Nucleic acid conjugated nanomaterials for enhanced molecular recognition

A biosensor integrating the electrochemical and fluorescence strategies for detection of aflatoxin B1 based on a dual-functionalized platform

BACKGROUND

Aflatoxin B1 (AFB1), is a potent hepatic carcinogen which causes cancer by inducing DNA changes in the liver cells. Variety of methods have been developed for detection of AFB1 which are based on single mode detection strategy. Fabrication of novel platform which are compatible for multimodal detection of AFB1 provide robust performance for reliable detection of AFB1. In this study, we aimed to develop a robust biosensing platform that combines electrochemical and fluorescence techniques for the sensitive and specific detection of Aflatoxin B1.

RESULTS

The sensing platform includes the magnetic core-shell Fe3O4@AuNPs and zeolitic imidazolate framework-8 (ZIF-8). In electrochemical mode, the applied voltametric approach was used through functionalization of glassy carbon electrode and exhibited a linear range between 0.5 and 10000 pg mL-1 with LOD of 0.32 pg mL-1. Fluorescence analysis was based on the FRET on/off status of FAM-functionalized aptamer deposited on the same platform. The FAM emission recovered by the addition of AFB1 concentration in the range of 6-60 fg mL-1 with the LOD of 0.20 fg mL-1. The real sample analysis demonstrated satisfactory relative recoveries in the range of 92.81-105.32 % and 91.66-106.66 % using the electrochemical and fluorescence methods, respectively, and its reliability was confirmed by the HPLC technique.

SIGNIFICANCE

The experimental results affirm that the proposed aptasensor serves as a sensitive, efficient, and precise platform for monitoring AFB1 in both electrochemical and fluorescence detection approaches. Proposed strategy showed efficient selectivity among different analytes and was reproducible. Furthermore, the applicability of biosensor was confirmed in food and biological samples.

Advancing Tumor Therapy: Development and Utilization of Protein-Based Nanoparticles

Protein-based nanoparticles (PNPs) in tumor therapy hold immense potential, combining targeted delivery, minimal toxicity, and customizable properties, thus paving the way for innovative approaches to cancer treatment. Understanding the various methods available for their production is crucial for researchers and scientists aiming to harness these nanoparticles for diverse applications, including tumor therapy, drug delivery, imaging, and tissue engineering. This review delves into the existing techniques for producing PNPs and PNP/drug complexes, while also exploring alternative novel approaches. The methods outlined in this study were divided into three key categories based on their shared procedural steps: solubility change, solvent substitution, and thin flow methods. This classification simplifies the understanding of the underlying mechanisms by offering a clear framework, providing several advantages over other categorizations. The review discusses the principles underlying each method, highlighting the factors influencing the nanoparticle size, morphology, stability, and functionality. It also addresses the challenges and considerations associated with each method, including the scalability, reproducibility, and biocompatibility. Future perspectives and emerging trends in PNPs' production are discussed, emphasizing the potential for innovative strategies to overcome current limitations, which will propel the field forward for biomedical and therapeutic applications.

Atomic force microscopy investigation of DNA denaturation on a highly oriented pyrolytic graphite surface

Understanding of DNA interaction with carbonaceous surfaces (including graphite, graphene and carbon nanotubes) is important for the development of DNA-based biosensors and other biotechnological devices. Though many issues related to DNA adsorption on graphitic surfaces have been studied, some important aspects of DNA interaction with graphite remain unclear. In this work, we use atomic force microscopy (AFM) equipped with super-sharp cantilevers to analyze the morphology and conformation of relatively long DNA molecule adsorbed on a highly oriented pyrolytic graphite (HOPG) surface. We have revealed the effect of DNA embedding into an organic monolayer of N,N'-(decane-1,10-diyl)-bis(tetraglycinamide) (GM), which may "freeze" DNA conformation on a HOPG surface during drying. The dependence of the mean squared point-to-point distance on the contour length suggests that DNA adsorbs on a bare HOPG by a "kinetic trapping" mechanism. For the first time, we have estimated the unfolded fraction of DNA upon contact with a HOPG surface (24 ± 5 %). The obtained results represent a novel experimental model for investigation of the conformation and morphology of DNA adsorbed on graphitic surfaces and provide with a new insight into DNA interaction with graphite.

