Development of biosensors with aptamers as bio-recognition element: the case of HIV-1 Tat protein

Aptamers targeting SARS-COV-2: a promising tool to fight against COVID-19

SARS-CoV-2, the causative agent of COVID-19, remains among the main causes of global mortality. Although antigen/antibody-based immunoassays and neutralizing antibodies targeting SARS-CoV-2 have been successfully developed over the past 2 years, they are often inefficient and unreliable for emerging SARS-CoV-2 variants. Novel approaches against SARS-CoV-2 and its variants are therefore urgently needed. Aptamers have been developed for the detection and inhibition of several different viruses such as HIV, influenza viruses, Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV. Aptamers targeting SARS-CoV-2 represent a promising tool in the fight against COVID-19, which is of paramount importance for the current and any future pandemics. This review presents recent advances and future trends in the development of aptamer-based approaches for SARS-CoV-2 diagnosis and treatment.

Aptamer-based rapid diagnosis for point-of-care application

Aptasensors have attracted considerable interest and widespread application in point-of-care testing worldwide. One of the biggest challenges of a point-of-care (POC) is the reduction of treatment time compared to central facilities that diagnose and monitor the applications. Over the past decades, biosensors have been introduced that offer more reliable, cost-effective, and accurate detection methods. Aptamer-based biosensors have unprecedented advantages over biosensors that use natural receptors such as antibodies and enzymes. In the current epidemic, point-of-care testing (POCT) is advantageous because it is easy to use, more accessible, faster to detect, and has high accuracy and sensitivity, reducing the burden of testing on healthcare systems. POCT is beneficial for daily epidemic control as well as early detection and treatment. This review provides detailed information on the various design strategies and virus detection methods using aptamer-based sensors. In addition, we discussed the importance of different aptamers and their detection principles. Aptasensors with higher sensitivity, specificity, and flexibility are critically discussed to establish simple, cost-effective, and rapid detection methods. POC-based aptasensors' diagnostic applications are classified and summarised based on infectious and infectious diseases. Finally, the design factors to be considered are outlined to meet the future of rapid POC-based sensors.

Aptamer-based biosensors for virus protein detection

Virus threatens life health seriously. The accurate early diagnosis of the virus is vital for clinical control and treatment of virus infection. Aptamers are small single-stranded oligonucleotides (DNAs or RNAs). In this review, we summarized aptasensors for virus detection in recent years according to the classification of the viral target protein, and illustrated common detection mechanisms in the aptasensors (colorimetry, fluorescence assay, surface plasmon resonance (SPR), surface-enhanced raman spectroscopy (SERS), electrochemical detection, and field-effect transistor (FET)). Furthermore, aptamers against different target proteins of viruses were summarized. The relationships between the different biomarkers of the viruses and the detection methods, and their performances were revealed. In addition, the challenges and future directions of aptasensors were discussed. This review will provide valuable references for constructing on-site aptasensors for detecting viruses, especially the SARS-CoV-2.

Advances in Aptamer-Based Biosensors and Cell-Internalizing SELEX Technology for Diagnostic and Therapeutic Application

Aptamers are a group of synthetic single-stranded nucleic acids. They are generated from a random library of single-stranded DNA or RNA by a technology named systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a repetitive process to select and identify suitable aptamers that show high affinity and specificity towards target cells. Great strides have been achieved in the design, construction, and use of aptamers up to this point. However, only a small number of aptamer-based applications have achieved widespread commercial and clinical acceptance. Additionally, finding more effective ways to acquire aptamers with high affinity remains a challenge. Therefore, it is crucial to thoroughly examine the existing dearth and advancement in aptamer-related technologies. This review focuses on aptamers that are generated by SELEX to detect pathogenic microorganisms and mammalian cells, as well as in cell-internalizing SELEX for diagnostic and therapeutic purposes. The development of novel aptamer-based biosensors using optical and electrical methods for microbial detection is reported. The applications and limitations of aptamers are also discussed.

Aptamers: A prospective tool for infectious diseases diagnosis

It is well known that people's health is seriously threatened by various pathogens (such as Mycobacterium tuberculosis, Treponema pallidum, Novel coronavirus, HIV, Mucor, etc.), which leads to heavy socioeconomic burdens. Therefore, early and accurate pathogen diagnosis is essential for timely and effective therapies. Up to now, diagnosing human contagious diseases at molecule and nano levels is remarkably difficult owing to insufficient valid probes when it comes to determining the biological markers of pathogens. Aptamers are a set of high‐specificity and high‐sensitivity plastic oligonucleotides screened in vitro via the selective expansion of ligands by exponential enrichment (SELEX). With the advent of aptamer‐based technologies, their merits have aroused mounting academic interest. In recent years, as new detection and treatment tools, nucleic acid aptamers have been extensively utilized in the field of biomedicine, such as pathogen detection, new drug development, clinical diagnosis, nanotechnology, etc. However, the traditional SELEX method is cumbersome and has a long screening cycle, and it takes several months to screen out aptamers with high specificity. With the persistent development of SELEX‐based aptamer screening technologies, the application scenarios of aptamers have become more and more extensive. The present research briefly reviews the research progress of nucleic acid aptamers in the field of biomedicine, especially in the diagnosis of contagious diseases.

