Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics

Strategies Employed to Design Biocompatible Metal Nanoparticles for Medical Science and Biotechnology Applications

The applicability of nanomaterials has evolved in biomedical domains thanks to advances in biocompatibility strategies and the mitigation of cytotoxic effects, allowing diagnostics, imaging, and therapeutic approaches. The application of nanoparticles (NP), particularly metal nanoparticles (mNPs), such as gold (Au) and silver (Ag), includes inherent challenges related to the material characteristics, surface modification, and bioconjugation techniques. By tailoring the surface properties through appropriate coating with biocompatible molecules or functionalization with active biomolecules, researchers can reach a harmonious interaction with biological systems or samples (mostly fluids or tissues). Thus, this review highlights the mechanisms associated with the obtention of biocompatible mNP and presents a comprehensive overview of methods that facilitate safe and efficient production. Therefore, we consider this review to be a valuable resource for all researchers navigating this dynamic field.

Simple and fast one-step FRET assay of therapeutic mAb bevacizumab using anti-idiotype DNA aptamer for process analytical technology

We developed an aptamer-based fluorescence resonance energy transfer (FRET) assay capable of recognizing therapeutic monoclonal antibody bevacizumab and rapidly quantifying its concentration with just one mixing step. In this assay, two fluorescent dyes (fluorescein and tetramethylrhodamine) labeled aptamers bind to two Fab regions on bevacizumab, and FRET fluorescence is observed when both dyes come into close proximity. We optimized this assay in three different formats, catering to a wide range of analytical needs. When applied to hybridoma culture samples in practical settings, this assay exhibited a signal response that was concentration-dependent, falling within the range of 50-2000 μg/mL. The coefficients of determination (r2) ranged from 0.998 to 0.999, and bias and precision results were within ±24.0 % and 20.3 %, respectively. Additionally, during thermal and UV stress testing, this assay demonstrated the ability to detect denatured samples in a manner comparable to conventional Size Exclusion Chromatography. Notably, it offers the added advantage of detecting decreases in binding activity without changes in molecular weight. In contrast to many existing process analytical technology tools, this assay not only identifies bevacizumab but also directly measures the quality attributes related to mAb efficacy, such as the binding activity. As a result, this assay holds great potential as a valuable platform for providing highly reliable quality attribute information in real-time. We consider this will make a significant contribution to the worldwide distribution of high-quality therapeutic mAbs in various aspects of antibody manufacturing, including production monitoring, quality control, commercial lot release, and stability testing.

Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation

The escalating threat of emerging diseases, often stemming from contaminants and lethal pathogens, has precipitated a heightened demand for sophisticated diagnostic tools. Within this landscape, the functional nucleic acid (FNA) biosensor, harnessing the power of single-stranded DNA (ssDNA), has emerged as a preeminent choice for target analyte detection. However, the dependence on ssDNA has raised difficulties in realizing it in biological samples. Therefore, the production of high-quality ssDNA from biological samples is critical. This review aims to discuss strategies for generating ssDNA from biological samples for integration into biosensors. Several innovative strategies for ssDNA generation have been deployed, encompassing techniques, such as asymmetric PCR, Exonuclease-PCR, isothermal amplification, biotin-streptavidin PCR, transcription-reverse transcription, ssDNA overhang generation, and urea denaturation PAGE. These approaches have been seamlessly integrated with biosensors for biological sample analysis, ushering in a new era of disease detection and monitoring. This amalgamation of ssDNA generation techniques with biosensing applications holds significant promise, not only in improving the speed and accuracy of diagnostic processes but also in fortifying the global response to deadly diseases, thereby underlining the pivotal role of cutting-edge biotechnology in public health and disease prevention.

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.

Epigenetic Regulation of Autophagy in Bone Metabolism

The skeletal system is crucial for supporting bodily functions, protecting vital organs, facilitating hematopoiesis, and storing essential minerals. Skeletal homeostasis, which includes aspects such as bone density, structural integrity, and regenerative processes, is essential for normal skeletal function. Autophagy, an intricate intracellular mechanism for degrading and recycling cellular components, plays a multifaceted role in bone metabolism. It involves sequestering cellular waste, damaged proteins, and organelles within autophagosomes, which are then degraded and recycled. Autophagy's impact on bone health varies depending on factors such as regulation, cell type, environmental cues, and physiological context. Despite being traditionally considered a cytoplasmic process, autophagy is subject to transcriptional and epigenetic regulation within the nucleus. However, the precise influence of epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNA expression, on cellular fate remains incompletely understood. The interplay between autophagy and epigenetic modifications adds complexity to bone cell regulation. This article provides an in-depth exploration of the intricate interplay between these two regulatory paradigms, with a focus on the epigenetic control of autophagy in bone metabolism. Such an understanding enhances our knowledge of bone metabolism-related disorders and offers insights for the development of targeted therapeutic strategies.

Bone marrow mesenchymal stem cells derived exosomal miRNAs can modulate diabetic bone-fat imbalance

Background

Diabetes mellitus is a chronic metabolic disease with systemic complications. Patient with diabetes have increased risks of bone fracture. Previous studies report that diabetes could affect bone metabolism, however, the underlying mechanism is still unclear.

Methods

We isolated exosomes secreted by bone marrow mesenchymal stem cells of normal and diabetic mice and test their effects on osteogenesis and adipogenesis. Then we screened the differential microRNAs by high-throughput sequencing and explored the function of key microRNA in vitro and in vivo.

Results

We find that lower bone mass and higher marrow fat accumulation, also called bone-fat imbalance, exists in diabetic mouse model. Exosomes secreted by normal bone marrow mesenchymal stem cells (BMSCs-Exos) enhanced osteogenesis and suppressed adipogenesis, while these effects were diminished in diabetic BMSCs-Exos. miR-221, as one of the highly expressed miRNAs within diabetic BMSCs-Exos, showed abilities of suppressing osteogenesis and promoting adipogenesis both in vitro and in vivo. Elevation of miR-221 level in normal BMSCs-Exos impairs the ability of regulating osteogenesis and adipogenesis. Intriguingly, using the aptamer delivery system, delivery normal BMSCs-Exos specifically to BMSCs increased bone mass, reduced marrow fat accumulation, and promoted bone regeneration in diabetic mice.

