Recent Advances in Biomolecular Detection Based on Aptamers and Nanoparticles

Nanostructured aptasensors for ricin detection and tumor therapy: exploring aptamer-protein interactions and conformational stability in biological complexities

Aptamers are distinctive single-stranded oligonucleotides derived through in vitro evolution, and exhibit exceptional ability in binding to target proteins. Structural modifications of aptamers can profoundly regulate their interactions with proteins, thereby influencing associated cellular behavior. Recent research focused on modulating aptamer-protein interaction in complex biological environments to regulate various biological processes. However, in such crowded conditions, aptamer conformation and stability are susceptible to nuclease degradation, which can impair stable binding to target. Ricin is recognized as a significant biological toxin protein, distinguished by its widespread availability, remarkable dissemination, and resilience including wide pH tolerance, remarkable thermostability, and solubility. RTA is an enzymatic subunit of ricin, that can inactivate approximately 2000 ribosomes per minute, rapidly halting protein synthesis, making it a powerful candidate for tumor therapy. By leveraging the potent cytotoxicity of ricin, coupled with the targeting precision of aptamers and the versatility of nanomaterials, a powerful approach emerges for both targeted tumor therapy and highly sensitive detection of ricin. Although there have been some insightful reports on aptamers applied in ricin detection, a systematic discussion remains limited. In this context, we provide an in-depth overview of techniques used to analyze aptamer-ricin interactions and explore the potential of ricin-aptamer interactions in clinical diagnosis.

Research and application discussion on new technology for detecting cadmium ions based on a near-red light carbon dot fluorescence quenching method

Cadmium ions are considered one of the most dangerous heavy metal pollutants. The human body does not require cadmium for growth and development, yet continuous intake of cadmium ions due to environmental pollution can lead to their accumulation in the body. This accumulation can result in damage to the urinary system and, in severe cases, pose life-threatening risks. The current conventional methods for analyzing heavy metals in the environment primarily include inductively coupled plasma mass spectrometry (ICP-MS), atomic absorption spectrometry (AAS), and inductively coupled plasma atomic emission spectrometry (ICP-AES). These methods are known for their drawbacks such as complex testing procedures, as well as expensive instrumentation and equipment. In this study, a novel technique for detecting cadmium ions using the near-red light carbon spot fluorescence burst method was developed. The near-infrared carbon dots (NIR-CDs) exhibited vibrant deep red fluorescence ranging from 625 to 710 nm, with a prominent peak at 685 nm. At a pH of 7 and a concentration of 0.1805 g L-1, the linear detection range for Cd2+ was determined to be 0.15-0.75 μM. The CDs demonstrated selectivity for Cd2+ detection, boasting an impressive detection limit of 0.397 nM. Mechanistic studies indicated that the interaction between red carbon dots and cadmium ions involved dynamic bursting of the ions. The practical application of the near-red light carbon spot fluorescence burst method for detecting cadmium ions could be further explored through the establishment of a Cd2+ recovery detection system.

Carbon nanomaterial-based aptasensors for rapid detection of foodborne pathogenic bacteria

Each year, millions of people suffer from foodborne illness due to the consumption of food contaminated with pathogenic bacteria, which severely challenges global health. Therefore, it is essential to recognize foodborne pathogens swiftly and correctly. However, conventional detection techniques for bacterial pathogens are labor-intensive, low selectivity, and time-consuming, highlighting a notable knowledge gap. A novel approach, aptamer-based biosensors (aptasensors) linked to carbon nanomaterials (CNs), has shown the potential to overcome these limitations and provide a more reliable method for detecting bacterial pathogens. Aptamers, short single-stranded DNA (ssDNA)/RNA molecules, serve as bio-recognition elements (BRE) due to their exceptionally high affinity and specificity in identifying foodborne pathogens such as Salmonella spp., Escherichia coli (E. coli), Listeria monocytogenes, Campylobacter jejuni, and other relevant pathogens commonly associated with foodborne illnesses. Carbon nanomaterials' high surface area-to-volume ratio contributes unique characteristics crucial for bacterial sensing, as it improves the binding capacity and signal amplification in the design of aptasensors. Furthermore, aptamers can bind to CNs and create aptasensors with improved signal specificity and sensitivity. Hence, this review intends to critically review the current literature on developing aptamer functionalized CN-based biosensors by transducer optical and electrochemical for detecting foodborne pathogens and explore the advantages and challenges associated with these biosensors. Aptasensors conjugated with CNs offers an efficient tool for identifying foodborne pathogenic bacteria that is both precise and sensitive to potentially replacing complex current techniques that are time-consuming.