Quartz Crystal Microbalance-Based Aptasensors for Medical Diagnosis

Aptamers are important materials for the specific determination of different disease-related biomarkers. Several methods have been enhanced to transform selected target molecule-specific aptamer bindings into measurable signals. A number of specific aptamer-based biosensors have been designed for potential applications in clinical diagnostics. Various methods in combination with a wide variety of nano-scale materials have been employed to develop aptamer-based biosensors to further increase sensitivity and detection limit for related target molecules. In this critical review, we highlight the advantages of aptamers as biorecognition elements in biosensors for target biomolecules. In recent years, it has been demonstrated that electrode material plays an important role in obtaining quick, label-free, simple, stable, and sensitive detection in biological analysis using piezoelectric devices. For this reason, we review the recent progress in growth of aptamer-based QCM biosensors for medical diagnoses, including virus, bacteria, cell, protein, and disease biomarker detection.

Recent Progress on Highly Selective and Sensitive Electrochemical Aptamer-based Sensors

Highly selective, sensitive, and stable biosensors are essential for the molecular level understanding of many physiological activities and diseases. Electrochemical aptamer-based (E-AB) sensor is an appealing platform for measurement in biological system, attributing to the combined advantages of high selectivity of the aptamer and high sensitivity of electrochemical analysis. This review summarizes the latest development of E-AB sensors, focuses on the modification strategies used in the fabrication of sensors and the sensing strategies for analytes of different sizes in biological system, and then looks forward to the challenges and prospects of the future development of electrochemical aptamer-based sensors.

Photoelectrochemical aptasensors for detection of viruses

Photoelectrochemistry (PEC) is a dynamic discipline studying the effect of light on photoelectrode or photosensitive material, and the conversion from solar energy into electrical power. The basic PEC process refers to the oxidation or reduction reactions between electrochemical active species in solution and photoactive materials that occurred at the electrode/electrolyte interface during illumination. In recent years, the PEC biosensing approaches have also been developed by the combination of the PEC technique with bioanalysis, where the interaction between biological recognition element and analyte influences a photocurrent signal. This involves the charge and energy transfer of PEC reaction between electron donor/acceptor and photoactive material upon light irradiation. Coupling the advantages of PEC bioanalysis and aptamers has provided new concepts for highly selective and sensitive biosensors development, applicable in human health monitoring and environmental protection. In a typical assay, a photoactive material converts the affinity binding properties of aptamers into a detectable electrical signal, presenting an innovative method for probing numerous aptamer-analyte interactions. Using different aptamer probes aiming for specific purposes, more sensing strategies with rational design and exquisite signaling mechanisms have been proposed. This review concentrated on the current topic of PEC aptasensors that are used for the detection of viruses. The prospects in this area are also discussed.

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2D Materials-Based Aptamer Biosensors: Present Status and Way Forward

Current advances in constructing functional nanomaterials and elegantly designed nanostructures have opened up new possibilities for the fabrication of viable field biosensors. Two-dimensional materials (2DMs) have fascinated much attention due to their chemical, optical, physicochemical, and electronic properties. They are ultrathin nanomaterials with unique properties such as high surface-to-volume ratio, surface charge, shape, high anisotropy, and adjustable chemical functionality. 2DMs such as graphene-based 2D materials, Silicate clays, layered double hydroxides (LDHs), MXenes, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs) offer intensified physicochemical and biological functionality and have proven to be very promising candidates for biological applications and technologies. 2DMs have a multivalent structure that can easily bind to single-stranded DNA/RNA (aptamers) through covalent, non-covalent, hydrogen bond, and π-stacking interactions, whereas aptamers have a small size, excellent chemical stability, and low immunogenicity with high affinity and specificity. This review discussed the potential of various 2D material-based aptasensor for diagnostic applications, e.g., protein detection, environmental monitoring, pathogens detection, etc.