Conclusion

We demonstrate that BMSCs derived exosomal miR-221 is a key regulator of diabetic osteoporosis, which may represent a potential therapeutic target for diabetes-related skeletal disorders.

A signal-on fluorescent aptasensor by sensitized Tb3+ luminescence for detection of melamine in milk

A fluorescent aptasensor based on sensitized terbium(III) luminescence was constructed to detect melamine in milk. Tb³⁺ as the fluorescence probe can be sensitized by a guanine-rich single-stranded DNA sequence, so the complementary sequence of the polythymidine aptamer (cDNA) was modified with six consecutive guanine bases (G6). In the absence of melamine, melamine aptamer combined with cDNA to form a double helix structure, and G6 hybridized with the extended cytosine bases in the aptamer, resulting in low fluorescence intensity of Tb³⁺. In the presence of melamine, cDNA was released due to the specific recognition of melamine to the aptamer, resulting in stronger sensitized fluorescence intensity of Tb³⁺. Under the optimum conditions, the linear concentration of melamine in the milk ranged from 1.0 μg/mL to 10.0 μg/mL. This aptasensor can be used for the accurate and rapid detection of melamine in milk with a detection limit of 0.02 μg/mL, and has the advantages of high sensitivity, high efficiency, simple operation and low cost.

Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles

The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.

Polymer Nanoparticles and Nanomotors Modified by DNA/RNA Aptamers and Antibodies in Targeted Therapy of Cancer

Polymer nanoparticles and nano/micromotors are novel nanostructures that are of increased interest especially in the diagnosis and therapy of cancer. These structures are modified by antibodies or nucleic acid aptamers and can recognize the cancer markers at the membrane of the cancer cells or in the intracellular side. They can serve as a cargo for targeted transport of drugs or nucleic acids in chemo- immuno- or gene therapy. The various mechanisms, such as enzyme, ultrasound, magnetic, electrical, or light, served as a driving force for nano/micromotors, allowing their transport into the cells. This review is focused on the recent achievements in the development of polymer nanoparticles and nano/micromotors modified by antibodies and nucleic acid aptamers. The methods of preparation of polymer nanoparticles, their structure and properties are provided together with those for synthesis and the application of nano/micromotors. The various mechanisms of the driving of nano/micromotors such as chemical, light, ultrasound, electric and magnetic fields are explained. The targeting drug delivery is based on the modification of nanostructures by receptors such as nucleic acid aptamers and antibodies. Special focus is therefore on the method of selection aptamers for recognition cancer markers as well as on the comparison of the properties of nucleic acid aptamers and antibodies. The methods of immobilization of aptamers at the nanoparticles and nano/micromotors are provided. Examples of applications of polymer nanoparticles and nano/micromotors in targeted delivery and in controlled drug release are presented. The future perspectives of biomimetic nanostructures in personalized nanomedicine are also discussed.

Fabrication of an electrochemical biodevice for ractopamine detection under a strategy of a double recognition of the aptamer/molecular imprinting polymer

The importance of RAC tracking in human biofluids has boosted many demands for designing an ultrasensitive tool to determine the trace value of the RAC from clinical, judicial, and forensic centers. In this study, an electrochemical biodevice has developed for the highly selective detection of this illegal feed additive under a double recognition strategy of the aptamer (Apt) and molecular imprinting polymer (MIP) on a glassy carbon electrode (GCE). The sensing relies on this fact that both the MIP and Apt act synergistically to trap the RAC molecules. The sensing surface fabrication steps have been monitored by some electrochemical techniques such as electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV(. The charge transfer resistance (R_ct) value of the redox probe as a representative of the biodevice response has increased linearly with the RAC concentration increasing in a dynamic range of 1 fM to 1.90 µM. The detection limit (LOD) value has been estimated to be 330 aM, lower than all of the reported methods in the RAC sensing. Furthermore, the practical feasibility of biodevice has been evaluated in some human blood serum and urine samples. This strategy offers some useful advantages in reliable detection of the RAC, which may help in the routine analysis, as mandated by regulatory agencies.

Ultrasensitive detection of amoxicillin by TiO2-g-C3N4@AuNPs impedimetric aptasensor: Fabrication, optimization, and mechanism

The trace amount of antibiotics in water can be enriched in the human body through the food chain, leading to extremely harmful effects on people's health. Therefore, it is urgent to develop new methods to detect trace pollutants in various aquatic phase. An analytical method utilizing the synergistic effect between the sensing strategy and catalytic material with high electron transfer capacity can be used to detect trace antibiotics. In this paper, an ultrasensitive impedimetric aptasensor was fabricated by the synergy between functionalized materials (TiO₂-g-C₃N₄) and gold nanoparticles (Au NPs). Due to the formation of the 'Au-S' bond between the thiol-aptamer and Au NPs, amoxicillin and the aptamer can be specifically recognized on the modified glassy carbon electrode (GCE), and the impedance signal increased rapidly. Meanwhile, the Box-Behnken Design (BBD) strategy was used to reduce the random error of the experiment, so that the prepared aptasensor has the highest sensitivity to the detection of amoxicillin. Under optimized conditions, the sensor successfully achieved the detection of amoxicillin in the ultra-low detection range (0.5-3 nM) and reached the ultra-low detection limit (0.2 nM). The detection strategy has good selectivity, reproducibility, and stability, and thus has good potential to detect amoxicillin in actual wastewater.

