Optimized aptamer-based next generation biosensor for the ultra-sensitive determination of SARS-CoV-2 S1 protein in saliva samples

COVID-19 is an infectious disease caused by the SARS-CoV-2 virus, which rapidly spread worldwide and resulted in a pandemic. Efficient and sensitive detection techniques have been devised since the onset of the epidemic and continue to be improved at present. Due to the crucial role of the SARS-CoV-2 S1 protein in facilitating the virus's entry into cells, efforts in detection and treatment have primarily centered upon this protein. In this study, a rapid, ultrasensitive, disposable, easy-to-use, cost-effective next generation biosensor based on optimized aptamer (Optimer, OPT) was developed by using a disposable pencil graphite electrode (PGE) and applied for the impedimetric determination of SARS-CoV-2 S1 protein. The S1 protein interacted with the OPT in the solution phase and then immobilized onto the PGE surface. Subsequently, measurements using electrochemical impedance spectroscopy (EIS) were conducted in a solution containing a redox probe of 1 mM [Fe(CN)6]3-/4-. Under optimum conditions, the limit of detection (LOD) for the S1 protein in buffer medium at concentrations ranging from 101 to 106 ag/mL was calculated as 8.80 ag/mL (0.11 aM). The selectivity of the developed biosensor was studied against MERS-CoV-S1 protein (MERS) and Influenza Hemagglutinin antigen (HA). Furthermore, the application of the biosensor in artificial saliva medium is demonstrated. The LOD was also calculated in artificial saliva medium in the concentration range of 101-105 ag/mL and calculated as 2.01 ag/mL (0.025 aM). This medium was also used to assess the selectivity of optimized-aptamer based biosensor.

Current Analytical Methods for the Sensitive Assay of New-Generation Ovarian Cancer Drugs in Pharmaceutical and Biological Samples

Ovarian cancer, which affects the female reproductive organs, is one of the most common types of cancer. Since this type of cancer has a high mortality rate from gynaecological cancers, the scientific community shows great interest in studies on its treatment. Chemotherapy, radiotherapy, and surgical treatment methods are used in its treatment. In the absence of targeted treatments in these treatment methods, side effects occur in patients, and patients show resistance to the drug. In addition, the underlying causes of ovarian cancer are still not fully known. The scientific world thinks that genetic factors, environmental conditions, and consumed foods may cause this cancer. The most important factor in the treatment of ovarian cancer is early diagnosis. Therefore, the drugs used in the treatment of ovarian cancer are platinum-based anticancer drugs. In addition to these drugs, the most preferred treatment method recently is targeted treatment approaches using poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors. In this review, studies on the sensitive analysis of the treatment methods of these new-generation drugs used in the treatment of ovarian cancer have been comprehensively examined. In addition, the basic features, structural aspects, and biological data of analytical methods used in treatments with new-generation drugs are explained. Analytical studies carried out in the literature in recent years aim to show future developments in how these new-generation drugs are used today and to guide future studies by comprehensively examining and explaining the structure-activity relationship, mechanism of action, toxicity, and pharmacokinetic studies. Finally, in this study, the methods used in the analysis of drugs used in the treatment of ovarian cancer and the studies conducted between 2015 and 2023 were discussed in detail.