Changes of Viscoelastic Properties of Aptamer-Based Sensing Layers Following Interaction with Listeria innocua

A multiharmonic quartz crystal microbalance (QCM) has been applied to study the viscoelastic properties of the aptamer-based sensing layers at the surface of a QCM transducer covered by neutravidin following interaction with bacteria Listeria innocua. Addition of bacteria in the concentration range 5 × 103-106 CFU/mL resulted in a decrease of resonant frequency and in an increase of dissipation. The frequency decrease has been lower than one would expect considering the dimension of the bacteria. This can be caused by lower penetration depth of the acoustics wave (approximately 120 nm) in comparison with the thickness of the bacterial layer (approximately 500 nm). Addition of E. coli at the surface of neutravidin as well as aptamer layers did not result in significant changes in frequency and dissipation. Using the Kelvin-Voight model the analysis of the viscoelastic properties of the sensing layers was performed and several parameters such as penetration depth, Γ, viscosity coefficient, η, and shear modulus, μ, were determined following various modifications of QCM transducer. The penetration depth decreased following adsorption of the neutravidin layer, which is evidence of the formation of a rigid protein structure. This value did not change significantly following adsorption of aptamers and Listeria innocua. Viscosity coefficient was higher for the neutravidin layer in comparison with the naked QCM transducer in a buffer. However, a further increase of viscosity coefficient took place following attachment of aptamers suggesting their softer structure. The interaction of Listeria innocua with the aptamer layer resulted in slight decrease of viscosity coefficient. The shearing modulus increased for the neutravidin layer and decreased following aptamer adsorption, while a slight increase of µ was observed after the addition of Listeria innocua.

Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections

The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.

Aptamers for Anti-Viral Therapeutics and Diagnostics

Viral infections cause a host of fatal diseases and seriously affect every form of life from bacteria to humans. Although most viral infections can receive appropriate treatment thereby limiting damage to life and livelihood with modern medicine and early diagnosis, new types of viral infections are continuously emerging that need to be properly and timely treated. As time is the most important factor in the progress of many deadly viral diseases, early detection becomes of paramount importance for effective treatment. Aptamers are small oligonucleotide molecules made by the systematic evolution of ligands by exponential enrichment (SELEX). Aptamers are characterized by being able to specifically bind to a target, much like antibodies. However, unlike antibodies, aptamers are easily synthesized, modified, and are able to target a wider range of substances, including proteins and carbohydrates. With these advantages in mind, many studies on aptamer-based viral diagnosis and treatments are currently in progress. The use of aptamers for viral diagnosis requires a system that recognizes the binding of viral molecules to aptamers in samples of blood, serum, plasma, or in virus-infected cells. From a therapeutic perspective, aptamers target viral particles or host cell receptors to prevent the interaction between the virus and host cells or target intracellular viral proteins to interrupt the life cycle of the virus within infected cells. In this paper, we review recent attempts to use aptamers for the diagnosis and treatment of various viral infections.

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.

An electrochemical label-free DNA impedimetric sensor with AuNP-modified glass fiber/carbonaceous electrode for the detection of HIV-1 DNA

In this study, a highly sensitive, electrochemical, and label-free DNA impedimetric sensor was developed using carbonized glass fiber-coal tar pitch (GF-CTP) electrodes supported with gold nanoparticles (AuNPs) for the detection of HIV-1 gene. Thiol-modified GF-CTP electrodes were prepared using amine crosslinking chemistry and AuNPs were self-assembled obtaining highly conductive nanoelectrodes, GF-CTP-ATP-Au. All steps of electrode modifications were characterized using electrochemical, spectroscopic, and microscopic methods. GF-CTP-ATP-Au electrode was then modified with a capture DNA probe (C-ssDNA) and optimized with a target DNA probe in terms of hybridization time and temperature between 30 and 180 min and 20-50 °C, respectively. Finally, the analytic performance of the developed ssDNA biosensor was evaluated using electrochemical impedance spectroscopy. The calibration of the sensor was obtained between 0.1 pM and 10 nM analyte working range. The limit of detection was calculated using signal to noise ratio of 3 (S/N = 3) as 13 fM. Moreover, interference results for two noncomplementary DNA probes were also tested to demonstrate non-specific ssDNA interactions. An electrochemical label-free DNA impedimetric sensor was successfully developed using a novel GF-CTP-ATP-Au electrode. This study suggests that highly sensitive DNA-based biosensors can be developed using relatively low-cost carbonaceous materials.