A Colorimetric Aptamer Sensor Based on the Enhanced Peroxidase Activity of Functionalized Graphene/Fe3O4-AuNPs for Detection of Lead (II) Ions

Lead (II) is regarded as one of the most hazardous heavy metals, and lead contamination has a serious impact on food chains, human health, and the environment. Herein, a colorimetric aptasensor based on the graphene/Fe3O4-AuNPs composites with enhanced peroxidase-like activity has been developed to monitor lead ions (Pb2+). In short, graphene/Fe3O4-AuNPs were fabricated and acted as an enzyme mimetic, so the color change could be observed by chromogenic reaction. The aptamer of Pb2+ was decorated on the surface of the amine magnetic beads by streptavidin–biotin interaction, and the complementary strands of the aptamer and target Pb2+ competed for the binding Pb2+ aptamer. In the presence of Pb2+, aptamers bonded the metal ions and were removed from the system by magnetic separation; the free cDNA was adsorbed onto the surface of the graphene/Fe3O4-AuNPs composites, thus inhibiting the catalytic activity and the color reaction. The absorbance of the reaction solution at 652 nm had a clear linear correlation with the Pb2+ concentration in the range of 1–300 ng/mL, and the limit of detection was 0.63 ng/mL. This assay is simple and convenient in operation, has good selectivity, and has been used to test tap water samples, which proves that it is capable for the routine monitoring of Pb2+.

Advances in aptasensor technology

Aptasensors form a class of biosensors that function on the basis of a biological recognition. An aptasensor is advantageous because it incorporates a unique biologic recognition element, i.e., an aptamer, coupled to a transducer to convert a biological interaction to readable signals that can be easily processed and reported. In such biosensors, the specificity of aptamers is comparable to and sometimes even better than that of antibodies. Using the SELEX technique, aptamers with high specificity and affinity to various targets can be isolated from large pools of different oligonucleotides. Nowadays, new modifications of the SELEX technique and, as a result, easy generation and synthesis of aptamers have led to the wide application of these materials as biological receptors in biosensors. In this regard, aptamers promise a bright future. In the present research a brief account is initially provided of the recent developments in aptasensors for various targets. Then, immobilization methods, design strategies, current limitations and future directions are discussed for aptasensors.

Electrochemiluminescent aptamer-sensor for alpha synuclein oligomer based on a metal-organic framework

The alpha synuclein (α-syn) oligomer is one of the biomarkers used for the early diagnosis of Parkinson's disease. In this paper, two electrochemiluminescent (ECL) biosensors with an aptamer as the recognition element for α-syn oligomer detection were prepared. A functionalized indium tin oxide (ITO) glass with metal-organic framework (MOF) materials provides an adequate sensing platform. Here the gold nanoparticles/metal organic frameworks (MOFs) composite (AuNPs@MOFs) using 3-aminopropyltrimethoxysilane as a binding agent, or to connect the MOFs onto the ITO directly via glutaraldehyde, both give a strong ECL emission for luminol, even under weak alkaline conditions. Thereafter, the thiolated or carboxylated aptamer was coalesced onto the MOF material functionalized electrode using an Au-S bond or amide bond via the classic 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide/N-hydroxysuccinimide (EDC-NHS) coupling, respectively. Thus, the ECL emission of the sensors significantly reduced after the specific binding of the α-syn oligomer to the aptamer. The good linear relationship of the ECL sensing signals upon the logarithm of the α-syn oligomer concentration were established, from 2.43 fM to 0.486 pM or 1.39 fM to 0.243 pM, and the limit of detection reached as low as 0.42 or 0.38 fM, for these two sensors. Both of the obtained sensors have the advantages of a high sensitivity, selectivity, and reproducibility and are capable of detecting the target in human serum.

Aptamer-Based Sensing of Small Organic Molecules by Measuring Levitation Coordinate of Single Microsphere in Combined Acoustic-Gravitational Field

We present aptamer-based sensing using a coupled acoustic-gravitational (CAG) field, which transduces a change in the density of a microparticle (MP) to a change in the levitation coordinate. A large density of the MP is initially induced by the binding of gold nanoparticles (AuNPs) on the MP through sandwich hybridization with aptamer DNA molecules. Targets added to the system interact with the aptamer DNA molecules to form complexes, and the duplex between the aptamer and the probe DNA molecules is dissociated. This leads to the release of AuNPs from the MP and a decrease in its density. As the target concentration increases, the levitation coordinate of the MP increases. From the levitation coordinate shift, we can determine the target concentration. The detection limits for adenosine triphosphate, dopamine, and ampicillin as test targets are 9.8 nM, 17 nM, and 160 pM, respectively. The dissociation constants for the aptamer-target complexes are quantitatively determined from the dependence of the levitation coordinate on the target concentration. This scheme is a useful analytical tool not only for the trace analyses of targets but also for the evaluation of aptamer-target interactions.

Enabling Molecular Gapping and Bridging on a Biosensing Surface via Electrochemical Cross-Linking and Cleavage

Protein detection in complicated biological samples requires robust design and a rigorous rinsing process. Many recently developed artificial targeting probes, however, often do not possess antibody-like binding strength that enables them to endure harsh biosensing conditions, and the classic 2-to-1 sandwich binding pattern is unavailable for many targets, often necessitating a complicated indirect signal conversion mechanism. Here, an attempt is made to provide innovative "covalent" solutions to such problems by employing peptide reactivity to form a covalent and robust biosensing structure upon target binding. Both the cross-coupling and cleavage of peptide chains are employed to achieve the classic 2-to-1 binding when only one targeting probe is available. Specifically, a targeting probe against the protein and a signaling probe are coimmobilized onto the sensing interface. The ratio between the two probes and their surface density is modulated so that direct cross-linking between the two immobilized probes is suppressed by the average distance between two such probes. Upon protein binding, the protein molecule may bridge that gap by itself. The signaling probe can carry any motif of signal amplification. And here a Cu-ion-complexed motif, which can exhibit peroxidase-like activity upon electrochemical agitation, is employed multipurposely as the catalyst for cross-linking, cleavage, and signal amplification. Three nonhomologous target proteins can be sensitively quantified in serum-spiked samples and clinical sample detection of one of them is also successful; these results suggest the potential of the proposed method in future clinical applications.

