An integrated microfluidic platform to perform uninterrupted SELEX cycles to screen affinity reagents specific to cardiovascular biomarkers

Design and application of microfluidics in aptamer SELEX and Aptasensors

Aptamers are excellent recognition molecules obtained from systematic evolution of ligands by exponential enrichment (SELEX) that have been extensively researched for constructing aptasensors. However, in the process from SELEX screening to the construction of aptasensors, there are many disadvantages, such as tedious and repetitive operations, interference from external factors, and low efficiency, which seriously limits their application scope and development. Introducing the microfluidic technology can realize the automation and intelligence of SELEX and aptasensing, improve the efficiency of SELEX, and enhance the detection performance and convenience of aptasensing. Hence, in this review, first the characteristics of various chips based on different driving forces are described. And then summarizing the design of microfluidic devices based on different SELEX methods and showing the strategies of microfluidic aptasensors based on different detection modes. Finally, discussing the difficulties and challenges encountered when microfluidic is integrated with the aptamer SELEX and the aptasensors.

Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review

In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.

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.

The molecular interaction of six single-stranded DNA aptamers to cardiac troponin I revealed by docking and molecular dynamics simulation

Cardiac troponin I (cTnI) is a cardiac biomarker for diagnosing ischemic heart disease and acute myocardial infarction. Current biochemical assays use antibodies (Abs) due to their high specificity and sensitivity. However, there are some limitations, such as the high-cost production of Abs due to complex instruments, reagents, and steps; the variability of Abs quality from batch to batch; the low stability at high temperatures; and the difficulty of chemical modification. Aptamer overcomes the limitations of antibodies, such as relatively lower cost, high reproducibility, high stability, and ease of being chemically modified. Aptamers are three-dimensional architectures of single-stranded RNA or DNA that bind to targets such as proteins. Six aptamers (Tro1-Tro6) with higher binding affinity than an antibody have been identified, but the molecular interaction has not been studied. In this study, six DNA aptamers were modeled and docked to cTnI protein. Molecular docking revealed that the interaction between all aptamer and cTnI happened in the similar cTnI region. The interaction between aptamer and cTnI involved hydrophobic interaction, hydrogen bonds, π-cation interactions, π-stack interactions, and salt-bridge formation. The calculated binding energy of all complexes was negative, which means that the complex formation was thermodynamically favorable. The electrostatic energy term was the main driving force of the interaction between all aptamer and cTnI. This study could be used to predict the behavior of further modified aptamer to improve aptamer performance.

Advancing the Diagnosis of Periprosthetic Joint Infections: Integrated Microfluidic Platform for Alpha-Defensins-Specific Aptamer Selection and Its Analytical Applications

Periprosthetic joint infections (PJIs) pose a significant challenge in orthopedic surgery, particularly total joint arthroplasty (TJA), due to the potential for implant failure and increased patient morbidity. Early and accurate detection of PJIs is crucial for timely intervention and better patient prognosis. Herein, we successfully screened a high-affinity aptamer targeting alpha-defensin complex human neutrophil protein 1-3 (HNP 1-3; potential PJI biomarkers in synovial fluid [SF]) for the first time using systematic evolution of ligands by exponential enrichment (SELEX) on an integrated microfluidic platform. The compact microfluidic device enabled efficient screening, with each round completed within <2 h, comprising five rounds of positive selection, two rounds of negative selection, and one round of competitive selection. A novel one-aptamer-one-antibody assay was further developed from the optimal aptamer screened, and it could accurately quantify HNP 1-3 in SF within 3 h with only ∼50 μL of SF. The assay demonstrated strong binding affinity and specificity for the target protein in SF. Thirteen PJI SF samples were accurately diagnosed and the assay was accurate over a wide dynamic range (0.32-100 mg/L). This study has showcased a rapid and accurate diagnostic tool for PJI detection, which should see widespread use in the clinic, holding promise for potential analytical applications in orthopedic surgery and improving patient care.

Comparative Study of Field-Effect Transistors Based on Graphene Oxide and CVD Graphene in Highly Sensitive NT-proBNP Aptasensors

Graphene-based materials are actively being investigated as sensing elements for the detection of different analytes. Both graphene grown by chemical vapor deposition (CVD) and graphene oxide (GO) produced by the modified Hummers' method are actively used in the development of biosensors. The production costs of CVD graphene- and GO-based sensors are similar; however, the question remains regarding the most efficient graphene-based material for the construction of point-of-care diagnostic devices. To this end, in this work, we compare CVD graphene aptasensors with the aptasensors based on reduced GO (rGO) for their capabilities in the detection of NT-proBNP, which serves as the gold standard biomarker for heart failure. Both types of aptasensors were developed using commercial gold interdigitated electrodes (IDEs) with either CVD graphene or GO formed on top as a channel of liquid-gated field-effect transistor (FET), yielding GFET and rGO-FET sensors, respectively. The functional properties of the two types of aptasensors were compared. Both demonstrate good dynamic range from 10 fg/mL to 100 pg/mL. The limit of detection for NT-proBNP in artificial saliva was 100 fg/mL and 1 pg/mL for rGO-FET- and GFET-based aptasensors, respectively. While CVD GFET demonstrates less variations in parameters, higher sensitivity was demonstrated by the rGO-FET due to its higher roughness and larger bandgap. The demonstrated low cost and scalability of technology for both types of graphene-based aptasensors may be applicable for the development of different graphene-based biosensors for rapid, stable, on-site, and highly sensitive detection of diverse biochemical markers.