Cooperative dynamics of DNA-grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami

Magnetic nanoparticles (MNPs) provide new opportunities for enzyme-free biosensing of nucleic acid biomarkers and magnetic actuation by patterning on DNA origami, yet how the DNA grafting density affects their dynamics and accessibility remains poorly understood. Here, we performed surface functionalization of MNPs with single-stranded DNA (ssDNA) via click chemistry with a tunable grafting density, which enables the encapsulation of single MNPs inside a functional polymeric layer. We used several complementary methods to show that particle translational and rotational dynamics exhibit a sigmoidal dependence on the ssDNA grafting density. At low densities, ssDNA strands adopt a coiled conformation that results in minor alterations to particle dynamics, while at high densities, they organize into polymer brushes that collectively influence particle dynamics. Intermediate ssDNA densities, where the dynamics are most sensitive to changes, show the highest magnetic biosensing sensitivity for the detection of target nucleic acids. Finally, we demonstrate that MNPs with high ssDNA grafting densities are required to efficiently couple to DNA origami. Our results establish ssDNA grafting density as a critical parameter for the functionalization of MNPs for magnetic biosensing and functionalization of DNA nanostructures.

Polydopamine functionalized dendritic fibrous silica nanoparticles as a generic platform for nucleic acid-based biosensing

Accurate and rapid detection of nucleic acid sequences is of utmost importance in various fields, including disease monitoring, clinical treatment, gene analysis and drug discovery. In this study, we developed a "turn-on" fluorescence biosensor that enables simple and highly efficient detection of nucleic acid biomarkers. Our approach involves the utilization of 6-carboxyfluorescein modified single-stranded DNA (FAM-ssDNA) as molecular recognition element, along with polydopamine-functionalized dendritic fibrous nanosilica (DFNS). FAM-ssDNA serves as both specific molecular recognition element for the target analyte and reporter capable of transducing a detectable signal through Watson-Crick base pairing. The polydopamine-functionalized DFNS (DFNS@DA) exhibits strong binding to FAM-ssDNA via polyvalent metal mediated coordination leading to effective quenching by fluorescence resonance energy transfer. In the presence of a complementary target sequence, FAM-ssDNA forms hybridized structure and detaches from DFNS@DA, which causes an increased fluorescence emission. The analytical system based on FAM-ssDNA and DFNS@DA demonstrates exceptional sensitivity, selectivity, and rapid response for the detection of nucleic acid sequences, leveraging the high adsorption and quenching properties of DFNS@DA. For the first proof of concept, we demonstrated the successful detection of microRNA (miR-21) in cancer cells using the FAM-ssDNA/DFNS@DA system. Our results highlight the promising capabilities of DFNS@DA and nucleic acid-based biosensors, offering a generic and cost-effective solution for the detection of nucleic acid-related biomarkers.

Effect of Lipid Corona on Phenylalanine-Functionalized Gold Nanoparticles to Develop Stable and Corona-Free Systems