Rational design of affinity ligands for bioseparation

Affinity adsorbents have been the cornerstone in protein purification. The selective nature of the molecular recognition interactions established between an affinity ligands and its target provide the basis for efficient capture and isolation of proteins. The plethora of affinity adsorbents available in the market reflects the importance of affinity chromatography in the bioseparation industry. Ligand discovery relies on the implementation of rational design techniques, which provides the foundation for the engineering of novel affinity ligands. The main goal for the design of affinity ligands is to discover or improve functionality, such as increased stability or selectivity. However, the methodologies must adapt to the current needs, namely to the number and diversity of biologicals being developed, and the availability of new tools for big data analysis and artificial intelligence. In this review, we offer an overview on the development of affinity ligands for bioseparation, including the evolution of rational design techniques, dating back to the years of early discovery up to the current and future trends in the field.

Gold-Decorated M13 I-Forms and S-Forms for Targeted Photothermal Lysis of Bacteria

With the emergence of multidrug-resistant bacteria, photothermal therapy has been proposed as an alternative to antibiotics for targeting and killing pathogens. In this study, two M13 bacteriophage polymorphs were studied as nanoscaffolds for plasmonic bactericidal agents. Receptor-binding proteins found on the pIII minor coat protein targeted Escherichia coli bacteria with F-pili (F⁺ strain), while a gold-binding peptide motif displayed on the pVIII major coat protein templated Au nanoparticles. Temperature-dependent exposure to a chloroform-water interface transformed the native filamentous phage into either rod-like or spheroid structures. The morphology, geometry, and size of the polymorphs, as well as the receptor-binding protein and host cell receptor interaction were studied using electron microscopy. Au/template structures were formed through incubation with Au colloid, and optical absorbance was measured. Despite the closely packed Au nanoparticle layer on the surface the viral scaffolds, electron microscopy confirmed that host receptor affinity was retained. Photothermal bactericidal studies were performed using 532 nm laser irradiation with a variety of powers and exposure times. Bacterial viability was assessed using colony count. With the shape-modified M13 scaffolds, up to 64% of E. coli were killed within 20 min. These studies demonstrate the promise of i-form and s-form polymorphs for the directed plasmonic-based photothermal killing of bacteria.

Polymerization nicking-triggered LAMP cascades enable exceptional signal amplification for aptamer-based label-free detection of trace proteins in human serum

Detecting molecular biomarkers in high sensitivity plays an important role in the diagnosis of various diseases at the early stage. Here, by combining the target-induced polymerization nicking reaction (TIPNR) with the loop-mediated isothermal amplification (LAMP), we describe an ultrasensitive and label-free aptamer-based sensing method for detecting low levels of proteins in human serum by using thrombin as the model target analyte. The target thrombin binds and causes spontaneous assembly of two distinct aptamer probes to form the templates for the polymerization nicking reaction recycling amplification to produce many forward inner primer sequences. Subsequently, downstream LAMP reactions are initiated by these sequences for the generation of tremendous DNA hairpins with various lengths via automated cyclic strand displacement reactions. The SYBR Green I organic dye further binds the many hairpins to show drastically amplified fluorescence for ultrasensitive detection of thrombin down to 3.6 fM in the linear range from 0.01 pM to 10 nM. Such a sensing method based on aptamers has high discrimination capability for the target molecules against other non-specific proteins and is applicable for diluted serum samples. With the successful demonstration of the substantial signal amplification ability and simplicity feature of this assay approach, highly sensitive and convenient detection of other disease biomarkers with this method can be envisioned in the near future.

Emerging biomaterials for downstream manufacturing of therapeutic proteins

Downstream processing is considered one of the most challenging phases of industrial manufacturing of therapeutic proteins, accounting for a large portion of the total production costs. The growing demand for therapeutic proteins in the biopharmaceutical market in addition to a significant rise in upstream titers have placed an increasing burden on the downstream purification process, which is often limited by high cost and insufficient capacities. To achieve efficient production and reduced costs, a variety of biomaterials have been exploited to improve the current techniques and also to develop superior alternatives. In this work, we discuss the significance of utilizing traditional biomaterials in downstream processing and review the recent progress in the development of new biomaterials for use in protein separation and purification. Several representative methods will be highlighted and discussed in detail, including affinity chromatography, non-affinity chromatography, membrane separations, magnetic separations, and precipitation/phase separations. STATEMENT OF SIGNIFICANCE: Nowadays, downstream processing of therapeutic proteins is facing great challenges created by the rapid increase of the market size and upstream titers, starving for significant improvements or innovations in current downstream unit operations. Biomaterials have been widely used in downstream manufacturing of proteins and efforts have been continuously devoted to developing more advanced biomaterials for the implementation of more efficient and economical purification methods. This review covers recent advances in the development and application of biomaterials specifically exploited for various chromatographic and non-chromatographic techniques, highlighting several promising alternative strategies.

An aptamer assay for aflatoxin B1 detection using Mg2+ mediated free zone capillary electrophoresis coupled with laser induced fluorescence

We described an aptamer based and Mg²⁺ mediated free zone capillary electrophoresis-laser induced fluorescence (CE-LIF) assay for aflatoxin B1 (AFB1) detection. This CE-LIF assay applied an anti-AFB1 aptamer with a single fluorescein (FAM) label at 5' end and a short complementary DNA (cDNA). In the absence of AFB1, the cDNA hybridized with the aptamer probe and formed a duplex DNA. The use of running buffer containing MgCl₂ allowed good isolation of the duplex DNA from the single stranded DNA in CE. We found introducing a biotin label on the cDNA further improved the isolation. When AFB1 existed in sample solution, the aptamer probe bound with AFB1, dissociating from the duplex DNA. Thus, the duplex DNA peak decreased, while the aptamer probe peak increased during CE-LIF analysis. We achieved detection of AFB1 by measuring the aptamer probe peak. The length of cDNA, the ratio of aptamer to cDNA, and the concentration of MgCl₂ in sample buffer and separation buffer had great effect on the aptamer based CE-LIF assay. Under optimized conditions, the detection limit of AFB1 was 0.2 nM, and the dynamic range was from 0.2 nM to 500 nM. Limit of quantitation was 0.5 nM. This CE-LIF assay enabled detection of AFB1 spiked in diluted human serum, diluted human urine, and corn flour samples. This assay exhibits potential for wide application as it integrates the rapidity, high sensitivity, low sample consumption of CE-LIF analysis and the strengths of aptamer.