Actuation for flexible and stretchable microdevices

Flexible and stretchable microdevices incorporate highly deformable structures, facilitating precise functionality at the micro- and millimetre scale. Flexible microdevices have showcased extensive utility in the fields of biomedicine, microfluidics, and soft robotics. Actuation plays a critical role in transforming energy between different forms, ensuring the effective operation of devices. However, when it comes to actuating flexible microdevices at the small millimetre or even microscale, translating actuation mechanisms from conventional rigid large-scale devices is not straightforward. The recent development of actuation mechanisms leverages the benefits of device flexibility, particularly in transforming conventional actuation concepts into more efficient approaches for flexible devices. Despite many reviews on soft robotics, flexible electronics, and flexible microfluidics, a specific and systematic review of the actuation mechanisms for flexible and stretchable microdevices is still lacking. Therefore, the present review aims to address this gap by providing a comprehensive overview of state-of-the-art actuation mechanisms for flexible and stretchable microdevices. We elaborate on the different actuation mechanisms based on fluid pressure, electric, magnetic, mechanical, and chemical sources, thoroughly examining and comparing the structure designs, characteristics, performance, advantages, and drawbacks of these diverse actuation mechanisms. Furthermore, the review explores the pivotal role of materials and fabrication techniques in the development of flexible and stretchable microdevices. Finally, we summarise the applications of these devices in biomedicine and soft robotics and provide perspectives on current and future research.

A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules

This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.

A self-driven, microfluidic, integrated-circuit biosensing chip for detecting four cardiovascular disease biomarkers

Cardiovascular diseases (CVDs) claimed the lives of nearly 21 million people worldwide in 2021, accounting for 30% of global deaths. However, one in five CVD patients is unaware that they have the disease, emphasizing the need for accurate biomarker monitoring. Herein we developed an integrated microfluidic system (IMS) for rapid quantification of four CVD biomarkers, including N-terminal pro B-type natriuretic peptide (NT-proBNP), fibrinogen, cardiac troponin I (cTnI), and C-reactive protein (CRP)- via aptamer-coated interdigitated electrodes (IDE) with integrated circuits (IC) and a self-driven IMS for sample treatment. The device was composed of plasma filtration, metering, and fluidic delay modules, and the former could extract 45% of plasma from a 20-μL blood sample; the metering module could quantify 5 μL of plasma within 90 s. Subsequently, the plasma was transported to a detection chamber, where IC-based IDE sensors made measurements within 5 min. The entire 15-min process allowed us to evaluate biomarkers across a wide dynamic range: NT-proBNP (0.1-10,000 pg/mL), fibrinogen (50-1,000 mg/dL), cTnI (0.1-10,000 pg/mL), and CRP (0.5-9 mg/L). Given that spiked blood samples were measured with reasonable accuracy (>80%), the IMS could see utility in CVD risk assessment and personalized medicine.

An integrated microfluidic system for automatic detection of cholangiocarcinoma cells from bile

Cholangiocarcinoma (CCA) is an aggressive cancer that originates from the epithelial cells lining the bile ducts. Due to its location deep within the body and nonspecific symptoms in the early stages, it is often diagnosed at the advanced stage, thus leading to worse prognosis. Circulating tumor cells within liquid biopsies (i.e. blood) have been considered as promising biomarkers for CCA diagnosis, though current methods for profiling them are not satisfactory in terms of sensitivity and specificity. Herein we developed a new cancer cell probing and immuno-tracking assay known as "CAPTURE", which was performed on an integrated microfluidic system (IMS) to automate CCA diagnosis from bile with a sample amount of only 1 mL. The assay utilized magnetic beads surface-coated with two affinity reagents, a nucleic acid aptamer (HN16) and a glycosaminoglycan (SCH 45-mix), for capturing cancer cells in bile; the "gold standard" anti-epithelial cell adhesion molecule was used as a comparison. In a single-blind test of 54 CCA-positive (+) and 102 CCA-negative (-) clinical samples, sensitivities and specificities of 96 and 80%, respectively, were documented with the CAPTURE assay on-bench. An IMS composed of a centrifugal module for sample pretreatment and a CAPTURE module for cell capture and staining was integrated with a new "vertical integration module" for detecting cancer cells from bile without human intervention. Furthermore, a novel micro-tier structure within the centrifugal module was designed to block passage of gallbladder stones with diameters >1 mm, thereby preventing their interference during the subsequent CAPTURE assay. Improved sensitivity and specificity (100 & 83%, respectively) by using three affinity reagents were achieved on the IMS when using 26 clinical bile samples, confirming its clinical bio-applicability for CCA diagnosis. This approach could be therefore used for early-stage CCA diagnostics, ideally enabling effective treatment, as well as reducing potential for relapse.

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.

A paper-based aptamer-sandwich assay for detection of HNP 1 as a biomarker for periprosthetic joint infections on an integrated microfluidic platform

BACKGROUND

Total joint arthroplasty (TJA) has significantly improved the quality of life for millions suffering from end-stage arthritis. However, periprosthetic joint infections (PJI) remain a serious complication, necessitating extensive interventions and prolonged antimicrobial treatments. The aging population is expected to lead to a rise in TJA cases, subsequently increasing the incidence of PJI, particularly in the elderly who face higher mortality rates. Current diagnostic methods for suspected PJI, such as radiographs and biochemical markers like CRP and ESR, exhibit limited sensitivity. Therefore, there is a critical need for a specific synovial fluid biomarker assay to enhance PJI diagnosis using specific SF-based assay.