DNA-based molecular recognition system for lactoferrin biosensing

The paper describes the development of a novel DNA oligonucleotide-based affinity bioreceptor that binds to lactoferrin, a glycoprotein-type immunomodulator. The research was performed using surface plasmon resonance method to investigate affinity of various types of oligonucleotides to the target protein. The 72 base pair-long 5'[(TAGAGGATCAAA)AAA]4TAGAGGATCAAA3' sequence with the highest affinity to lactoferrin was selected for further investigations. Kinetic analysis of the interaction between selected DNA and lactoferrin provided rate and equilibrium constants: ka = (2.49 ± 0.03)∙104 M-1∙s-1, kd = (1.89 ± 0.02)∙10-3 s-1, KA = (0.13 ± 0.05)∙108 M-1, and KD = (7.61 ± 0.18)∙10-8 M. Thermodynamic study conducted to determine the ΔH0, ΔS0, and ΔG0 for van't Hoff characteristic in the temperature range of 291.15-305.15 K, revealed the complex formation as endothermic and entropically driven. The chosen DNA sequence's selectivity towards lactoferrin was confirmed with interferents' response constituting <3 % of the response to lactoferrin. SPR analysis justified utility of the designed DNA oligonucleotide for Lf determination, with LOD of 4.42∙10-9 M. Finally, the interaction between lactoferrin and DNA was confirmed by electrochemical impedance spectroscopy, providing the basis for further quantitative assay of lactoferrin using the developed DNA-based bioreceptor. The interactions were performed under immobilized DNA ligand conditions, thus reflecting the sensor's surface, which facilitates their transfer to other label-free biosensor technologies.

Aptasensor for Impedimetric Detection of Lysozyme

The impedimetric detection of a protein, lysozyme (LYS), was carried out herein by aptamer-immobilized single-use pencil graphite electrodes (PGEs). The aptamer was immobilized onto electrochemically activated surface of electrode without using any chemical agents, or any types of nanomaterials. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) techniques were applied to analyze the electrochemical behavior of unmodified PGE and aptamer immobilized PGE. The interaction of aptamer with its target protein, LYS, was then investigated by EIS. The limit of detection for LYS was found to be 1.44 μg/mL (equals to 100.65 nM). The developed aptasensor specific to LYS presented high selectivity against to bovine serum albumin and thrombin.

Surface plasmon resonance aptasensor for detection of human activated protein C

The aim of this study is a highly sensitive and selective label-free surface plasmon resonance (SPR) aptasensor preparation for the specific detection of human activated protein C (APC). In the first step, DNA aptamer was complexed with N-methacryloyl-L-cysteine (MAC) monomer. Then, cyanamide and 2-hydroxyethyl methacrylate solution was mixed with the DNA-Apt/MAC complex. Two different SPR sensors (Random-DNA and HEMA-MAC polymeric films) were also prepared by following the same experimental procedure. The characterization of SPR aptasensors was done by contact angle, atomic force microscopy, and ellipsometer analysis. Selectivity studies of SPR aptasensors were performed in the presence of bovine serum albumin, hemoglobin and myoglobin. Desorption studies were performed by using 0.025 M NaCl solution. The limit of detection (LOD) and limit of quantification (LOQ) values of DNA-Apt SPR aptasensor was determined as 1.5 ng/mL and 5.2 ng/mL.

Voltammetric Aptasensor Based on Magnetic Beads Assay for Detection of Human Activated Protein C

Aptamers are defined as new generation of nucleic acids, which has recently presented promising specifications over to antibodies. An increasing number of electrochemical studies related to aptamer-based sensors, so-called aptasensors have been introduced in the literature. Herein, the interaction between human activated protein C (APC) and its cognate DNA aptamer (DNA APT) was performed at the surface of magnetic beads (MBs), followed by voltammetric detection using disposable graphite electrodes (PGEs).

Voltammetric aptasensors for protein disease biomarkers detection: A review

An electrochemical aptasensor is a compact analytical device where the bioreceptor (aptamer) is coupled to a transducer surface to convert a biological interaction into a measurable signal (current) that can be easily processed, recorded and displayed. Since the discovery of the Systematic Evolution of Ligands by Enrichment (SELEX) methodology, the selection of aptamers and their application as bioreceptors has become a promising tool in the design of electrochemical aptasensors. Aptamers present several advantages that highlight their usefulness as bioreceptors such as chemical stability, cost effectiveness and ease of modification towards detection and immobilization at different transducer surfaces. In this review, a special emphasis is given to the potential use of electrochemical aptasensors for the detection of protein disease biomarkers using voltammetry techniques. Methods for the immobilization of aptamers onto electrode surfaces are discussed, as well as different electrochemical strategies that can be used for the design of aptasensors.