Molecularly imprinted polymer-decorated signal on-off ratiometric electrochemical sensor for selective and robust dopamine detection

Dopamine (DA), as one of the central neurotransmitters, plays an important role in many physiological and pathological processes. Detection of DA is critical to diagnose and monitor some neurological diseases. In this work, a novel on-off ratiometric electrochemical sensor with molecularly imprinted polymers (MIPs) as target molecule recognizer has been developed for selective and accurate detection of DA. Nanoporous gold (NPG) was electrodeposited on bare gold electrode, which not only benefited the output signal amplification, but also provided enlarged surface for immobilization of polythionine (pThi) and MIPs. Oxidation of DA and pThi served as response signal and internal reference signal, respectively. The oxidation peak currents of DA at +0.12 V increased with increasing the concentration of DA, while the peak currents of pThi at -0.2 V decreased simultaneously. Due to the specificity from MIPs and the built-in correction from pThi, the fabricated sensor showed excellent performance in view of selectivity and reproducibility. It's worth to mention that even if the surface area and morphology of working electrode underwent huge variation deliberately, the assay deviation among these ratiometric sensors was largely reduced around 10 times. The proposed sensor demonstrated a broad dynamic range of 0.3-100 μM, as well as a low detection limit of 0.1 μM (S/N = 3). Moreover, superior anti-interfering ability toward DA detection was obtained despite the presence of interferents at high concentration in artificial cerebrospinal fluid (aCSF). Therefore, this work is expected to provide an alternative pathway for constructing ratiometric electrochemical sensor and offer reliable determination of small molecules with high selectivity and stability.

Subtyping of influenza A H1N1 virus using a label-free electrochemical biosensor based on the DNA aptamer targeting the stem region of HA protein

Rapid subtyping of influenza viruses in clinical laboratories has been increasingly important because three subtypes (seasonal H1N1, H3N2, and 2009 H1N1) of influenza A virus currently disseminated in humans have variable susceptibilities to antiviral drug. Herein, we present DNA aptamers for selective detection of influenza A H1N1 (seasonal and 2009 pandemic H1N1) viruses by targeting recombinant influenza A mini-hemagglutinin (mini-HA) protein (the stable stem region of HA) and whole H1N1 viruses. The dissociation constants (K_D) of aptamer candidates V46 and V57 were 19.2 nM and 29.6 nM, respectively, according to electrochemical characterization (differential pulse voltammetry), demonstrating strong binding to mini-HA. In comparison, the K_D of the influenza virus antibodies is in the range of 1 μM-10 nM. Aptamer V46 showed higher specificity and binding affinity to the mini-HA protein and H1N1 subtypes, and it was also incorporated into an indium tin oxide-based electrochemical sensor, showing sensitive and specific detection of H1N1 viruses, with a limit of detection (LOD) of 3.7 plaque-forming units per mL. The binding affinity, specificity, and LOD achieved with the electrochemical sensor suggest that it can be used for rapid subtyping of H1N1. We also propose that this aptamer can be used for the neutralization of H1N1 subtypes, suggesting potential therapeutic and diagnostic applications.

Advances on Aptamers against Protozoan Parasites

Aptamers are single-stranded DNA or RNA sequences with a unique three-dimensional structure that allows them to recognize a particular target with high affinity. Although their specific recognition activity could make them similar to monoclonal antibodies, their ability to bind to a large range of non-immunogenic targets greatly expands their potential as tools for diagnosis, therapeutic agents, detection of food risks, biosensors, detection of toxins, drug carriers, and nanoparticle markers, among others. One aptamer named Pegaptanib is currently used for treating macular degeneration associated with age, and many other aptamers are in different clinical stages of development of evaluation for various human diseases. In the area of parasitology, research on aptamers has been growing rapidly in the past few years. Here we describe the development of aptamers raised against the main protozoan parasites that affect hundreds of millions of people in underdeveloped and developing countries, remaining a major health concern worldwide, i.e. Trypanosoma spp., Plasmodium spp., Leishmania spp., Entamoeba histolytica, and Cryptosporidium parvuum. The latest progress made in this area confirmed that DNA and RNA aptamers represent attractive alternative molecules in the search for new tools to detect and treat these parasitic infections that affect human health worldwide.

Antimicrobial Peptides: Powerful Biorecognition Elements to Detect Bacteria in Biosensing Technologies

Bacterial infections represent a serious threat in modern medicine. In particular, biofilm treatment in clinical settings is challenging, as biofilms are very resistant to conventional antibiotic therapy and may spread infecting other tissues. To address this problem, biosensing technologies are emerging as a powerful solution to detect and identify bacterial pathogens at the very early stages of the infection, thus allowing rapid and effective treatments before biofilms are formed. Biosensors typically consist of two main parts, a biorecognition moiety that interacts with the target (i.e., bacteria) and a platform that transduces such interaction into a measurable signal. This review will focus on the development of impedimetric biosensors using antimicrobial peptides (AMPs) as biorecognition elements. AMPs belong to the innate immune system of living organisms and are very effective in interacting with bacterial membranes. They offer unique advantages compared to other classical bioreceptor molecules such as enzymes or antibodies. Moreover, impedance-based sensors allow the development of label-free, rapid, sensitive, specific and cost-effective sensing platforms. In summary, AMPs and impedimetric transducers combine excellent properties to produce robust biosensors for the early detection of bacterial infections.