RESULTS

This study introduces a novel microfluidic chip with a paper-based aptamer-sandwich assay for the quantitative detection of HNP 1, a crucial PJI biomarker, in synovial fluid. The assay leverages the advantages of aptamers over antibodies, demonstrating high selectivity and affinity for target molecules. The integration of a nitrocellulose (NC) membrane onto the microfluidic platform represents a significant advancement, reducing background signals and simplifying the assay procedure without intricate procedure and pre-treatment. The NC membrane-based microfluidic device offers rapid, cost-effective, and highly sensitive detection of HNP 1, with a limit of detection of 0.5 mg L-1. The microfluidic device demonstrates exceptional performance, detecting up to four clinical samples in approximately 42 min on a single chip with 100 % accuracy, as confirmed by analysis of 12 clinical samples and comparison with "gold-standard". Moreover, the assay exhibits a wide dynamic range of 0.5-100 mg L-1, underscoring its potential as a powerful tool for PJI diagnosis in clinical settings.

SIGNIFICANCE

This work introduces a paper-based microfluidic system tailored for rapid HNP 1 detection using synovial fluid near joint region (and not serum via blood) for better diagnosis. The innovative paper-based aptamer-sandwich assay yields results within 42-min. Significantly, it boasts a wide dynamic range, detecting levels from an impressive 0.5 mg L-1, crucial in the 2.6 mg L-1 threshold region. This heightened sensitivity and expansive detection capability establish our assay as a leader in PJI diagnostics, promising unmatched precision and efficiency in clinical applications.

Highly-specific aptamer targeting SARS-CoV-2 S1 protein screened on an automatic integrated microfluidic system for COVID-19 diagnosis

Variants of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) have evolved such that it may be challenging for diagnosis and clinical treatment of the pandemic coronavirus disease-19 (COVID-19). Compared with developed SARS-CoV-2 diagnostic tools recently, aptamers may exhibit some advantages, including high specificity/affinity, longer shelf life (vs. antibodies), and could be easily prepared. Herein an integrated microfluidic system was developed to automatically carry out one novel screening process based on the systematic evolution of ligands by exponential enrichment (SELEX) for screening aptamers specific with SARS-CoV-2. The new screening process started with five rounds of positive selection (with the S1 protein of SARS-CoV-2). In addition, including non-target viruses (influenza A and B), human respiratory tract-related cancer cells (adenocarcinoma human alveolar basal epithelial cells and dysplastic oral keratinocytes), and upper respiratory tract-related infectious bacteria (including methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae), and human saliva were involved to increase the specificity of the screened aptamer during the negative selection. Totally, all 10 rounds could be completed within 20 h. The dissociation constant of the selected aptamer was determined to be 63.0 nM with S1 protein. Limits of detection for Wuhan and Omicron clinical strains were found to be satisfactory for clinical applications (i.e. 4.80 × 10¹ and 1.95 × 10² copies/mL, respectively). Moreover, the developed aptamer was verified to be capable of capturing inactivated SARS-CoV-2 viruses, eight SARS-CoV-2 pseudo-viruses, and clinical isolates of SARS-CoV-2 viruses. For high-variable emerging viruses, this developed integrated microfluidic system can be used to rapidly select highly-specific aptamers based on the novel SELEX methods to deal with infectious diseases in the future.

Tools and techniques for the discovery of therapeutic aptamers: recent advances

INTRODUCTION

The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers.

AREAS COVERED

The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility.

EXPERT OPINION

The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.

Aptamer-Based Point-of-Care Devices: Emerging Technologies and Integration of Computational Methods

Recent innovations in point-of-care (POC) diagnostic technologies have paved a critical road for the improved application of biomedicine through the deployment of accurate and affordable programs into resource-scarce settings. The utilization of antibodies as a bio-recognition element in POC devices is currently limited due to obstacles associated with cost and production, impeding its widespread adoption. One promising alternative, on the other hand, is aptamer integration, i.e., short sequences of single-stranded DNA and RNA structures. The advantageous properties of these molecules are as follows: small molecular size, amenability to chemical modification, low- or nonimmunogenic characteristics, and their reproducibility within a short generation time. The utilization of these aforementioned features is critical in developing sensitive and portable POC systems. Furthermore, the deficiencies related to past experimental efforts to improve biosensor schematics, including the design of biorecognition elements, can be tackled with the integration of computational tools. These complementary tools enable the prediction of the reliability and functionality of the molecular structure of aptamers. In this review, we have overviewed the usage of aptamers in the development of novel and portable POC devices, in addition to highlighting the insights that simulations and other computational methods can provide into the use of aptamer modeling for POC integration.

Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations

Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.

One-step impedimetric NT-proBNP aptasensor targeting cardiac insufficiency in artificial saliva

Currently, sensitive and accurate approaches for diagnosis, rapid assessment, and cardiac biomarker monitoring in patients with heart failure are needed. In this context, the advantages of aptamers over traditional antibodies have been employed to fabricate a single-step impedimetric N-terminal pro b-type natriuretic peptide (NT-proBNP)-modified gold microelectrode array. The development of an electrochemical aptasensing platform was based on the coimmobilization of alkanethiol self-assembled monolayers and amine-terminated aptamer that specifically recognized cardiac NT-proBNP protein resulting in charge electron transfer. Electroimpedimetric signals of the sensor were observed to be linear to the NT-proBNP concentrations in the range of 5.0 × 10^-3 to 1.0 pg mL^-1 (R² = 0.9624), while achieving a low detection limit of 5.0 × 10^-3 pg mL^-1. Clinically relevant detection levels for NT-proBNP were achieved in a simple, rapid, and label-free measurement using artificial saliva, which was highlighted to be specific, regenerative, and selective over potential interferers occurring during the processes of cardiac insufficiency, Therefore, the novel NT-proBNP aptasensor is a promising point-of-care tool exhibiting safe, non-invasive, affordable, and non-prescription home use accessible to overcome the limitations associated with conventional ELISA and previous aptasensing.