Conventional gold nanoparticles (Au NPs) have many limitations, such as aggregation and subsequent precipitation in the medium of high ionic strength and protein molecules. Furthermore, when exposed to biological fluids, nanoparticles form a protein corona, which controls different biological processes such as the circulation lifetime, drug release profile, biodistribution, and in vivo cellular distribution. These limitations reduce the functionality of Au NPs in targeted delivery, bioimaging, gene delivery, drug delivery, and other biomedical applications. To circumvent these problems, there are numerous attempts to design corona-free and stable nanoparticles. Here, we report for the first time that lipid corona (coating of lipid) formation on phenylalanine-functionalized Au NPs (AuPhe NPs) imparts excellent stability against the high ionic strength of bivalent metal ions, amino acids, and proteins of different charges as compared to bare nanoparticles. Moreover, this work is focused on the ability of lipid corona formation on AuPhe NPs to prevent protein adsorption in the presence of cell culture medium (CCM), oppositely charged protein (e.g., histone 3), and human serum albumin (HSA). The results demonstrate that the lipid corona successfully protects the AuPhe NPs from protein adsorption, leading to the development of corona-free character. This unique achievement has profound implications for enhancing the biomedical utility and safety of these nanoparticles.

Differential local ordering of mixed crowders determines effective size and stability of ss-DNA capped gold nanoparticle

Understanding the influence of a crowded intracellular environment on the structure and solvation of DNA functionalized gold nanoparticles (ss-DNA AuNP) is necessary for designing applications in nanomedicine. In this study, the effect of single (Gly, Ser, Lys) and mixture of amino acids (Gly+Ser, Gly+Lys, Ser+Lys) at crowded concentrations is examined on the structure of the ss-DNA AuNP using molecular dynamics simulations. Using the structural estimators such as pair correlation functions and ligand shell positional fluctuations, the solvation entropy is estimated. Combining the AuNP-solvent interaction energy with the solvation entropy estimates, the free energy of solvation of the AuNP in crowded solutions is computed. The solvation entropy favours the solvation free energy which becomes more favourable for larger effective size of AuNP in crowded solutions relative to that in water. The effective size of AuNP depends on the different propensity of the crowders to adsorb on Au surface, with the smallest crowder (Gly) having the highest propensity inducing the least effective AuNP size as compared to other single crowder solutions. In mixed crowded solutions of amino acids of variable size and chemistry, distinctive local adsorption of the crowders on the gold surface is observed that controls the additive or non-additive crowding effects which govern an increase (in Gly+Ser) or decrease (in Gly+Lys) in nanoparticle effective size respectively. The results shed light into the fundamental understanding of the influence of intracellular crowding on structure of ss-DNA AuNP and plausible employability of crowding as a tool to design programmable self-assembly of functionalized nanoparticles.

Nanoparticles-assisted aptamer biosensing for the detection of environmental pathogens

Given the importance of public health, it is crucial to develop quick, targeted, highly sensitive, and accurate technologies to monitor pathogenic microbes in response to the growing concerns of food and environmental safety. Although conventional approaches for microbiological detection are available, they are laborious, and often skill demanding. Therefore, such approaches are incompetent in the on-site or high-throughput assessment of pathogenic microbes. Numerous efforts have been made to develop biosensors that use nucleic acid aptamer as the biorecognition element, which would avoid the abovementioned limitations. Incorporating nanomaterials (NMs) into aptamer-based biosensors (aptasensors) improves their sensitivity and specificity, opening exciting possibilities for various applications, such as bioanalysis of food and environmental samples. Over the last decade, nanomaterial-conjugated aptasensors have seen a steadily rising demand. To this end, the main goal of this study is to demonstrate the novelty in the design of nanomaterial-conjugated aptasensors and how they can be used to detect different pathogenic microbes in water and food. The intent of this paper is to evaluate the cutting-edge techniques that have appeared in nano-aptasensors throughout the past few years, such as manufacturing procedures, analytical credibility, and sensing mechanisms. Additionally, the fundamental performance parameters of aptasensing techniques (such as detection limits, and sensing ranges response) were also used to evaluate their practical applicability. Finally, it is anticipated that this study will inspire innovative ideas and techniques for the construction and use of aptasensors for monitoring pathogenic microorganisms in food, drinks, recreational water, and wastewater.

Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers

Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.