Slow Off-Rate Modified Aptamer (SOMAmer) as a Novel Reagent in Immunoassay Development for Accurate Soluble Glypican-3 Quantification in Clinical Samples

Accurate quantification of soluble glypican-3 in clinical samples using immunoassays is challenging, because of the lack of appropriate antibody reagents to provide a full spectrum measurement of all potential soluble glypican-3 fragments in vivo. Glypican-3 SOMAmer (slow off-rate modified aptamer) is a novel reagent that binds, with high affinity, to a far distinct epitope of glypican-3, when compared to all available antibody reagents generated in-house. This paper describes an integrated analytical approach to rational selection of key reagents based on molecular characterization by epitope mapping, with the focus on our work using a SOMAmer as a new reagent to address development challenges with traditional antibody reagents for the soluble glypican-3 immunoassay. A qualified SOMAmer-based assay was developed and used for soluble glypican-3 quantification in hepatocellular carcinoma (HCC) patient samples. The assay demonstrated good sensitivity, accuracy, and precision. Data correlated with those obtained using the traditional antibody-based assay were used to confirm the clinically relevant soluble glypican-3 forms in vivo. This result was reinforced by a liquid chromatography tandem mass spectrometry (LC-MS/MS) assay quantifying signature peptides generated from trypsin digestion. The work presented here offers an integrated strategy for qualifying aptamers as an alternative affinity platform for immunoassay reagents that can enable speedy assay development, especially when traditional antibody reagents cannot meet assay requirements.

In Silico Selection Approach to Develop DNA Aptamers for a Stem-like Cell Subpopulation of Non-small Lung Cancer Adenocarcinoma Cell Line A549

Background

Detection of circulating lung cancer cells with cancer-stem like characteristics would represent an improved tool for disease prognosis. However, current antibodies based methods have some disadvantages and therefore cell SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was used to develop DNA aptamers, recognizing cell surface markers of non-small lung carcinoma (NSLC) cells.

Materials and methods

The human adenocarcinoma cell line A549 was used for selection in seven cell SELEX cycles. We used human blood leukocytes for negative selection, and lung stem cell protein marker CD90 antibody binding A549 cells for positive selection.

Results

The obtained oligonucleotide sequences after the seventh SELEX cycle were subjected to in silico selection analysis based on three independent types of bioinformatics approaches, selecting two closely related aptamer candidates in terms of consensus sequences, structural motifs, binding affinity (Kd) and stability (ΔG). We selected and identified the aptamer A155_18 with very good binding characteristics to A459 cells, selected for CD90 antibody binding. The calculated phylogenetic tree showed that aptamers A155_18 and the known A549 cell aptamer S6 have a close structural relationship. MEME sequence analysis showed that they share two unique motifs, not present in other sequences.

Conclusions

The novel aptamer A155_18 has strong binding affinity for A549 lung carcinoma cell line subpopulation that is expressing stem cell marker CD90, indicating a possible stemness, characteristic for the A459 line, or a subpopulation present within this cell line. This aptamer can be applied as diagnostic tool, identifying NSLC circulating cells.

High performance affinity chromatography and related separation methods for the analysis of biological and pharmaceutical agents

The last few decades have witnessed the development of many high-performance separation methods that use biologically related binding agents. The combination of HPLC with these binding agents results in a technique known as high performance affinity chromatography (HPAC). This review will discuss the general principles of HPAC and related techniques, with an emphasis on their use for the analysis of biological compounds and pharmaceutical agents. Various types of binding agents for these methods will be considered, including antibodies, immunoglobulin-binding proteins, aptamers, enzymes, lectins, transport proteins, lipids, and carbohydrates. Formats that will be discussed for these methods range from the direct detection of an analyte to indirect detection based on chromatographic immunoassays, as well as schemes based on analyte extraction or depletion, post-column detection, and multi-column systems. The use of biological agents in HPLC for chiral separations will also be considered, along with the use of HPAC as a tool to screen or study biological interactions. Various examples will be presented to illustrate these approaches and their applications in fields such as biochemistry, clinical chemistry, and pharmaceutical research.

Electrochemical biosensing based on protein-directed carbon nanospheres embedded with SnOx and TiO2 nanocrystals for sensitive detection of tobramycin

A series of nanocomposites comprised of homogeneous mesoporous carbon nanospheres embedded with SnO_x (x = 0, 1, or 2) and TiO₂ nanocrystals using bovine serum albumin (BSA) as template followed by calcinated at different temperatures (300, 500, 700, and 900°C) were prepared, and were denoted as SnO_x@TiO₂@mC. Then a novel electrochemical biosensing strategy for detecting tobramycin (TOB) based on the nanocomposites was constructed. The as-prepared SnO_x@TiO₂@mC nanocomposites not only possess high specific surface area and good electrochemical activity but also exhibit strong bioaffinity with the aptamer strands, therefore, they were applied as the scaffold for anchoring TOB-targeted aptamer and further used to sensitively detect trace TOB in aqueous solutions. By comparing the electrochemical biosensing responses toward TOB detection based on the four SnO_x@TiO₂@mC nanocomposites, the biosensing system constructed with SnO_x@TiO₂@mC₉₀₀ (derived at 900°C) demonstrated the highest determination efficiency, high selectivity, and good stability. In particular, the new proposed aptasensing method based on SnO_x@TiO₂@mC nanocomposite exhibits considerable potential for the quantitative detection of TOB in the biomedical field.

Aptamer-Based Carboxyl-Terminated Nanocrystalline Diamond Sensing Arrays for Adenosine Triphosphate Detection

Here, we propose simple diamond functionalization by carboxyl termination for adenosine triphosphate (ATP) detection by an aptamer. The high-sensitivity label-free aptamer sensor for ATP detection was fabricated on nanocrystalline diamond (NCD). Carboxyl termination of the NCD surface by vacuum ultraviolet excimer laser and fluorine termination of the background region as a passivated layer were investigated by X-ray photoelectron spectroscopy. Single strand DNA (amide modification) was used as the supporting biomolecule to immobilize into the diamond surface via carboxyl termination and become a double strand with aptamer. ATP detection by aptamer was observed as a 66% fluorescence signal intensity decrease of the hybridization intensity signal. The sensor operation was also investigated by the field-effect characteristics. The shift of the drain current–drain voltage characteristics was used as the indicator for detection of ATP. From the field-effect characteristics, the shift of the drain current–drain voltage was observed in the negative direction. The negative charge direction shows that the aptamer is capable of detecting ATP. The ability of the sensor to detect ATP was investigated by fabricating a field-effect transistor on the modified NCD surface.