Electrochemical DNAzyme-based biosensors for disease diagnosis

DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.

A comparative study of aptamer isolation by conventional and microfluidic strategies

Aptamers are single-stranded oligonucleotide molecules that bind with high affinity and specificity to a wide range of target molecules. The method of systematic evolution of ligands by exponential enrichment (SELEX) plays an essential role in the isolation of aptamers from a randomized oligonucleotide library. To date, significant modifications and improvements of the SELEX process have been achieved, engendering various forms of SELEX from conventional SELEX to microfluidics-based full-chip SELEX. While full-chip SELEX is generally considered advantageous over conventional SELEX, there has not yet been a conclusive comparison between the methods. Herein, we present a comparative study of three SELEX strategies for aptamer isolation, including those using conventional agarose bead-based partitioning, microfluidic affinity selection, and fully integrated microfluidic affinity selection and PCR amplification. Using immunoglobulin E (IgE) as a model target molecule, we compare these strategies in terms of the time and cost for each step of the SELEX process including affinity selection, amplification, and oligonucleotide conditioning. Target-binding oligonucleotides in the enriched pools are sequenced and compared to assess the relative efficacy of the SELEX strategies. We show that the microfluidic strategies are more time- and cost-efficient than conventional SELEX.

Aptamer-based Emerging Tools for Viral Biomarker Detection: A Focus on SARS-CoV-2

Viral infections can cause fatal illnesses to humans as well as animals. Early detection of viruses is therefore crucial to provide effective treatment to patients. Recently, the Covid-19 pandemic has undoubtedly given an alarming call to develop rapid and sensitive detection platforms. The viral diagnostic tools need to be fast, affordable, and easy to operate with high sensitivity and specificity equivalent or superior to the currently used diagnostic methods. The present detection methods include direct detection of viral antigens or measuring the response of antibodies to viral infections. However, the sensitivity and quantification of the virus are still a significant challenge. Detection tools employing synthetic binding molecules like aptamers may provide several advantages over the conventional methods that use antibodies in the assay format. Aptamers are highly stable and tailorable molecules and are therefore ideal for detection and chemical sensing applications. This review article discusses various advances made in aptamer-based viral detection platforms, including electrochemical, optical, and colorimetric methods to detect viruses, specifically SARS-Cov-2. Considering the several advantages, aptamers could be game-changing in designing high-throughput biosensors for viruses and other biomedical applications in the future.

Microfluidic isolation of aptamers with affinity towards multiple myeloma monoclonal immunoglobulins

Multiple myeloma (MM) is a bone marrow cancer of resident plasma cells that affects 125,000 patients in the U.S. with about 30,000 new cases per year. Its signature is the clonal proliferation of a single plasma cell that secretes a patient specific monoclonal immunoglobulin (M-Ig). Targeting the M-Ig in patient serum could allow sensitive and noninvasive identification of minimal residual disease in multiple myeloma. Aptamers, which are single-stranded oligonucleotides with affinity and specificity to a target molecule, have recently been introduced as affinity reagents for recognition of MM M-Igs. Here we exploit microfluidic SELEX technology to enable rapid and efficient generation of aptamers against M-Ig proteins from MM patients. We first characterize the technology by isolating aptamers with affinity towards the monoclonal antibody rituximab as a model M-Ig and then apply the technology to isolating aptamers specifically targeting M-Igs obtained from serum samples of MM patients. We demonstrate that high-affinity DNA aptamers (KD < 50 nM) for M-Ig proteins from a patient sample could be isolated via microfluidic SELEX within approximately 12 h and using less than 100 micrograms of patient M-Ig. Such aptamers can potentially be used in personalized monitoring of minimal residual disease in MM patients.

One-Step Photochemical Immobilization of Aptamer on Graphene for Label-Free Detection of NT-proBNP

A novel photochemical technological route for one-step functionalization of a graphene surface with an azide-modified DNA aptamer for biomarkers is developed. The methodology is demonstrated for the functionalization of a DNA aptamer for an N-terminal B-type natriuretic peptide (NT-proBNP) heart failure biomarker on the surface of a graphene channel within a system based on a liquid-gated graphene field effect transistor (GFET). The limit of detection (LOD) of the aptamer-functionalized sensor is 0.01 pg/mL with short response time (75 s) for clinically relevant concentrations of the cardiac biomarker, which could be of relevance for point-of-care (POC) applications. The novel methodology could be applicable for the development of different graphene-based biosensors for fast, stable, real-time, and highly sensitive detection of disease markers.