An integrated microfluidic platform for selective and real-time detection of thrombin biomarkers using a graphene FET

Lab-on-a-chip technology offers an ideal platform for low-cost, reliable, and easy-to-use diagnostics of key biomarkers needed for early screening of diseases and other health concerns. In this work, a graphene field-effect transistor (GFET) functionalized with target-binding aptamers is used as a biosensor for the detection of thrombin protein biomarker. Furthermore, this GFET is integrated with a microfluidic device for enhanced sensing performances in terms of detection limit, sensitivity, and continuous monitoring. Under this platform, a picomolar limit of detection was achieved for measuring thrombin; in our experiment measured as low as 2.6 pM. FTIR, Raman and UV-Vis spectroscopy measurements were performed to confirm the device functionalization steps. Based on the concentration-dependent calibration curve, a dissociation constant of KD = 375.8 pM was obtained. Continuous real-time measurements were also conducted under a constant gate voltage (VGS) to observe the transient response of the sensor when analyte was introduced to the device. The target selectivity of the sensor platform was evaluated and confirmed by challenging the GFET biosensor with various concentrations of lysozyme protein. The results suggest that this device technology has the potential to be used as a general diagnostic platform for measuring clinically relevant biomarkers for point-of-care applications.

Lab-on-a-Chip Systems for Aptamer-Based Biosensing

Aptamers are oligonucleotides or peptides that are selected from a pool of random sequences that exhibit high affinity toward a specific biomolecular species of interest. Therefore, they are ideal for use as recognition elements and ligands for binding to the target. In recent years, aptamers have gained a great deal of attention in the field of biosensing as the next-generation target receptors that could potentially replace the functions of antibodies. Consequently, it is increasingly becoming popular to integrate aptamers into a variety of sensing platforms to enhance specificity and selectivity in analyte detection. Simultaneously, as the fields of lab-on-a-chip (LOC) technology, point-of-care (POC) diagnostics, and personal medicine become topics of great interest, integration of such aptamer-based sensors with LOC devices are showing promising results as evidenced by the recent growth of literature in this area. The focus of this review article is to highlight the recent progress in aptamer-based biosensor development with emphasis on the integration between aptamers and the various forms of LOC devices including microfluidic chips and paper-based microfluidics. As aptamers are extremely versatile in terms of their utilization in different detection principles, a broad range of techniques are covered including electrochemical, optical, colorimetric, and gravimetric sensing as well as surface acoustics waves and transistor-based detection.

Spectrophotometric ellipsometry based Tat-protein RNA-aptasensor for HIV-1 diagnosis

Rapid and reliable diagnosis of Human Immunodeficiency Virus (HIV) Type I that causes autoimmune deficiency syndrome (AIDS) is still important today. In this study, the HIV-I Tat (trans-activator of transcription) protein-specific RNA-aptamer (antiTat) and spectroscopic ellipsometer were preferred to increase specificity and sensitivity in the diagnosis. The ellipsometry is a well-known characterization tool for the ultra-thin films, where polarization state changes show surface deposition in terms of the ellipsometric angles, psi (Ψ) and delta (Δ). Here, we reported the HIV-Tat protein detection performance of antiTat aptamers both for the spectroscopic ellipsometry (SE) and for the surface plasmon resonance enhanced total internal reflection ellipsometry (SPReTIRE), first time. Detection limits for antiTat aptamers with various configurations were in the range of nM-pM protein in the buffer solution. For instance, SPRe-TIRE configuration revealed a detection limit of 1 pM (or about 1.5 pg/mL) for HIV-Tat protein in the range of 1.0-500 nM.

An in-tube aptamer/gold nanoparticles coated capillary solid-phase microextraction for separation of adenosine in serum and urine samples

As an endogenous nucleoside, adenosine was significant for the diagnosis and treatment of some diseases, such as schizophrenia. However, due to the complicated matrix interference, it was difficult to monitor trace or ultra-trace adenosine directly in bio-samples. In this contribution, a novel in-tube SPME technique based on aptamer/Au nanoparticles coated open tubular fused-silica capillary was established to separate and enrich adenosine in bio-samples with high affinity. Therefore, a uniform and dense AuNPs layer was coated on the inner surface of the open tubular capillary, and then adenosine aptamer was immobilized on AuNPs with a high capacity of 2.44 μg per 27-cm capillary. As a result, the capillary shown high selectivity to adenosine with a selectivity factor of 14.4 when compared with the scrambled aptamer/AuNPs coated capillary. Also, the extraction amount of adenosine was 2.8-24.8 times higher than those of its structural analogs and contrast, such as guanosine, uridine, cytidine, thymidine, and toluic acid. After the optimization of extraction conditions, the aptamer/AuNPs coated in-tube SPME-HPLC method was developed for the adenosine assay with the linear range of 0.002-0.100 μg mL^-1 and the detection limit of 0.45 ng mL^-1. Subsequently, the approach was applied for trace adenosine monitoring in human serum and urine samples. It showed a strong performance of reducing matrix interference and improving sensitivity, and the spiking recoveries of 89.9-92.6% and 91.1-94.5% were achieved respectively.