Microfluidic Optical Aptasensor for Small Molecules Based on Analyte-Tuned Growth of Gold Nanoseeds and Machine Learning-Enhanced Spectrum Analysis: Rapid Detection of Mycotoxins

Natural toxins, mainly small molecules, are a category of chemical hazards in agri-food systems that pose threats to both public health and food security. Current standard methods for monitoring these toxins, predominantly based on liquid chromatography-mass spectrometry, are costly, labor-intensive, and complex. This study presents the development of a novel microfluidic optical aptasensor for rapid detection of small molecules based on analyte-tuned growth of gold nanoseeds combined with machine learning-enhanced spectrum analysis. We discovered and optimized a previously unreported growth pattern of aptamer-coated nanoparticles in the presence of different concentrations of analyte, enabling the detection of a major mycotoxin in food. The entire analysis was miniaturized on a customized microfluidic platform, allowing for automated spectral acquisition with precise liquid manipulation. A machine learning model, based on random forest with feature engineering, was developed and evaluated for spectrum analysis, significantly enhancing the prediction of mycotoxin concentrations. This approach extended the detection limit determined by the conventional method (∼72 ppb with high variation) to a wider range of 10 ppb to 100 ppm with high accuracy (overall mean absolute percentage error of 5.7%). The developed analytical tool provides a promising solution for detecting small molecules and monitoring chemical hazards in agri-food systems and the environment.

Immunodetection of Poorly Soluble Substances: Limitations and Their Overcoming

Immunoassays based on the specific antigen-antibody interactions are efficient tools to detect various compounds and estimate their content. Usually, these assays are implemented in water-saline media with composition close to physiological conditions. However, many substances are insoluble or cannot be molecularly dispersed in such media, which objectively creates problems when interacting in aquatic environments. Thus, obtaining immunoreactants and implementing immunoassays of these substances need special methodological solutions. Hydrophobicity of antigens as well as their limited ability to functionalization and conjugation are often overlooked when developing immunoassays for these compounds. The main key finding is the possibility to influence the behavior of hydrophobic compounds for immunoassays, which requires specific approaches summarized in the review. Using the examples of two groups of compounds-surfactants (alkyl- and bisphenols) and fullerenes, we systematized the existing knowledge and experience in the development of immunoassays. This review addresses the challenges of immunodetection of poorly soluble substances and proposes solutions such as the use of hydrotropes, other solubilization techniques, and alternative receptors (aptamers and molecularly imprinted polymers).

Polyethyleneimine capped silver nanoclusters based turn-off-on fluorescence sensor for the determination of glutathione

A polyethyleneimine capped silver nanoclusters (PEI-AgNCs) based turn-off-on fluorescence sensor has been developed to determine glutathione (GSH) effectively. The fluorescence intensity of silver nanoclusters (AgNCs) has been quenched by Cu(II) and recovered by adding GSH. The quenching of fluorescence intensity of PEI-AgNCs by Cu(II) and recovery of the emission intensity of PEI-AgNCs after the addition of GSH is supposed to be ground state adduct formation. Due to the greater affinity of Cu(II) towards GSH compared to that to PEI-AgNCs, the defragmentation of PEI-AgNCs-Cu(II) adduct occurs after the addition of GSH to the solution, resulting in the recovery of emission intensity of PEI-AgNCs. Characterisation studies of the probe have been done using FT-IR spectroscopy, XPS analysis, XRD analysis, UV-visible and Fluorescence spectrophotometry, EDX spectroscopy and TEM analysis. Different experimental parameters were optimised. Under optimised analytical conditions, the sensor showed a wide linear range for the quantification of GSH from 1.00 × 10-4 M to 3.00 × 10-6 M with a detection limit (LOD) of 8.00 × 10-7 M. Selectivity and interference studies were done in the presence of different structurally similar and coexisting species of GSH in blood. The practical utility of the proposed sensor has been validated in artificial blood serum.