A Review on Aptamers Selection and Application in Heart Diseases Diagnosis

Biomarkers detection and quantification in biological fluids play a key role in the screening, diagnosing and treating several diseases. Recently, a large number of aptamers have been selected and applied for the sensing of different biomarkers. Combined with different transducers, aptamers provide simple and rapid tools that allow highly sensitive and selective detection. Cardiology requires an accurate assessment of cardiac biomarkers for a complete diagnosis of cardiovascular diseases. The analysis is generally performed by immunoassays using antibodies as biorecognition elements. This review paper focuses on using aptamers as a promising alternative for antibodies in cardiac biomarkers biosensing. First, the different aptamers specific to the most important cardiac biomarkers are Troponin I, the peptide of B-type natriuretic peptide and myoglobin. Then, in the second part, we overview the electrochemical aptasensors principle and characteristics reported in the literature in the last five years.

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.

On-chip selection of adenosine aptamer using graphene oxide-coated magnetic nanoparticles

Systematic evolution of ligands by exponential enrichment (SELEX) is a method that is generally used for developing aptamers, which have arisen the promising alternatives for antibodies. However, conventional SELEX methods have limitations, such as a limited selection of target molecules, time-consuming and complex fabrication processes, and labor-intensive processes, which result in low selection yields. Here, we used (i) graphene oxide (GO)-coated magnetic nanoparticles in the selection process for separation and label-free detection and (ii) a multilayered microfluidic device manufactured using a three-dimensionally printed mold that is equipped with automated control valves to achieve precise fluid flows. The developed on-chip aptamer selection device and GO-coated magnetic nanoparticles were used to screen aptamer candidates for adenosine in eight cycles of the selection process within approximately 2 h for each cycle. Based on results from isothermal titration calorimetry, an aptamer with a dissociation constant of 18.6 ± 1.5 μM was selected. Therefore, the on-chip platform based on GO-coated magnetic nanoparticles provides a novel label-free screening technology for biosensors and micro/nanobiotechnology for achieving high-quality aptamers.

Surface acoustic wave-assisted microfluidic isolation of aptamers

Aptamers are synthetic single-stranded nucleic acid molecules that bind to biochemical targets with high affinity and specificity. The method of systematic evolution of ligands by exponential enrichment (SELEX) is widely used to isolate aptamers from randomized oligonucleotides. Recently, microfluidic technology has been applied to improve the efficiency and reduce the cost in SELEX processes. In this work, we present an approach that exploits surface acoustic waves to improve the affinity selection process in microfluidic SELEX. Acoustic streaming is used to enhance the interactions of the solution-based oligonucleotide molecules with microbead-immobilized target molecules, allowing the identification of high-affinity aptamer candidates in a more efficient manner. For demonstration, a DNA aptamer is isolated within three rounds of selection in 5 h to specifically bind to immunoglobulin E, a representative target protein, with an equilibrium dissociation constant of approximately 22.6 nM.

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.

Compatibility of Popular Three-Dimensional Printed Microfluidics Materials with In Vitro Enzymatic Reactions

3D printed microfluidics offer several advantages over conventional planar microfabrication techniques including fabrication of 3D microstructures, rapid prototyping, and inertness. While 3D printed materials have been studied for their biocompatibility in cell and tissue culture applications, their compatibility for in vitro biochemistry and molecular biology has not been systematically investigated. Here, we evaluate the compatibility of several common enzymatic reactions in the context of 3D-printed microfluidics: (1) polymerase chain reaction (PCR), (2) T7 in vitro transcription, (3) mammalian in vitro translation, and (4) reverse transcription. Surprisingly, all the materials tested significantly inhibit one or more of these in vitro enzymatic reactions. Inclusion of BSA mitigates only some of these inhibitory effects. Overall, inhibition appears to be due to a combination of the surface properties of the resins as well as soluble components (leachate) originating in the matrix.

Aptamer selection against alpha-defensin human neutrophil peptide 1 on an integrated microfluidic system for diagnosis of periprosthetic joint infections

Periprosthetic joint infections (PJIs) arising from joint arthroplasty are dreadful, yet difficult to diagnose in subtle cases. Definite diagnosis requires microbiological culture to confirm the causative pathogens. However, up to 40% of culture-negative PJI needs other surrogate biomarkers such as human neutrophil peptide 1 (HNP 1) to improve diagnostic accuracy or gauge therapeutic responses. To devise a diagnostic method, systematic evolution of ligands by exponential enrichment (SELEX) (five rounds) was used to screen PJI biomarkers on a compact (20 × 20 × 35 cm), integrated microfluidic system equipped with two separate Peltier devices and one magnetic control module where an aptamer with high affinity and specificity for HNP 1, which has been used as one of the synovial fluid (SF) biomarkers for detecting PJI, was identified for the first time. Two rounds of negative selection (with immunoglobulin G & human serum album) on-chip followed by one round of unique "competitive selection" with SF extracted from PJI patients validated the specificity of the HNP 1 aptamer. The dissociation constant was measured to be 19 nM. The applicability of SF HNP 1 levels for diagnosing PJI was then verified by a new aptamer-based enzyme-linked immunosorbent assay (ELISA)-like assay. It is envisioned that this new aptamer and the associated assay could be used in future clinical applications.