DNAzyme-aptamer or aptamer-DNAzyme paradigm: Biochemical approach for aflatoxin analysis

DNAzyme and aptamer conjugations have already been used for sensitive and accurate detection of several molecules. In this study, we tested the relationship between conjugation orientation of DNAzyme and aflatoxin B1 aptamer and their subsequent peroxidase activity. Circular dichroism (CD) spectroscopy and biochemical analysis were used here to differentiate between these two conjugation patterns. Results showed that DNAzyme-aptamer has more catalytic activity and efficiency than aptamer-DNAzyme. Thereby, DNAzyme-aptamer with its superior efficiency can be used for design and development of more sensitive aflatoxin B1 DNA based biosensors.

DNA aptamer probes for detection of estrogen receptor α positive carcinomas

Estrogen receptor alpha (ERα) also known as NR3A1 (nuclear receptor subfamily 3, group A, member 1) is a ligand-activated transcription factor. It is an important biomarker for breast cancer metastasis. In the present study, we report a novel DNA aptamer candidate against estrogen receptor (ER) alpha structure. The enriched aptamer candidate was obtained after 14 iterative cycles of in vitro protein-SELEX process. Isothermal calorimetry study suggests the nanomolar sensitivity of the candidate ER_Apt1 to its target protein. Fluorescence- and chemiluminescence-binding assays confirm the specificity of the candidate aptamer to ER alpha positive breast cancer cell line. Comparative analysis of ER_Apt1 to ER alpha monoclonal antibody was also performed to analyze the expression of ER alpha in various malignant cancer cell line. Cytochemical and immunohistochemistry assay indicates its potential use as a diagnostic agent against ERα positive carcinomas. The nucleotide aptamer sequences described in the present study can be used for the detection, treatment, prophylaxis and diagnosis of ERα-related disorder.

MicroRNAs in bone development and their diagnostic and therapeutic potentials in osteoporosis

MicroRNAs (miRNAs) are small non-coding RNAs approximately 22 nucleotides in length. miRNAs play an important role in the posttranscriptional regulation of gene expression via translational repression and targeting messenger RNA for degradation. In vivo and in vitro evidence has established the importance of miRNAs in physiology and developmental processes such as cell proliferation, differentiation, survival and apoptosis. miRNA dysregulation is associated with the pathogenesis of cardiovascular diseases, metabolic syndromes, and degenerative diseases. An increasing number of miRNAs have been found to play an important role in bone homeostasis. In this review, the roles of miRNAs in the regulation of bone formation and resorption as well as miRNAs that regulate key transcription factors of osteogenesis are discussed. A special emphasis is given to miRNAs whose direct targets have been identified. The miRNAs that contribute to the pathogenesis of osteoporosis and their therapeutic potential are also considered.

Fluorescence based fiber optic and planar waveguide biosensors. A review

The application of optical biosensors, specifically those that use optical fibers and planar waveguides, has escalated throughout the years in many fields, including environmental analysis, food safety and clinical diagnosis. Fluorescence is, without doubt, the most popular transducer signal used in these devices because of its higher selectivity and sensitivity, but most of all due to its wide versatility. This paper focuses on the working principles and configurations of fluorescence-based fiber optic and planar waveguide biosensors and will review biological recognition elements, sensing schemes, as well as some major and recent applications, published in the last ten years. The main goal is to provide the reader a general overview of a field that requires the joint collaboration of researchers of many different areas, including chemistry, physics, biology, engineering, and material science.

RNA aptamers as genetic control devices: the potential of riboswitches as synthetic elements for regulating gene expression

RNA utilizes many different mechanisms to control gene expression. Among the regulatory elements that respond to external stimuli, riboswitches are a prominent and elegant example. They consist solely of RNA and couple binding of a small molecule ligand to the so-called "aptamer domain" with a conformational change in the downstream "expression platform" which then determines system output. The modular organization of riboswitches and the relative ease with which ligand-binding RNA aptamers can be selected in vitro against almost any molecule have led to the rapid and widespread adoption of engineered riboswitches as artificial genetic control devices in biotechnology and synthetic biology over the past decade. This review highlights proof-of-principle applications to demonstrate the versatility and robustness of engineered riboswitches in regulating gene expression in pro- and eukaryotes. It then focuses on strategies and parameters to identify aptamers that can be integrated into synthetic riboswitches that are functional in vivo, before finishing with a reflection on how to improve the regulatory properties of engineered riboswitches, so that we can not only further expand riboswitch applicability, but also finally fully exploit their potential as control elements in regulating gene expression.

Modern affinity reagents: Recombinant antibodies and aptamers

Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research.

Computing with synthetic protocells

In this article we present a new kind of computing device that uses biochemical reactions networks as building blocks to implement logic gates. The architecture of a computing machine relies on these generic and composable building blocks, computation units, that can be used in multiple instances to perform complex boolean functions. Standard logical operations are implemented by biochemical networks, encapsulated and insulated within synthetic vesicles called protocells. These protocells are capable of exchanging energy and information with each other through transmembrane electron transfer. In the paradigm of computation we propose, protoputing, a machine can solve only one problem and therefore has to be built specifically. Thus, the programming phase in the standard computing paradigm is represented in our approach by the set of assembly instructions (specific attachments) that directs the wiring of the protocells that constitute the machine itself. To demonstrate the computing power of protocellular machines, we apply it to solve a NP-complete problem, known to be very demanding in computing power, the 3-SAT problem. We show how to program the assembly of a machine that can verify the satisfiability of a given boolean formula. Then we show how to use the massive parallelism of these machines to verify in less than 20 min all the valuations of the input variables and output a fluorescent signal when the formula is satisfiable or no signal at all otherwise.