Biomimetic Nanoparticles for the Diagnosis and Therapy of Atherosclerosis

Atherosclerosis (AS) is a chronic inflammation of blood vessels, which often has no obvious symptoms in the early stage of the disease, but when atherosclerotic plaques are formed, they often cause lumen blockage, and even plaque rupture leads to thrombosis, that is the essential factor of cardiovascular events, for example myocardial infarction, cerebral infarction, and renal atrophy. Therefore, it is considerably significant for the early recognition and precise therapy of plaque. Biomimetic nanoparticles (BNPs), especially those coated with cell membranes, can retain the biological function of cell membranes or cells, which has led to extensive research and application in the diagnosis and treatment of AS in recent years. In this review, we summarized the roles of various key cells in AS progression, the construction of biomimetic nanoparticles based on these key cells as well as their applications in AS diagnosis and therapy. Furthermore, we give a challenge and prospect of biomimetic nanoparticles in AS, hoping to elevate their application quality and the possibility of clinical translation.

Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives

Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.

Gold Nanoparticles in Nanobiotechnology: From Synthesis to Biosensing Applications

Nanobiotechnology has ushered in a new era of scientific discovery where the unique properties of nanomaterials, such as gold nanoparticles, have been harnessed for a wide array of applications. This review explores gold nanoparticles' synthesis, properties, and multidisciplinary applications, focusing on their role as biosensors. Gold nanoparticles possess exceptional physicochemical attributes, including size-dependent optical properties, biocompatibility, and ease of functionalization, making them promising candidates for the development of biosensing platforms. The review begins by providing a comprehensive overview of gold nanoparticle synthesis techniques, highlighting the advantages and disadvantages of various approaches. It then delves into the remarkable properties that underpin their success in biosensing, such as localized surface plasmon resonance and enhanced surface area. The discussion also includes the functionalization strategies that enable specific binding to biomolecules, enhancing the sensitivity and selectivity of gold-nanoparticle-based biosensors. Furthermore, this review surveys the diverse applications of gold nanoparticles in biosensing, encompassing diagnostics, environmental monitoring, and drug delivery. The multidisciplinary nature of these applications underscores the versatility and potential of gold nanoparticles in addressing complex challenges in healthcare and environmental science. The review emphasizes the pressing need for further exploration and research in the field of nanobiotechnology, particularly regarding the synthesis, properties, and biosensing applications of gold nanoparticles. With their exceptional physicochemical attributes and versatile functionalities, gold nanoparticles present a promising avenue for addressing complex challenges in healthcare and environmental science, making it imperative to advance our understanding of their synthesis, properties, and applications for enhanced biosensing capabilities and broader scientific innovation.

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.

Nanotechnology improves the detection of bacteria: Recent advances and future perspectives

Nanotechnology has advanced significantly, particularly in biomedicine, showing promise for nanomaterial applications. Bacterial infections pose persistent public health challenges due to the lack of rapid pathogen detection methods, resulting in antibiotic overuse and bacterial resistance, threatening the human microbiome. Nanotechnology offers a solution through nanoparticle-based materials facilitating early bacterial detection and combating resistance. This study explores recent research on nanoparticle development for controlling microbial infections using various nanotechnology-driven detection methods. These approaches include Surface Plasmon Resonance (SPR) Sensors, Surface-Enhanced Raman Scattering (SERS) Sensors, Optoelectronic-based sensors, Bacteriophage-Based Sensors, and nanotechnology-based aptasensors. These technologies provide precise bacteria detection, enabling targeted treatment and infection prevention. Integrating nanoparticles into detection approaches holds promise for enhancing patient outcomes and mitigating harmful bacteria spread in healthcare settings.

Classification and applications of nanomaterials in vitro diagnosis

With the rapid development of clinical diagnosis and treatment, many traditional and conventional in vitro diagnosis technologies are unable to meet the demands of clinical medicine development. In this situation, nanomaterials are rapidly developing and widely used in the field of in vitro diagnosis. Nanomaterials have distinct size-dependent physical or chemical properties, and their optical, magnetic, electrical, thermal, and biological properties can be modulated at the nanoscale by changing their size, shape, chemical composition, and surface functional groups, particularly because they have a larger specific surface area than macromaterials. They provide an amount of space to modify different molecules on their surface, allowing them to detect small substances, nucleic acids, proteins, and microorganisms. Combining nanomaterials with in vitro diagnosis is expected to result in lower detection limits, higher sensitivity, and stronger selectivity. In this review, we will discuss the classfication and properties of some common nanomaterials, as well as their applications in protein, nucleic acids, and other aspect detection and analysis for in vitro diagnosis, especially on aging-related nanodiagnostics. Finally, it is summarized with guidelines for in vitro diagnosis.