Paper based microfluidics: A forecast toward the most affordable and rapid point-of-care devices

The microfluidic industry has evolved through years with acquired scientific knowledge from different, and already developed industries. Consequently, a wide range of materials like silicon from the electronic industry to all the way, silicone, from the chemical engineering industry, has been spotted to solve similar challenges. Although a typical microfluidic chip, fabricated from glass or polymer substrates offers definite benefits, however, paper-based microfluidic analytical devices (μPADs) possess numerous special benefits for practical implementation at a lower price. Owing to these features, in recent years, paper microfluidics has drawn immense interest from researchers in industry and academia alike. These devices have wider applications with advantages like lower cost, speedy detection, user-easiness, biocompatibility, sensitivity, and specificity etc. when compared to other microfluidic devices. Therefore, these sensitive but affordable devices fit themselves into point-of-care (POC) testing with features in demand like natural disposability, situational flexibility, and the capability to store and analyze the target at the point of requirement. Gradually, advancements in fabrication technologies, assay development techniques, and improved packaging capabilities, have contributed significantly to the real-time identification and health investigation through paper microfluidics; however, the growth has not been limited to the biomedical field; industries like electronics, energy storage and many more have expanded substantially. Here, we represent an overall state of the paper-based microfluidic technology by covering the fundamentals, working principles, different fabrication procedures, applications for various needs and then to make things more practical, the real-life scenario and practical challenges involved in launching a device into the market have been revealed. To conclude, recent contribution of μPADs in the 2020 pandemic and potential future possibilities have been reviewed.

Aptamer grafted nanoparticle as targeted therapeutic tool for the treatment of breast cancer

Breast carcinomas repeat their number and grow exponentially making it extremely frequent malignancy among women. Approximately, 70-80% of early diagnosed or non-metastatic conditions are treatable while the metastatic cases are considered ineffective to treat with current ample amount of therapy. Target based anti-cancer treatment has been in the limelight for decades and is perceived significant consideration of scientists. Aptamers are the 'coming of age' therapeutic approach, selected using an appropriate tool from the library of sequences. Aptamers are non-immunogenic, stable, and high-affinity ligand which are poised to reach the clinical benchmark. With the heed in nanoparticle application, the delivery of aptamer to the specific site could be enhanced which also protects them from nuclease degradation. Moreover, nanoparticles due to robust structure, high drug entrapment, and modifiable release of cargo could serve as a successful candidate in the treatment of breast carcinoma. This review would showcase the method and modified method of selection of aptamers, aptamers that were able to make its way towards clinical trial and their targetability and selectivity towards breast cancers. The appropriate usage of aptamer-based biosensor in breast cancer diagnosis have also been discussed.

Nanomaterial-based aptasensors as an efficient substitute for cardiovascular disease diagnosis: Future of smart biosensors

As a major cause of deaths in developed countries, cardiovascular disease (CVD) has been a big burden for human health systems. Its early and rapid detection is crucial to efficiently apply appropriate on time therapy and to ultimately reduce the associated mortality rate. Aptamers, known as single-stranded DNA/RNA or oligonucleotides containing receptors and/or catalytic properties, have been widely employed in biodetection platforms due to their beneficial properties. Like antibodies, aptamers have served as artificial target receptors in affinity biosensors. Currently, advanced biosensors with improved sensitivity and specificity are fabricated by the synergistic combination of aptamers and diverse nanomaterials. Herein, we review the current development and applications of nanomaterial-based aptasensors for the recognition of CVD biomarkers with special emphasis on electrochemical and optical technologies. The performance of aptasensors has been assessed further in terms of key quality assurance metrics along with discussions on recent technologies developed for the amplification of signals with enhanced portability.

The Application of Microfluidic Technologies in Aptamer Selection

Aptamers are sequences of single-strand oligonucleotides (DNA or RNA) with potential binding capability to specific target molecules, which are increasingly used as agents for analysis, diagnosis, and medical treatment. Aptamers are generated by a selection method named systematic evolution of ligands by exponential enrichment (SELEX). Numerous SELEX methods have been developed for aptamer selections. However, the conventional SELEX methods still suffer from high labor intensity, low operation efficiency, and low success rate. Thus, the applications of aptamer with desired properties are limited. With their advantages of low cost, high speed, and upgraded extent of automation, microfluidic technologies have become promising tools for rapid and high throughput aptamer selection. This paper reviews current progresses of such microfluidic systems for aptamer selection. Comparisons of selection performances with discussions on principles, structure, operations, as well as advantages and limitations of various microfluidic-based aptamer selection methods are provided.

A review of biosensors for the detection of B-type natriuretic peptide as an important cardiovascular biomarker

Heart disease, as the most serious threat to human health globally, is responsible for rising mortality rates, largely due to lifestyle and diet. Unfortunately, the main problem for patients at high risk of heart disease is the validation of prognostic tests. To this end, the detection of cardiovascular biomarkers has been employed to obtain pathological and physiological information in order to improve prognosis and early-stage diagnosis of chronic heart failure. Short-term changes in B-type natriuretic peptide are known as a standard and important biomarker for diagnosis of heart failure. The most important problem for detection is low concentration and short half-life in the blood. The normal concentration of BNP in blood is less than 7 nM (25 pg/mL), which increases significantly to more than 80 pg/mL. Therefore, the development of new biosensors with better sensitivity, detection limit, and dynamic range than current commercial kits is urgently needed. This review classifies the biosensors designed for detection of BNP into electrochemical, optical, microfluidic, and lateral-flow immunoassay techniques. The review clearly demonstrates that a variety of immunoassay, aptasensor, enzymatic and catalytic nanomaterials, and fluorophores have been successfully employed for detection of BNP at low attomolar ranges. Dtection of B-type natriuretic peptide with biosensors.