Inspired Beyond Nature: Three Decades of Spherical Nucleic Acids and Colloidal Crystal Engineering with DNA

The conception, synthesis, and invention of a nanostructure, now known as the spherical nucleic acid, or SNA, in 1996 marked the advent of a new field of chemistry. Over the past three decades, the SNA and its analogous anisotropic equivalents have provided an avenue for us to think about some of the most fundamental concepts in chemistry in new ways and led to technologies that are significantly impacting fields from medicine to materials science. A prime example is colloidal crystal engineering with DNA, the framework for using SNAs and related structures to synthesize programmable matter. Herein, we document the evolution of this framework, which was initially inspired by nature, and describe how it now allows researchers to chart paths to move beyond it, as programmable matter with real-world significance is envisioned and created.

Melting of dsDNA attached with AuNPs

DNA-linked gold nanoparticles (DNA-AuNPs) are combined nanomaterials that contain the optical and electronic properties of AuNPs with the unique functions of DNA. These hybrid systems are used in various nanobiotechnology, medical, and pharmaceutical sciences (Löwe et al. in FEBS J 287(23):5039, 2020; Speer et al. in Annu Rev Biophys 51:267, 2022). In recent years, there has been an increasing interest in studying the behavior of DNA-AuNPs in the presence of molecular solvents. In the present work, we study the thermal melting of DNA-linked gold nanoparticles (DNA-AuNP). In the first part of the study, we find the melting profile of short heterogeneous DNA-linked AuNP in the presence of solvent in the solution. We also study the effect of the location of the gold nanoparticle attached to the DNA molecule. In this case, we move the location of the AuNP from one end to the other. We found that while the melting temperature is susceptible to the location of the AuNP when it is near the ends, there is a region in the middle section of the chain where the melting temperature remains constant.

Nanomaterials enabled and enhanced DNA-based biosensors

DNA has excellent molecular recognition properties. At the same time, DNA has a programmable structure, high stability, and can be easily modified, making DNA attractive for biosensor design. To convert DNA hybridization or aptamer binding events to physically detectable signals, various nanomaterials have been extensively exploited to take advantage of their optical and surface properties. A popular sensing scheme is through the adsorption of a fluorescently-labeled DNA probe, where detection is achieved by target-induced probe desorption and fluorescence recovery. Another method is to use DNA to protect the colloidal stability of nanomaterials, where subsequent target binding can decrease the protection ability and induce aggregation; this method has mainly been used for gold nanoparticles. This Perspective summarizes some of our work in examining the sensing mechanisms, and we articulate the importance of the understanding of DNA/surface and target/surface interactions for the development of practical DNA-based biosensors.

Computer Aided Development of Nucleic Acid Applications in Nanotechnologies

Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.

Metal organic frameworks as advanced functional materials for aptasensor design

BACKGROUND

Advancement in coordination chemistry has achieved an impressive development of metal organic frameworks (MOFs) as the supramolecular hybrid materials, comprising harmonized metal nodes with organic ligands. Scope and approach: MOFs offer the unique properties of easy synthesis, nanoscale structure, adjustable size and morphology, high porosity, large surface area, supreme chemical tunability and stability, and biocompatibility. The features provide an exceptional opportunity for the widely usage of MOFs in the different scientific fields, e.g. biomedicine, electrocatalysis, food safety, energy storage, environmental surveillance, and biosensing platforms. The synergistic incorporation of the aptamer advantages and the superiorities of MOFs attains the novel MOF-based aptasensors. The excellent selectivity and sensitivity of the MOF-based aptasensors nominate them as efficient lab-on-chip tools for cost-effective, label-free, portable, and real-time monitoring of diverse targets.

KEY FINDINGS AND CONCLUSIONS

Here, we review the achievements in the sensor design by cooperation of MOF motifs and aptamers with the conspicuous potential of determining the targets. Finally, some results are expressed that provide a valuable viewpoint for developing the novel MOF-based test strips in the future.