Signal amplification strategy of DNA self-assembled biosensor and typical applications in pathogenic microorganism detection

Biosensors have emerged as ideal analytical devices for various bio-applications owing to their low cost, convenience, and portability, which offer great potential for improving global healthcare. DNA self-assembly techniques have been enriched with the development of innovative amplification strategies, such as dispersion-to-localization of catalytic hairpin assembly, and dumbbell hybridization chain reaction, which hold great significance for building biosensors capable of realizing sensitive, rapid and multiplexed detection of pathogenic microorganisms. Here, focusing primarily on the signal amplification strategies based on DNA self-assembly, we concisely summarized the strengths and weaknesses of diverse isothermal nucleic acid amplification techniques. Subsequently, both single-layer and cascade amplification strategies based on traditional catalytic hairpin assembly and hybridization chain reaction were critically explored. Furthermore, a comprehensive overview of the recent advances in DNA self-assembled biosensors for the detection of pathogenic microorganisms is presented to summarize methods for biorecognition and signal amplification. Finally, a brief discussion is provided about the current challenges and future directions of DNA self-assembled biosensors.

Biosensors for the detection of pathogenic bacteria: current status and future perspectives

Pathogenic microorganisms pose significant threats to human health, food safety and environmental integrity. Rapid and accurate detection of these pathogens is essential to mitigate their impact. Fast, sensitive detection methods such as biosensors also play a critical role in preventing outbreaks and controlling their spread. In recent years, biosensors have emerged as a revolutionary technology for pathogen detection. This review aims to present the current developments in biosensor technology, investigate the methods by which these developments are used in the detection of pathogenic bacteria and highlight future perspectives on the subject.

Recent Advances in Metallic Nanostructures-assisted Biosensors for Medical Diagnosis and Therapy

The field of nanotechnology has witnessed remarkable progress in recent years, particularly in its application to medical diagnosis and therapy. Metallic nanostructures-assisted biosensors have emerged as a powerful and versatile platform, offering unprecedented opportunities for sensitive, specific, and minimally invasive diagnostic techniques, as well as innovative therapeutic interventions. These biosensors exploit the molecular interactions occurring between biomolecules, such as antibodies, enzymes, aptamers, or nucleic acids, and metallic surfaces to induce observable alterations in multiple physical attributes, encompassing electrical, optical, colorimetric, and electrochemical signals. These interactions yield measurable data concerning the existence and concentration of particular biomolecules. The inherent characteristics of metal nanostructures, such as conductivity, plasmon resonance, and catalytic activity, serve to amplify both sensitivity and specificity in these biosensors. This review provides an in-depth exploration of the latest advancements in metallic nanostructures-assisted biosensors, highlighting their transformative impact on medical science and envisioning their potential in shaping the future of personalized healthcare.

Novel Microsynthesis of High-Yield Gold Nanoparticles to Accelerate Research in Biosensing and Other Bioapplications

Gold nanoparticles (AuNPs) exhibit unique properties that make them appealing for applications in biosensing and other emerging fields. Despite the availability of numerous synthesis methods, important questions remain to be addressed regarding the volume effect on the synthesis yield and quality of AuNPs in the light of biosensing research. The present study addresses these issues by developing a novel microvolumetric citrate-reduction method to improve the synthesis of AuNPs, which were characterized by electronic microscopy, energy dispersive spectroscopy, zeta potential and colorimetric analysis. A comparison of the novel microsynthesis method with the standard Turkevich method demonstrated its superior performance in terms of yield, monodispersity, rapidity (in one step), reproducibility, and stability. The analytical behavior of AuNPs-based aptasensors prepared by microsynthesis was investigated using kanamycin detection and showed higher reproducibility and improved detection limits (3.4 times) compared to those of Turkevich AuNPs. Finally, the effect of pH was studied to demonstrate the suitability of the method for the screening of AuNP synthesis parameters that are of direct interest in biosensing research; the results showed an optimal pH range between 5.0 and 5.5. In summary, the approach described herein has the potential to improve research capabilities in biosensing, with the added benefits of lowering costs and minimizing waste generation in line with current trends in green nanotechnology.