Recent Achievements in Electrochemical and Surface Plasmon Resonance Aptasensors for Mycotoxins Detection

Mycotoxins are secondary metabolites of fungi that contaminate agriculture products. Their release in the environment can cause severe damage to human health. Aptasensors are compact analytical devices that are intended for the fast and reliable detection of various species able to specifically interact with aptamers attached to the transducer surface. In this review, assembly of electrochemical and surface plasmon resonance (SPR) aptasensors are considered with emphasis on the mechanism of signal generation. Moreover, the properties of mycotoxins and the aptamers selected for their recognition are briefly considered. The analytical performance of biosensors developed within last three years makes it possible to determine mycotoxin residues in water and agriculture/food products on the levels below their maximal admissible concentrations. Requirements for the development of sample treatment and future trends in aptasensors are also discussed.

A multiplexed nanoliter array-based microfluidic platform for quick, automatic antimicrobial susceptibility testing

Antimicrobial resistance stemming from indiscriminate usage of antibiotics has emerged as a global healthcare issue with substantial economic implications. The inefficacy of commonly used antibiotics combined with superfluous consumption has worsened the issue. Rapid antimicrobial susceptibility testing (AST) to antibiotics can be advantageous in thwarting bacterial infections. Therefore, this study developed a simple nanoliter array-based microfluidic platform for performing rapid AST, which can handle and manipulate liquids both in nanoliter and microliter volumes. The platform consisted of two microfluidic devices, one for performing AST and another for diluting antibiotics and these two were suitably integrated. The microfluidic device used for generating microarrays for AST experiments is single-layered (no air layer) and has no active microvalves and air hole, which makes the device easy to fabricate and use. The loading process ensures uniform distribution of bacteria and relies on displacing the air from microarrays through porous polydimethylsiloxane membranes. Furthermore, the chip for dilution consisted of active microfluidic components, and could prepare and test seven different concentrations of antibiotics, which make the platform multiplexed and be capable of evaluating minimum inhibitory concentrations (MICs), a clinically relevant parameter. MIC determination requires less number of bacteria (∼2000) and hence shortens the pre-culture step, i.e. bacteria culture in blood and urine. This automated system demonstrated AST and evaluated MICs using Escherichia coli and two antibiotics, including ampicillin and streptomycin, and the results were ascertained using a gold standard method. It only took 8-9 h to perform AST, which is substantially less compared to a conventional process and hence is of high clinical utility.

Advances in Screening and Development of Therapeutic Aptamers Against Cancer Cells

Cancer has become the leading cause of death in recent years. As great advances in medical treatment, emerging therapies of various cancers have been developed. Current treatments include surgery, radiotherapy, chemotherapy, immunotherapy, and targeted therapy. Aptamers are synthetic ssDNA or RNA. They can bind tightly to target molecules due to their unique tertiary structure. It is easy for aptamers to be screened, synthesized, programmed, and chemically modified. Aptamers are emerging targeted drugs that hold great potentials, called therapeutic aptamers. There are few types of therapeutic aptamers that have already been approved by the US Food and Drug Administration (FDA) for disease treatment. Now more and more therapeutic aptamers are in the stage of preclinical research or clinical trials. This review summarized the screening and development of therapeutic aptamers against different types of cancer cells.

A malachite green light-up aptasensor for the detection of theophylline

Biosensors are of interest for the quantitative detection of small molecules (metabolites, drugs and contaminants for instance). To this end, fluorescence is a widely used technique that is easily associated to aptamers. Light-up aptamers constitute a particular class of oligonucleotides that, specifically induce fluorescence emission when binding to cognate fluorogenic ligands such as malachite green (MG). We engineered a dual aptasensor for theophylline (Th) based on the combination of switching hairpin aptamers specific for MG on the one hand and for Th on the other hand, hence their names: malaswitch (Msw) and theoswitch (Thsw). The two aptaswitches form a loop-loop or kissing Msw-Thsw complex only in the presence of theophylline, allowing binding of MG, subsequently generating a fluorescent signal. The combination of the best Msw and Thsw variants, MswG12 and Thsw19.1, results in a 20-fold fluorescence enhancement of MG at saturating theophylline concentration. This aptasensor discriminates between theophylline and its analogues caffeine and theobromine. Kissing aptaswitches derived from light-up aptamers constitute a novel sensing device.

Pumpless, modular, microphysiological systems enabling tunable perfusion for long-term cultivation of endothelialized lumens

Given the increased recognition of the importance of physiologically relevant microenvironments when designing in vitro assays, microphysiological systems (MPS) that mimic the critical function and structure of tissues and organs have gained considerable attention as alternatives to traditional experimental models. Accordingly, the field is growing rapidly, and some promising MPS are being tested for use in pharmaceutical development and toxicological testing. However, most MPS are complex and require additional infrastructure, which limits their successful translation. Here, we present a pumpless, modular MPS consisting of 1) a resistance module that controls flow rate and 2) a physiologically relevant, three-dimensional blood vessel module. Flow is provided by an attached reservoir tank that feeds fluid into the resistance channel via hydrostatic pressure. The flow rate is controlled by the height of the media in the tank and the resistance channel's dimensions. The flow from the resistance module is streamed into the blood vessel module using a liquid bridge. We utilize optical coherence tomography (OCT) to measure fluid velocity at regions of interest. The endothelial cells cultured in the MPS remain viable for up to 14 days and demonstrate the functional characteristics of the human blood vessels verified by tight junction expression and diffusion assay. Our results show that a modular MPS can simulate a functional endothelium in vitro while simplifying the operation of the MPS. The simplicity of the system allows for modifications to incorporate other microenvironmental components and to build other organ-modeling systems easily.