Electrochemical detection of N-homocysteinylated BSA in the fetal bovine serum medium

The immobilization of bovine serum albumin (BSA), homocysteine-thiolactone (HTL) andN-homocysteinylated BSA (N-Hcy-BSA) onto the surface of each PGE was performed by passive adsorption and the electrochemical detection of these components was investigated individually.

Voltammetric aptasensor combined with magnetic beads assay developed for detection of human activated protein C

A sensitive and selective label free voltammetric aptasensor based on magnetic beads assay was performed for the first time in our study for monitoring of human activated protein C (APC), which is a serine protease (i.e., key enzyme of the protein C pathway). An amino modified DNA aptamer (DNA APT) was covalently immobilized onto the surface of carboxylated magnetic beads (MBs), and then, the specific interaction between DNA APT and its cognate protein, APC, was performed at the surface of MBs. Similarly a biotinylated DNA APT was immobilized onto the surface of streptavidin coated MBs. Before and after interaction process, the oxidation signal of guanine was measured at disposable pencil graphite electrode (PGE) surface in combination with differential pulse voltammetry (DPV) technique and accordingly, the decrease at the guanine signal was evaluated. The biomolecular recognition of APC was successfully achieved with a low detection limit found as 2.35 µg mL(-1) by using MB-COOH based assay. Moreover, the selectivity of this aptasensor assay was tested in the presence of numerous proteins and other biomolecules: protein C (PC), thrombin (THR), bovine serum albumin (BSA), factor Va (FVa) and chromogenic substrate (KS).

Dendrimer enriched single-use aptasensor for impedimetric detection of activated protein C

A novel impedimetric aptasensor for detection of human activated protein C (APC) was introduced for the first time in the present study. An enhanced sensor response was obtained using poly(amidoamine) (PAMAM) dendrimer having 16 succinamic acid surface groups (generation 2, G2-PS), that was modified onto the surface of screen printed graphite electrode (G2-PS/SPE). An amino modified DNA aptamer was then immobilized onto the surface of G2-PS modified SPE. The selective interaction of APT with its cognate protein, APC was investigated using different electrochemical techniques; differential pulse voltammetry (DPV), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The microscopic characterization was consecutively performed before/after each modification/interaction step using scanning electron microscopy (SEM) and atomic force microscopy (AFM). The selectivity of aptasensor was tested in the presence of numerous proteins; protein C, thrombin, bovine serum albumin, factor Va and chromogenic substrate in different buffer mediums. The APC detection in the artificial serum; fetal bovine serum (FBS) was also performed impedimetrically. This dendrimer modified aptasensor technology brings several advantages: being single-use, fast screening with low-cost per measurement and resulting in sensitive detection of APC with the detection limits of 0.74 μg/mL (0.46 pmol in 35 μL sample) in buffer medium, and 2.03 μg/mL (1.27 pmol in 35 μL sample) in serum.

Thrombin aptasensing with inherently electroactive graphene oxide nanoplatelets as labels

Graphene and its associated materials are commonly used as the transducing platform in biosensing. We propose a different approach for the application of graphene in biosensing. Here, we utilized graphene oxide nanoplatelets as the inherently electroactive labels for the aptasensing of thrombin. The basis of detection lies in the ability of graphene oxide to be electrochemically reduced, thereby providing a well-defined reduction wave; one graphene oxide nanoplatelet of dimension 50 × 50 nm can provide a reduction signal by accepting ~22,000 electrons. We demonstrate that by using graphene oxide nanoplatelets as an inherently electroactive label, we can detect thrombin in the concentration range of 3 pM-0.3 μM, with good selectivity of the aptamer towards interferences by bovine serum albumin, immunoglobulin G and avidin. Therefore, the inherently electroactive graphene oxide nanoplatelets are a material which can serve as an electroactive label, in a manner similar to metallic nanoparticles.