HIV biosensors for early diagnosis of infection: The intertwine of nanotechnology with sensing strategies

Human immunodeficiency virus (HIV) is a lentivirus that leads to acquired immunodeficiency syndrome (AIDS). With increasing awareness of AIDS emerging as a global public health threat, different HIV testing kits have been developed to detect antibodies (Ab) directed toward different parts of HIV. A great limitation of these tests is that they can not detect HIV antibodies during early virus infection. Therefore, to overcome this challenge, a wide range of biosensors have been developed for early diagnosis of HIV infection. A significant amount of these studies have been focused on the application of nanomaterials for improving the sensitivity and accuracy of the sensing methods. Following an introduction into this field, a first section of this review covers the synthesis and applicability of such nanomaterials as metal nanoparticles (NPs), quantum dots (QDs), carbon-based nanomaterials and metal nanoclusters (NCs). A second larger section covers the latest developments concerning nanomaterial-based biosensors for HIV diagnosis, with paying a special attention to the determination of CD4⁺ cells as a hall mark of HIV infection, HIV gene, HIV p24 core protein, HIV p17 peptide, HIV-1 virus-like particles (VLPs) and HIV related enzymes, particularly those that are passed on from the virus to the CD⁴⁺ T lymphocytes and are necessary for viral reproduction within the host cell. These studies are described in detail along with their diverse principles/mechanisms (e.g. electrochemistry, fluorescence, electromagnetic-piezoelectric, surface plasmon resonance (SPR), surface enhanced Raman spectroscopy (SERS) and colorimetry). Despite the significant progress in HIV biosensing in the last years, there is a great need for the development of point-of-care (POC) technologies which are affordable, robust, easy to use, portable, and possessing sufficient quantitative accuracy to enable clinical decision making. In the final section, the focus is on the portable sensing devices as a new standard of POC and personalized diagnostics.

Application of Aptamers in Virus Detection and Antiviral Therapy

Viral infections can cause serious diseases for humans and animals. Accurate and early detection of viruses is often crucial for clinical diagnosis and therapy. Aptamers are mostly single-stranded nucleotide sequences that are artificially synthesized by an in vitro technology known as the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Similar to antibodies, aptamers bind specifically to their targets. However, compared with antibody, aptamers are easy to synthesize and modify and can bind to a broad range of targets. Thus, aptamers are promising for detecting viruses and treating viral infections. In this review, we briefly introduce aptamer-based biosensors (aptasensors) and describe their applications in rapid detection of viruses and as antiviral agents in treating infections. We summarize available data about the use of aptamers to detect and inhibit viruses. Furthermore, for the first time, we list aptamers specific to different viruses that have been screened out but have not yet been used for detecting viruses or treating viral infections. Finally, we analyze barriers and developing perspectives in the application of aptamer-based virus detection and therapeutics.

High-performance interactive analysis of split aptamer and HIV-1 Tat on multiwall carbon nanotube-modified field-effect transistor

Interaction between split RNA aptamer and the clinically important target, HIV-1 Tat was investigated on a biosensing surface transduced by functionally choreographed multiwall carbon nanotubes (MWCNTs). Acid oxidation was performed to functionalize MWCNTs with carboxyl functional groups. X-ray photoelectron spectroscopy analysis had profound ~2.91% increment in overall oxygen group and ~1% increment was noticed with a specific carboxyl content owing to CO and OCO bonding. The interaction between split RNA aptamer and HIV-1 Tat protein was quantified by electrical measurements with the current signal (I_ds) over a gate voltage (V_gs). Initially, 34.4 mV gate voltage shift was observed by the immobilization of aptamer on MWCNT. With aptamer and HIV-1 Tat interaction, the current flow was decreased with the concomitant gate voltage shift of 23.5 mV. The attainment of sensitivity with split aptamer and HIV-1 Tat interaction on the fabricated device was 600 pM. To ensure the genuine interaction of aptamer with HIV-1 Tat, other HIV-1 proteins, Nef and p24 were interacted with aptamer and they displayed the negligible interferences with gate voltage shift of 3.5 mV and 5.7 mV, which shows 4 and 2.5 folds lesser than HIV-1 Tat interaction, respectively.

Immunomagnetic antibody plus aptamer pseudo-DNA nanocatenane followed by rolling circle amplication for highly-sensitive CTC detection

Biosensing and detecting the rare circulating tumor cells (CTCs) in complex blood samples are a great challenge but necessary for cancer metastasis prevention. Here we show a novel highly-sensitive biosensing system for detecting CTCs in whole blood. The system is composed of Her2-coated immunomagnetic beads and an anti-EpCAM aptamer assembled pseudo-DNA nanocatenane (PDN) for dual targeting and separating CTCs, in conjunction with the rolling circle amplification (RCA) and molecular beacon (MB) system for CTCs signal amplification. The Her-2-coated beads separated CTCs from blood after their elution from a magnetic column. The unique PDN, which is a tailor-designed self-assembly of three circular DNAs that are inter-locked with independent and non-interfered templates for periodic RCA process, binds EpCAM-rich CTCs. In the presence of the RCA primer, phi29 DNA polymerase and MB, the system collaboratively generated the amplified fluorescent signals for highly-sensitive detection of CTCs. Through this system, we achieved the limit of detection less than 10 CTCs/mL blood, and quantified the number of CTCs in patient blood, which is proportional to the patient cancer status. Our technique is highly-sensitive, practicable and convenient enough for clinical detection of breast CTCs.

Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases

The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.

Thrombin Assessment on Nanostructured Label-Free Aptamer-Based Sensors: A Mapping Investigation via Surface-Enhanced Raman Spectroscopy

Aptamers, synthetic single-stranded DNA or RNA molecules, can be regarded as a valuable improvement to develop novel ad hoc sensors to diagnose several clinical pathologies. Their intrinsic potential is related to the high specificity and sensitivity to the selected target biomarkers, being capable of detecting very low concentrations and thus allowing an early diagnosis of a possible disease. This kind of probe can be usefully integrated into a number of different devices in order to provide a reliable acquisition of the analyte and properly elaborate the related signal. The study presents the fabrication and characterization of a label-free aptamer sensor designed using a gold-coated silicon nanostructured substrate to map the target molecule by means of surface-enhanced Raman spectroscopy (SERS). As a proof, thrombin was used as a model at four different concentrations (i.e., 0.0873, 0.873, 8.73, and 87.3 nM). SERS mapping analysis was carried out considering each representative band of the aptamer-thrombin complex (centered at 822, 1140, and 1558 cm⁻¹) and then combining them in order to acquire a comprehensive and unambiguous measure of the target. In both cases, a valuable correlation was evaluated, even if the first approach can suffer from some limitations in the third band related to lower definition of the characteristic peak compared to those in the other two bands.

Aptamers in HIV research diagnosis and therapy

Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range. Stable and nontoxic aptamers could be selected for a wide range of ligands including small molecules to large proteins. Aptamers have shown tremendous potential and have found multipurpose application in the field of therapeutic, diagnostic, biosensor and bio-imaging. While their mechanism of action can be similar to that of monoclonal antibodies, aptamers provide additional advantages in terms of production cost, simpler regulatory approval and lower immunogenicity as they are synthesized chemically. Human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), which causes significant morbidity and mortality with a significant consequent decrease in the quality of patient's lives. While cART has led to good viral control, people living with HIV now suffer from non-HIV comorbidities due to viral protein expression that cannot be controlled by cART. Hence pathophysiological mechanisms that govern these comorbidities with a focus on therapies that neutralize these HIV effects gained increased attention. Recent advances in HIV/AIDS research have identified several molecular targets and for the development of therapeutic and diagnostic using aptamers against HIV/AIDS. This review presents recent advances in aptamers technology for potential application in HIV diagnostics and therapeutics towards improving the quality of life of people living with HIV.

Ready-to-use protein G-conjugated gold nanorods for biosensing and biomedical applications

BACKGROUND

Gold nanorods (GNRs) display unique capacity to absorb and scatter near infrared light, which arises from their peculiar composition of surface plasmon resonances. For this reason, GNRs have become an innovative material of great hope in nanomedicine, in particular for imaging and therapy of cancer, as well as in photonic sensing of biological agents and toxic compounds for e.g. biomedical diagnostics, forensic analysis and environmental monitoring. As the use of GNRs is becoming more and more popular, in all these contexts, there is emerging a latent need for simple and versatile protocols for their modification with targeting units that may convey high specificity for any analyte of interest of an end-user.

RESULTS

We introduce protein G-coated GNRs as a versatile solution for the oriented immobilization of antibodies in a single step of mixing. We assess this strategy against more standard covalent binding of antibodies, in terms of biocompatibility and efficiency of molecular recognition in buffer, serum and plasma, in the context of the development of a direct immunoenzymatic assay. In both cases, we estimate an average of around 30 events of molecular recognition per particle. In addition, we disclose a convenient protocol to store these particles for months in a freezer, without any detrimental effect.

CONCLUSIONS

The biocompatibility and efficiency of molecular recognition is similar in either case of GNRs that are modified with antibodies by covalent binding or oriented immobilization through protein G. However, protein G-coated GNRs are most attractive for an end-user, owing to their unique versatility and ease of bioconjugation with antibodies of her/his choice.