From Enzymatic Dopamine Biosensors to OECT Biosensors of Dopamine

Neurotransmitters are an important category of substances used inside the nervous system, whose detection with biosensors has been seriously addressed in the last decades. Dopamine, a neurotransmitter from the catecholamine family, was recently discovered to have implications for cardiac arrest or muscle contractions. In addition to having many other neuro-psychiatric implications, dopamine can be detected in blood, urine, and sweat. This review highlights the importance of biosensors as influential tools for dopamine recognition. The first part of this article is related to an introduction to biosensors for neurotransmitters, with a focus on dopamine. The regular methods in their detection are expensive and require high expertise personnel. A major direction of evolution of these biosensors has expanded with the integration of active biological materials suitable for molecular recognition near electronic devices. Secondly, for dopamine in particular, the miniaturized biosensors offer excellent sensitivity and specificity and offer cheaper detection than conventional spectrometry, while their linear detection ranges from the last years fall exactly on the clinical intervals. Thirdly, the applications of novel nanomaterials and biomaterials to these biosensors are discussed. Older generations, metabolism-based or enzymatic biosensors, could not detect concentrations below the micro-molar range. But new generations of biosensors combine aptamer receptors and organic electrochemical transistors, OECTs, as transducers. They have pushed the detection limit to the pico-molar and even femto-molar ranges, which fully correspond to the usual ranges of clinical detection of human dopamine in body humors that cover 0.1 ÷ 10 nM. In addition, if ten years ago the use of natural dopamine receptors on cell membranes seemed impossible for biosensors, the actual technology allows co-integrate transistors and vesicles with natural receptors of dopamine, like G protein-coupled receptors. The technology is still complicated, but the uni-molecular detection selectivity is promising.

Strategies for targeted gene delivery using lipid nanoparticles and cell-derived nanovesicles

Gene therapy is a promising approach for the treatment of many diseases. However, the effective delivery of the cargo without degradation in vivo is one of the major hurdles. With the advent of lipid nanoparticles (LNPs) and cell-derived nanovesicles (CDNs), gene delivery holds a very promising future. The targeting of these nanosystems is a prerequisite for effective transfection with minimal side-effects. In this review, we highlight the emerging strategies utilized for the effective targeting of LNPs and CDNs, and we summarize the preparation methodologies for LNPs and CDNs. We have also highlighted the non-ligand targeting of LNPs toward certain organs based on their composition. It is highly expected that continuing the developments in the targeting approaches of LNPs and CDNs for the delivery system will further promote them in clinical translation.

Rapid Detection of Microparticles Using a Microfluidic Resistive Pulse Sensor Based on Bipolar Pulse-Width Multiplexing

Rapid and accurate analysis of micro/nano bio-objects (e.g., cells, biomolecules) is crucial in clinical diagnostics and drug discovery. While a traditional resistive pulse sensor can provide multiple kinds of information (size, count, surface charge, etc.) about analytes, it has low throughput. We present a unique bipolar pulse-width, multiplexing-based resistive pulse sensor for high-throughput analysis of microparticles. Signal multiplexing is enabled by exposing the central electrode at different locations inside the parallel sensing channels. Together with two common electrodes, the central electrode encodes the electrical signal from each sensing channel, generating specific bipolar template waveforms with different pulse widths. Only one DC source is needed as input, and only one combined electrical output is collected. The combined signal can be demodulated using correlation analysis and a unique iterative cancellation scheme. The accuracy of particle counting and sizing was validated using mixtures of various sized microparticles. Results showed errors of 2.6% and 6.1% in sizing and counting, respectively. We further demonstrated its accuracy for cell analysis using HeLa cells.

Recent Advances in the DNA-Mediated Multi-Mode Analytical Methods for Biological Samples

DNA-mediated nanotechnology has become a research hot spot in recent decades and is widely used in the field of biosensing analysis due to its distinctive properties of precise programmability, easy synthesis and high stability. Multi-mode analytical methods can provide sensitive, accurate and complementary analytical information by merging two or more detection techniques with higher analytical throughput and efficiency. Currently, the development of DNA-mediated multi-mode analytical methods by integrating DNA-mediated nanotechnology with multi-mode analytical methods has been proved to be an effective assay for greatly enhancing the selectivity, sensitivity and accuracy, as well as detection throughput, for complex biological analysis. In this paper, the recent progress in the preparation of typical DNA-mediated multi-mode probes is reviewed from the aspect of deoxyribozyme, aptamer, templated-DNA and G-quadruplex-mediated strategies. Then, the advances in DNA-mediated multi-mode analytical methods for biological samples are summarized in detail. Moreover, the corresponding current applications for biomarker analysis, bioimaging analysis and biological monitoring are introduced. Finally, a proper summary is given and future prospective trends are discussed, hopefully providing useful information to the readers in this research field.

Special Issue in "Nanomaterials and Their Applications in Sensing and Biosensing"

The identification of the target molecule is required for rapid and reliable clinical diagnosis and disease monitoring [...].