2D MOF Nanosensor-Integrated Digital Droplet Microfluidic Flow Cytometry for In Situ Detection of Multiple miRNAs in Single CTC Cells

Current circulating tumor cells (CTCs) detection strategies based on surface epithelial markers suffer from low specificity in distinguishing between CTCs and epithelial cells in hematopoietic cell population. Tumor-associated miRNAs within CTCs are emerging as new biomarkers due to their high correlation with tumor development and progress. However, in-situ simultaneous analysis of multiple miRNAs in single CTC cell is still challenging. To overcome this limitation, a digital droplet microfluidic flow cytometry based on biofunctionalized 2D metal-organic framework nanosensor (Nano-DMFC) is developed for in situ detection of dual miRNAs simultaneously in single living breast cancer cells. Here, 2D MOF-based fluorescent resonance energy transfer (FRET) nanosensors are established by conjugating dual-color fluorescence dye-labeled DNA probes on MOF nanosheet surface. In the Nano-DMFC, 2D MOF-based nanoprobes are precisely microinjected into each single-cell encapsulated droplets to achieve dual miRNA characterization in single cancer cell. This Nano-DMFC platform successfully detects dual miRNAs at single-cell resolution in 10 mixed positive MCF-7 cells out of 10 000 negative epithelial cells in serum biomimic samples. Moreover, this Nano-DMFC platform shows good reproductivity in the recovery experiment of spiked blood samples, which demonstrate the high potential for CTC-based cancer early diagnosis and prognosis.

Stabilization of Gold Nanoparticles by Hairpin DNA and Implications for Label-Free Colorimetric Biosensors

With extremely high extinction coefficients and other unique optical properties, gold nanoparticles (AuNPs) have received growing interest in developing biosensors. DNA hairpin structures are very popular probes for the detection of not only complementary DNA or RNA but also aptamer targets. This work aims to understand the effect of the structure and sequence of hairpin DNA for the stabilization of AuNPs and its implications in AuNP-based label-free colorimetric biosensors. A series of hairpin DNA with various loop sizes from 4 to 26 bases and sequences (random sequences, poly-A and poly-T) were tested, but they showed similar abilities to protect AuNPs from aggregation. Using hairpin DNA with a tail under the same conditions, optimal protection was achieved with a six-base or longer tail. DNA hairpins are likely adsorbed via their tail regions or with their terminal bases if no tail is present. Molecular dynamics simulations showed that the rigidity of the hairpin loop region disfavored its adsorption to AuNPs, while the flexible tail region is favored. Finally, a DNA sensing assay was conducted using different structured DNA, where hairpin DNA with a tail doubled the sensitivity compared to the tail-free hairpin.

Nucleic acid-based electrochemical biosensors for rapid clinical diagnosis: advances, challenges, and opportunities

Clinical diagnostic tests should be quick, reliable, simple to perform, and affordable for diagnosis and treatment of diseases. In this regard, owing to their novel properties, biosensors have attracted the attention of scientists as well as end-users. They are efficient, stable, and relatively cheap. Biosensors have broad applications in medical diagnosis, including point-of-care (POC) monitoring, forensics, and biomedical research. The electrochemical nucleic acid (NA) biosensor, the latest invention in this field, combines the sensitivity of electroanalytical methods with the inherent bioselectivity of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The NA biosensor exploits the affinity of single-stranded DNA/RNA for its complementary strand and is used to detect complementary sequences of NA based on hybridization. After the NA component in the sensor detects the analyte, a catalytic reaction or binding event that generates an electrical signal in the transducer ensues. Since 2000, much progress has been made in this field, but there are still numerous challenges. This critical review describes the advances, challenges, and prospects of NA-based electrochemical biosensors for clinical diagnosis. It includes the basic principles, classification, sensing enhancement strategies, and applications of biosensors as well as their advantages, limitations, and future prospects, and thus it should be useful to academics as well as industry in the improvement and application of EC NA biosensors.