Streptavidin Modified ZnO Film Bulk Acoustic Resonator for Detection of Tumor Marker Mucin 1

A ZnO-based film bulk acoustic resonator has been fabricated using a magnetron sputtering technology, which was employed as a biosensor for detection of mucin 1. The resonant frequency of the thin-film bulk acoustic resonator was located near at 1503.3 MHz. The average electromechanical coupling factor [Formula: see text] and quality factor Q were 2.39 % and 224, respectively. Using the specific binding system of avidin-biotin, the streptavidin was self-assembled on the top gold electrode as the sensitive layer to indirectly test the MUC1 molecules. The resonant frequency of the biosensor decreases in response to the mass loading in range of 20-500 nM. The sensor modified with the streptavidin exhibits a high sensitivity of 4642.6 Hz/nM and a good selectivity.

A G-quadruplex-selective luminescent iridium(III) complex and its application by long lifetime

BACKGROUND

The G-quadruplex motif has been widely used for the construction of analytical detection platforms due to its rich structural polymorphism and flexibility. Luminescent assays are often limited due to the interference from endogenous fluorophores in biological samples.

METHODS

To address this challenge, a novel long lifetime iridium(III) complex 1 was synthesized and used to construct a G-quadruplex-based assay for detecting prostate specific antigen (PSA) in aqueous solution. PSA is a common biomarker in serum and used as a model for demonstration in this work.

RESULTS

The PSA assay has achieved a detection limit of 40.8pg·mL^-1, and shows high selectivity towards PSA over other proteins. Additionally, the assay could function in diluted human serum by using time-resolved luminescent spectroscopy, with good linearity from 1 to 10ng·mL^-1 of PSA, which is adequate to detect the PSA levels for physiological (<4ng·mL^-1) and clinical (4-10ng·mL^-1) applications.

CONCLUSIONS

The assay was successfully constructed. As revealed from time-resolved method, the long lifetime property of iridium(III) complex 1 plays an important role in distinguishing phosphorescence signals from short-life auto-fluorescence of human serum.

GENERAL SIGNIFICANCE

Luminescent transition metal complexes offer several advantages over other widely used organic fluorophores, such as long phosphorescence lifetime, large Stokes shift and modular syntheses. In addition, the assay could work effectively in diluted human serum using time-resolved luminescent spectroscopy, it therefore could be potentially developed to monitor PSA in biological samples. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

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).

Luminescence switch-on assay of interferon-gamma using a G-quadruplex-selective iridium(III) complex

In this study, we synthesized a series of 9 luminescent iridium(III) complexes and studied their ability to function as luminescent probes for G-quadruplex DNA. The iridium(III) complex 8 [Ir(pbtz)2(dtbpy)]PF6 (where pbtz = 2-phenylbenzo[d]thiazole; dtbpy = 4,4'-di-tert-butyl-2,2'-bipyridine) showed high selectivity for G-quadruplex DNA over single-stranded and double-stranded DNA, and was subsequently utilized for the development of a label-free oligonucleotide-based assay for interferon-gamma (IFN-γ), an important biomarker for a range of immune and infectious diseases, in aqueous solution. We further demonstrated that this assay could monitor IFN-γ levels even in the presence of cellular debris. This assay represents the first G-quadruplex-based assay for IFN-γ detection described in the literature.

Aptamers in analytics

Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.

Label-free and sensitive aptasensor based on dendritic gold nanostructures on functionalized SBA-15 for determination of chloramphenicol

A highly sensitive and low-cost electrochemical aptasensor was developed for the determination of chloramphenicol (CAP). The system was based on a CAP-binding aptamer, a molecular recognition element, and 1,4-diazabicyclo[2.2.2]octane (DABCO)-supported mesoporous silica SBA-15 on the surface of a screen-printed graphite electrode for formation of dendritic gold nanostructures and improving the performance and conductivity of the biosensor. Hemin has been applied as an electrochemical indicator which interacted with the guanine bases of the aptamer. In the absence of CAP, hemin binds to the aptamer and produces a weak differential pulse voltammetric (DPV) signal. The presence of CAP led to stabilization of the folded aptamer, which generated an amplified DPV signal. The peak current of hemin increased linearly with the concentration of CAP. Under optimal conditions, two linear ranges were obtained from 0.03 to 0.15 μM and 0.15 to 7.0 μM, respectively, and the detection limit was 4.0 nM. The prepared biosensor has good selectivity against other non-target drugs. Thus, the sensor could provide a promising platform for the fabrication of aptasensors. The feasibility of using this aptasensor was demonstrated by determination of CAP in a human blood serum sample.

