on its potential application in biosensing.

Remote biosensor for the determination of trypsin by using nanoporous anodic alumina as a three-dimensional nanostructured material

The determination of trypsin in the human real sample is a routine medical investigation to assess the pancreatic disease. Herein, we fabricated an interferometric reflectance spectroscopy based biosensor for the determination trypsin. For this purpose, urease and fluorescein 5(6)-isothiocyanate (FLITC) were immobilized on the nanoporous anodic alumina (NAA). The operation principle of the proposed biosensor is based on the change in the pH of the solution during the reaction of urease and urea and therefore change in the light-absorbing ability of FLITC in the presence of trypsin. The reaction of the urease enzyme with urea increased the pH of the solution because of producing ammonia. This increase in the pH of solution increased the light-absorbing ability of the immobilized FLITC on NAA and therefore the intensity of the reflected light from the NAA to the charge-coupled device detector decreased. In the presence of trypsin, the catalytic activity of immobilized urease on NAA decreased. This decrease in the activity of urease enzyme consequent on the decrease in the amount of the generated ammonia. Therefore, the immobilized FLITC on the NAA did not absorb more light and consciously, the intensity of the light reflected light into the detector increased. The proposed biosensor exhibited a good response to the concentration of trypsin in the range of 0.25–20 μg.mL⁻¹ with the limit of detection of 0.06 μg.mL⁻¹.