Aptamer modules as sensors and detectors

Aptamers comprise a range of molecular recognition scaffolds that can be engineered to bind to a legion of different proteins and other targets with excellent specificity and affinity. Because these non-natural oligonucleotides are accessible entirely synthetically, aptamers can be equipped with all sorts of reporter groups and can be coupled to many different carriers, surfaces, nanoparticles, or other biomolecules. They can be used in a highly modular fashion and often recognize their targets by a mechanism in which the aptamer undergoes considerable structural rearrangement, which can be exploited for transducing a binding event into a signal. As a consequence, aptamers have been adapted to a huge variety of "read-out configurations" and are increasingly used as capture agents in many different bioanalytical methods. But despite considerable success with these applications, many remaining challenges must still be overcome for the more widespread incorporation of aptasensors in clinical and environmental biosensing and diagnostics to take place. Some particularly noteworthy progress on this front is currently being made with aptasensor configurations that can be used for the multiplexed sensing of many analytes in parallel. In this Account, we describe some of the concepts involved in transducing the binding of a ligand into a signal through various physico-chemical interactions. Research in this area usually involves the combination of the molecular biology of proteins and nucleic acids with biotechnology, synthetic chemistry, physical chemistry, and surface physics. We begin with a brief introduction of the properties and characteristics that qualify aptamers as capture agents for many different analytes and their suitability as highly versatile biosensor components. We then address approaches that apply to surface acoustic wave configurations, drawing largely from our own contributions to aptasensor development, before moving on to describe previous and recent progress in multiplexed aptasensors. Obtaining proteome-wide profiles in cells, organs, organisms, or full populations requires the ability to accurately measure many different analytes in small sample volumes over a broad dynamic range. Multiplexed sensing is an invaluable tool in this endeavor. We discuss what we consider the biggest obstacles to the broader clinical use of aptasensor-based diagnostics and our perspective on how they can be surmounted. Finally,we explore the tremendous potential of aptamer-based sensors that can specifically discriminate between diseased and healthy cells. Progress in these areas will greatly expand the range of aptasensor applications, leading to enhanced diagnosis of diseases in clinical practice and, ultimately, improved patient care.

Label-free impedimetric aptasensor for lysozyme detection based on carbon nanotube-modified screen-printed electrodes

We report on the direct electrochemical detection of aptamer-protein interactions, namely between a DNA aptamer and lysozyme (LYS) based on electrochemical impedance spectroscopy (EIS) technique. First, the affinity of the aptamer to LYS and control proteins was presented by using filter retention assay. An amino-modified version of the DNA aptamer-recognizing lysozyme was covalently immobilized on the surface of multiwalled carbon nanotube-modified screen-printed electrodes (MWCNT-SPEs), which were employed for measurements and have improved properties compared with bare SPEs. This carbon nanotube setup enabled the reliable monitoring of the interaction of lysozyme with its cognate aptamer by EIS transduction of the resistance to charge transfer (R(ct)) in the presence of 2.5 mM [Fe(CN)₆]³⁻/⁴⁻. This assay system provides a means for the label-free, concentration-dependent, and selective detection of lysozyme with an observed detection limit of 12.09 μg/ml (equal to 862 nM).

Nucleic acid aptamers: ideal reagents for point-of-care diagnostics?