Aptamer for imaging and therapeutic targeting of brain tumor glioblastoma

Aptamers are short single-stranded nucleic acids (RNA or ssDNA), identified by an in vitro selection process, denominated SELEX, from a partially random oligonucleotide library. They bind to a molecular target, a protein or other complex macromolecular structures of interest with high affinity and specificity, comparable to those of antibodies. Recently, aptamer selection protocols were developed for targeting living cells, including tumors. Chemical modifications of the aptamers and modalities of their detection and delivery systems are already available with high selectivity and targeting ability for the desired cancer cell type, making them promising for diagnosis and therapy. Glioblastoma multiformae represents the most malignant and fatal stage of glioma, and is also the most frequent brain tumor. Glioblastoma-specific aptamers were developed by either targeting the whole cell surface or known glioma biomarkers. These aptamers may gain importance for imaging, tumor cell isolation from biopsies and drug delivery. In biomedical imaging techniques, aptamers coupled with radionuclide or fluorescent labels, bioconjugates and nanoparticles offer an advanced, noninvasive manner for defining the glioblastoma tissue border. Though single modality aptamer imaging probes have some limitations, these are overcome by the use of multimodal probes. Due to selectivity and chemical characteristics, aptamers can be coupled to functionalized nanoparticles and loaded with a drug, appeared promising for in vivo targeting of glioblastoma. Finally, aptamers are effective mediators for gene silencing when coupled to small interfering RNA and a viral vector, thus providing a novel tool with enhanced targeting capability in drug delivery, designed for tailored treatment of glioblastoma patients.

Recent advances in nanoparticle based aptasensors for food contaminants

Food safety and hazard analysis is a prime concern of human life, thus quality assessment of food and water is the need of the day. Recent advances in nano-biotechnology play a significant role in providing possible solutions for developing highly sensitive and affordable detection tools for food analysis. Nanomaterials based aptasensors hold great potential to overcome the drawbacks of conventional analytical techniques. Aptamers comprise a novel class of highly specific bio-recognition elements which are produced by SELEX (systematic evolution of ligands by exponential enrichment) process. They bind to target molecules by folding into 3D structures that can discriminate different chiral compounds. The flexibility in making modifications in aptamers contribute to the design of biosensors, enabling the generation of bio-recognition elements for a wide variety of target molecules. Nanomaterials such as metal nanoparticles, metal nanoclusters, metal oxide nanoparticles, metal and carbon quantum dots, graphene, carbon nanotubes and nanocomposites enable higher sensitivity by signal amplification and introduce several novel transduction principles such as enhanced chemiluminescence, fluorescence, Raman signals, electrochemical signals, enhanced catalytic activity, and super-paramagnetic properties to the biosensor. Although there are a few reviews published recently which deal with the potential of aptamers in various fields, none are devoted exclusively to the potential of aptasensors based on nanomaterials for the analysis of food contaminants. Hence, the current review discusses several transduction systems and their principles used in aptamer based nanosensors which have been developed in the past five years, the challenges faced in their designing, along with their strengths and limitations.

In-line coupling of an aptamer based miniaturized monolithic affinity preconcentration unit with capillary electrophoresis and Laser Induced Fluorescence detection

A composite 30-cm capillary was prepared. The head of the capillary was a 1.5-cm original and miniaturized aptamer-based monolithic affinity support that was in-line coupled to the end of the capillary used for capillary electrophoresis (CE) with laser induced fluorescence (LIF) detection. The device was used for the preconcentration, separation and quantification of ochratoxin A (OTA) as a test solute. The 1.5-cm preconcentration unit consists of a fritless affinity monolithic bonded with 5'-SH-modified oligonucleotide aptamers. A vinyl spacer was used for thiol-ene photoclick chemistry with a 5min irradiation at 365nm. Photografting allowed to confine the binding reaction to the desired silica monolithic segment, upstream the empty section of the CE capillary using an UV mask. The photografting procedure was optimized preparing 10-cm capillary monoliths for nano-LC. The retention factors of cationic solutes in ion-exchange nano-LC allowed to follow the aptamer binding on the monolith. The reproducibility of the photografting process was satisfactory with inter-capillary variation lower than 10%. The aptamer bonding density can be increased by successive graftings of 100μM aptamer concentration solution (5pmol/cm/grafting). The optimal conditions to successfully perform the in-line coupling (preconcentration, elution and separation of OTA) with the composite capillary were adjusted depending on individual requirements of each step but also insuring compatibility. Under optimized conditions, OTA was successfully preconcentrated and quantified down to 0.1pg (percolation of 2.65μL of a 40ng/L OTA solution). A quantitative recovery of OTA (93±2%) was achieved in a single elution of 30pg percolated OTA amount. The reproducibility of the overall process was satisfactory with a relative standard deviation lower than 10% with negligible non-specific adsorption. This device was applied for the preconcentration and analysis of OTA in beer and wine at the ppb level within a total analysis time of 30min.

Development of ssDNA aptamers as potent inhibitors of Mycobacterium tuberculosis acetohydroxyacid synthase

Acetohydroxyacid synthase (AHAS) from Mycobacterium tuberculosis (Mtb) is a promising potential drug target for an emerging class of new anti-tuberculosis agents. In this study, we identify short (30-mer) single-stranded DNA aptamers as a novel class of potent inhibitors of Mtb-AHAS through an in vitro DNA-SELEX method. Among all tested aptamers, two candidate aptamers (Mtb-Apt1 and Mtb-Apt6) demonstrated the greatest inhibitory potential against Mtb-AHAS activity with IC50 values in the low nanomolar range (28.94±0.002 and 22.35±0.001 nM respectively). Interestingly, inhibition kinetics analysis of these aptamers showed different modes of enzyme inhibition (competitive and mixed type of inhibition respectively). Secondary structure-guided mutational modification analysis of Mtb-Apt1 and Mtb-Apt6 identified the minimal region responsible for their inhibitory action and consequently led to 17-mer and 20-mer shortened aptamers that retained equivalent or greater inhibitory potential. Notably, a modeling and docking exercise investigated the binding site of these two potent inhibitory aptamers on the target protein and showed possible involvement of some key catalytic dimer interface residues of AHAS in the DNA-protein interactions that lead to its potent inhibition. Importantly, these two short candidate aptamers, Mtb-Apt1 (17-mer) and Mtb-Apt6 (20-mer), also demonstrated significant growth inhibition against multidrug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) strains of tuberculosis with very low MIC of 5.36 μg/ml and 6.24 μg/ml, respectively and no significant cytotoxicity against mammalian cell line. This is the first report of functional inhibitory aptamers against Mtb-AHAS and provides the basis for development of these aptamers as novel and strong anti-tuberculosis agents.