Recent Progress in Aptamer Discoveries and Modifications for Therapeutic Applications

Aptamers are oligonucleotide sequences with a length of about 25-80 bases which have abilities to bind to specific target molecules that rival those of monoclonal antibodies. They are attracting great attention in diverse clinical translations on account of their various advantages, including prolonged storage life, little batch-to-batch differences, very low immunogenicity, and feasibility of chemical modifications for enhancing stability, prolonging the half-life in serum, and targeted delivery. In this Review, we demonstrate the emerging aptamer discovery technologies in developing advanced techniques for producing aptamers with high performance consistently and efficiently as well as requiring less cost and resources but offering a great chance of success. Further, the diverse modifications of aptamers for therapeutic applications including therapeutic agents, aptamer-drug conjugates, and targeted delivery materials are comprehensively summarized.

Aptamer-Functionalized Microdevices for Bioanalysis

Aptamers have drawn great attention in the field of biological research and disease diagnosis for the remarkable advantages as recognition elements. They show unique superiority for facile selection, desirable thermal stability, flexible engineering, and low immunogenicity, complementing the use of conventional antibodies. Aptamer-functionalized microdevices offer promising properties for bioanalysis applications because of the compact sizes, minimal reaction volume, high throughput, operational feasibility, and controlled preciseness. In this review, we first introduce the innovative technologies in the selection of aptamers with microdevices and then highlight some advanced applications of aptamer-functionalized microdevices in bioanalysis field for diverse targets. Aptamer-functionalized microfluidic devices, microarrays, and paper-based and other interface-based microdevices are all bioanalysis platforms with huge potential in the near future. Finally, the major challenges of these microdevices applied in bioanalysis are discussed and future perspectives are also envisioned.

SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques

DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.

Liquid biopsy technologies for hematological diseases

Since the discovery of circulating tumor cells in 1869, technological advances in studying circulating biomarkers from patients' blood have made the diagnosis of nonhematologic cancers less invasive. Technological advances in the detection and analysis of biomarkers provide new opportunities for the characterization of other disease types. When compared with traditional biopsies, liquid biopsy markers, such as exfoliated bladder cancer cells, circulating cell-free DNA (cfDNA), and extracellular vesicles (EV), are considered more convenient than conventional biopsies. Liquid biopsy markers undoubtedly have the potential to influence disease management and treatment dynamics. Our main focuses of this review will be the cell-based, gene-based, and protein-based key liquid biopsy markers (including EV and cfDNA) in disease detection, and discuss the research progress of these biomarkers used in conjunction with liquid biopsy. First, we highlighted the key technologies that have been broadly adopted used in hematological diseases. Second, we introduced the latest technological developments for the specific detection of cardiovascular disease, leukemia, and coronavirus disease. Finally, we concluded with perspectives on these research areas, focusing on the role of microfluidic technology and artificial intelligence in point-of-care medical applications. We believe that the noninvasive capabilities of these technologies have great potential in the development of diagnostics and can influence treatment options, thereby advancing precision disease management.

Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach

This study introduces a computational method to design a new aptamer with higher binding affinity to a special target in comparison with the experimentally available aptamers. The method is called step by step mutation based on MD simulation, which includes some steps. First, MD simulation is performed for the SELEX-introduced (native) aptamer in the presence of the target. Afterwards, conformational factor (P_i) is calculated for the simulated system, which obtains the affinity of the aptamer residues to the target. A nucleotide exchange is done for the residue with the least P_i parameter to the nucleotide with the highest P_i value that results in a mutant aptamer. MD simulation is performed for the target-mutant complex, and P_i values are calculated again. The nucleotide exchange is performed similarly, and the designing process is proceeded repeatedly that results in a mutant with the improved specificity to the target. The aptamer affinity to the target is also determined in each step through calculating the binding Gibbs energy (ΔG_Bind) as a reliable parameter. The introduced strategy is utilized efficiently to design a mutant aptamer with improved specificity toward sulfadimethoxine (SDM) antibiotic as a case study. The great difference in the ΔG_Bind values about 579.856 kJ mol^-1 highlights that the M5 mutant possesses the improved specificity toward SDM in comparison with the native aptamer. Besides, the selectivity of the M5 aptamer toward SDM is examined among some conventional interfering compounds by using MD simulation that confirms the applicability of the designed aptamer for further experimental studies.

Exploring Circulating Tumor Cells in Cholangiocarcinoma Using a Novel Glycosaminoglycan Probe on a Microfluidic Platform

The search of alternative approaches to epithelial cell adhesion molecule (EpCAM), for the isolation of circulating tumor cells (CTC), is on the rise. This work attempts at evaluating the feasibility of using a new glycosaminoglycan, SCH45, as a probe to isolate CTCs from the peripheral blood of 65 advanced/metastatic cholangiocarcinoma (CCA) patients. The positive enrichment of CTCs from 1 mL of blood using SCH45-bound magnetic beads and subsequent staining on an integrated microfluidic platform is demonstrated. Results detailing CTC concentrations averaging ≥1 CTCs mL^-1 of blood are shown, and a conventional protein biomarker, EpCAM, has been used to corroborate the finding that 100% of the patients possess CTCs in their blood. Studies detailing the use of CTCs in the prognostic monitoring and treatment effectiveness of advanced/metastatic CCA are scarce, and the isolation of CTCs from all CCA patients tested has not been reported yet. A strong correlation between CTC counts and disease progression at the time of and/or in advance of radiographic imaging in patients receiving chemotherapy is also reported. This study is one of its kind with the new probe and reduced sample volume and has potential for use in CCA diagnosis and prognosis in the near future.