HIV-1 Tat biosensor: Current development and trends for early detection strategies

Human immunodeficiency virus (HIV) has infected almost 35 million people worldwide. Various tests have been developed to detect the presence of HIV during the early stages of the disease in order to reduce the risk of transmission to other humans. The HIV-1 Tat protein is one of the proteins present in HIV that are released abundantly approximately 2-4 weeks after infection. In this review, we have outlined various strategies for detecting the Tat protein, which helps transcribe the virus and enhances replication. Detection strategies presented include immunoassays, biosensors and gene expression, which utilize antibodies or aptamers as common probes to sense the presence of Tat. Alternatively, measuring the levels of gene transcription is a direct method of analysing the HIV gene to confirm the presence of Tat. By detection of the Tat protein, virus transmission can be detected in high-risk individuals in the early stages of the disease to reduce the risk of an HIV pandemic.

Aptasensors for viral diagnostics

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We discuss progress in aptamer-based detection of viruses.

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We consider the use of aptasensors for point-of-care diagnostics of viruses.

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Aptamers have distinct advantages over antibodies for virus recognition.

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There is strong demand for multiplexed diagnostic measurement of pathogens.

Novel viral diagnostic tools need to be affordable, fast, accurate and easy to use with sensitivity and specificity equivalent or superior to current standards. At present, viral diagnostics are based on direct detection of viral components or indirect detection by measuring antibodies generated in response to viral infection. While sensitivity of detection and quantification are still important challenges, we expect major advances from new assay formats and synthetic binding molecules, such as aptamers. Compared to traditional antibody-based detection, aptamers could provide faster adaptation to continuously evolving virus strains and higher discriminating capacity between specific virus serotypes. Aptamers are very stable and easily modifiable, so are ideal molecules for detection and chemical sensing applications. Here, we review the use of aptasensors for detection of viral pathogens and consider the feasibility of aptasensors to become standard devices for point-of-care diagnostics of viruses.

Deploying aptameric sensing technology for rapid pandemic monitoring

The genome of virulent strains may possess the ability to mutate by means of antigenic shift and/or antigenic drift as well as being resistant to antibiotics with time. The outbreak and spread of these virulent diseases including avian influenza (H1N1), severe acute respiratory syndrome (SARS-Corona virus), cholera (Vibrio cholera), tuberculosis (Mycobacterium tuberculosis), Ebola hemorrhagic fever (Ebola Virus) and AIDS (HIV-1) necessitate urgent attention to develop diagnostic protocols and assays for rapid detection and screening. Rapid and accurate detection of first cases with certainty will contribute significantly in preventing disease transmission and escalation to pandemic levels. As a result, there is a need to develop technologies that can meet the heavy demand of an all-embedded, inexpensive, specific and fast biosensing for the detection and screening of pathogens in active or latent forms to offer quick diagnosis and early treatments in order to avoid disease aggravation and unnecessary late treatment costs. Nucleic acid aptamers are short, single-stranded RNA or DNA sequences that can selectively bind to specific cellular and biomolecular targets. Aptamers, as new-age bioaffinity probes, have the necessary biophysical characteristics for improved pathogen detection. This article seeks to review global pandemic situations in relation to advances in pathogen detection systems. It particularly discusses aptameric biosensing and establishes application opportunities for effective pandemic monitoring. Insights into the application of continuous polymeric supports as the synthetic base for aptamer coupling to provide the needed convective mass transport for rapid screening is also presented.

An electrochemical molecular recognition-based aptasensor for multiple protein detection

This article reports a simple electrochemical approach for the detection of multiple proteins (thrombin and lysozyme) using Dabcyl-labeled aptamer modified metal nanoparticles (DLAPs). DLAPs were immobilized on β-cyclodextrins (β-CDs) modified electrode by means of host-guest self-assembly. During the time of detection, the aptamers' structure will change due to the specific binding with corresponding proteins that forced DLAPs far away from the electrode that had been modified by β-CDs. Thus, the capture of target proteins onto DLAPs was translated via the electrochemical current signal offered by metal nanoparticles. Linearity of the aptasensor for quantitative measurements was demonstrated. Determinations of proteins in human real serum samples were also performed to demonstrate detection in real clinical samples.

Aptamers against pathogenic microorganisms

An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.

A review on immobilised aptamers for high throughput biomolecular detection and screening

The discovery of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has led to the generation of aptamers from libraries of nucleic acids. Concomitantly, aptamer-target recognition and its potential biomedical applications have become a major research endeavour. Aptamers possess unique properties that make them superior biological receptors to antibodies with a plethora of target molecules. Some specific areas of opportunities explored for aptamer-target interactions include biochemical analysis, cell signalling and targeting, biomolecular purification processes, pathogen detection and, clinical diagnosis and therapy. Most of these potential applications rely on the effective immobilisation of aptamers on support systems to probe target species. Hence, recent research focus is geared towards immobilising aptamers as oligosorbents for biodetection and bioscreening. This article seeks to review advances in immobilised aptameric binding with associated successful milestones and respective limitations. A proposal for high throughput bioscreening using continuous polymeric adsorbents is also presented.