Nucleic acid aptamers have many of the properties that make for effective reagents in point-of-care diagnostic devices and whilst superficially similar to antibodies as affinity reagents the scope for engineering them to fit this role is considerable. Synthesis of aptamers allows for the incorporation of functionality for both immobilisation and electrochemical signalling in a way that is compatible with the 'strip' type sensors familiar in enzyme sensors, such as those for glucose. Control of the structure of DNA aptamers through Watson-Crick base pairing allows for different electrochemical assay formats, whilst ferrocenes provide a versatile redox label and insights into the interactions between the aptamer and its target are obtained through both cyclic and square-wave voltammetries. Square-wave voltammetry in particular demonstrates good analytical utility. Two different approaches were used to assemble aptamer/redox probe structures on the surface of gold electrodes and both showed "signal on" behaviour (i.e. the current increases in the presence of analyte) although the two different methods appear to give quite distinct surface coatings.

Nanoparticles in molecular diagnostics

The aim of this chapter is to provide an overview of the available and emerging molecular diagnostic methods that take advantage of the unique nanoscale properties of nanoparticles (NPs) to increase the sensitivity, detection capabilities, ease of operation, and portability of the biodetection assemblies. The focus will be on noble metal NPs, especially gold NPs, fluorescent NPs, especially quantum dots, and magnetic NPs, the three main players in the development of probes for biological sensing. The chapter is divided into four sections: a first section covering the unique physicochemical properties of NPs of relevance for their utilization in molecular diagnostics; the second section dedicated to applications of NPs in molecular diagnostics by nucleic acid detection; and the third section with major applications of NPs in the area of immunoassays. Finally, a concluding section highlights the most promising advances in the area and presents future perspectives.

ADLOC: an aptamer-displacement assay based on luminescent oxygen channeling

Functional nucleic acids, such as aptamers and allosteric ribozymes, can sense their ligands specifically, thereby undergoing structural alterations that can be converted into a detectable signal. The direct coupling of molecular recognition to signal generation enables the production of versatile reporters that can be applied as molecular probes for various purposes, including high-throughput screening. Here we describe an unprecedented type of a nucleic acid-based sensor system and show that it is amenable to high-throughput screening (HTS) applications. The approach detects the displacement of an aptamer from its bound protein partner by means of luminescent oxygen channeling. In a proof-of-principle study we demonstrate that the format is feasible for efficient identification of small drug-like molecules that bind to a protein target, in this case to the Sec7 domain of cytohesin. We extended the approach to a new cytohesin-specific single chain DNA aptamer, C10.41, which exhibits a similar binding behavior to cytohesins but has the advantage of being more stable and easier to synthesize and to modify than the RNA-aptamer M69. The results obtained with both aptamers indicate the general suitability of the aptamer-displacement assay based on luminescent oxygen channelling (ADLOC) for HTS. We also analyzed the potential for false positive hits and identified from a library of 18,000 drug-like small molecules two compounds as strong singlet-oxygen quenchers. With full automation and the use of commercially available plate readers, we estimate that the ADLOC-based assay described here could be used to screen at least 100,000 compounds per day.

Screening and improvement of an anti-VEGF DNA aptamer

To obtain an aptamer with a high affinity for vascular endothelial growth factor (VEGF), we focused on the receptor-binding domain (RBD) of VEGF as a target epitope. Three rounds of screening gave Vap7, which bound to the VEGF isoforms VEGF(121) and VEGF(165) with K(D) values of 1.0 nM and 20 nM, respectively. Moreover, Vap7 showed specificity within the VEGF family. Secondary structure predictions and circular dicrhoism suggested that Vap7 folds into a G-quadruplex structure. We obtained a mutant aptamer that contains only this region of the aptamer sequence. This truncated mutant (V7t1) bound to both VEGF(121) and VEGF(165) with K(D) values of 1.1 nM and 1.4 nM, respectively. Its sequence was 5'-TGTGGGGGTGGACGGGCCGGGTAGA-3', and it appeared to form a G-quadruplex structure. We also produced an aptamer heterodimer consisting of our previously derived aptamer (del5-1), which binds to the heparin-binding domain of VEGF, linked to V7t1. The resulting heterodimer bound strongly to VEGF(165) with a K(D) value of 4.7 x 10(2) pM.