A simple and ultrasensitive metal-organic framework-based aptasensor for fluorescence detection of ethanolamine

In this research, a facile fluorescence aptasensor was designed for the ultrasensitive determination of ethanolamine (ETA) as an aliphatic amino alcohol molecule with harmful side effects for human health. Zeolitic imidazolate framework-8 (ZIF-8) as an efficient metal-organic framework was applied to quench the fluorescence emission of the FAM-labeled ETA aptamer. The presence of ETA could recover the fluorescence response under the optimal experimental conditions. ETA could be sensitively detected by the designed aptasensor in the linear concentration range of 0.1 nM-20 µM with the detection limit of 14.38 pM. The designed aptasensor was utilized to determine ETA in milk and serum samples with the detection limits of 17.86 and 15.21 pM, respectively. The aptasensor with the remarkable features of high sensitivity, simplicity and feasibility holds the supreme potential to construct a low-cost portable sensing method for food safety control, human diagnostics, and environmental monitoring with coupling to the microfluidic paper-based devices.

Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects

Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.

Current progress in aptamer-based sensing tools for ultra-low level monitoring of Alzheimer's disease biomarkers

Alzheimer's disease (AD) as common late-life dementia is pathologically associated with the irreversible and progressive disorder, misfolding, deposition, and accumulation of the brain proteins. Especially, the formation of fibrous amyloid plaques by aggregation of amyloid-β peptides is the pathological cause of this neurologic disorder disease. Besides, tau protein isoforms destabilize the microtubule filaments through post-translational modifications and induce nerve cells' death. Amyloid-β peptides and tau proteins are considered as the critical symptom and reliable molecular biomarkers for the early diagnosis of AD. AD is characterized by impaired thinking proficiencies, cognitive decline, memory loss, and behavioral disability. Since there is no efficacious therapy for AD at present, the development of precise sensing tools for the early diagnosis of this disease is essential and crucial. Aptamer-based biosensors (aptasensors) have acquired utmost importance in the field of AD healthcare, due to excellent sensitivity and specificity, ease-of-use, cost-effectiveness, portability, and rapid assay time. Here, we highlight the recent developments and novel perspectives in the field of aptasensor design to quantitatively monitor the AD biomarkers. Finally, some results are represented to achieve a promising viewpoint for introducing the novel aptasensor test kits in the future.

Signal enhancing strategies in aptasensors for the detection of small molecular contaminants by nanomaterials and nucleic acid amplification

Small molecular contaminants (such as mycotoxins, antibiotics, pesticide residues, etc.) in food and environment have given rise to many biological and ecological toxicities, which has attracted worldwide attention in recent years. Meanwhile, due to the advantages of aptamers such as high specificity and stability, easy synthesis and modification, as well as low cost and immunogenicity, various aptasensors for the detection of small molecular contaminants have been flourishing. An aptasensor as a whole is composed of an aptamer-based target recognizer and a signal transducer, which are fields of concentrated research. In the practical detection applications, in order to achieve the quantitative detection of small molecular contaminants at low abundance in real samples, a large number of signal enhancing strategies have been utilized in the development of aptasensors. Recent years is a vintage period for efficient signal enhancing strategies of aptasensors by the aid of nanomaterials and nucleic acid amplification that are applied in the elements for target recognition and signal conversion. Therefore, this paper meticulously reviews the signal enhancing strategies based on nanomaterials (including the (quasi-)zero-dimensional, one-dimensional, two-dimensional and three-dimensional nanomaterials) and nucleic acid amplification (including enzyme-assisted nucleic acid amplification and enzyme-free nucleic acid amplification). Furthermore, the challenges and future trends of the abovementioned signal enhancing strategies for application are also discussed in order to inspire the practitioners in the research and development of aptasensors for small molecular contaminants.

Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms

Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10^-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.

Nanotechnology based solutions to combat zoonotic viruses with special attention to SARS, MERS, and COVID 19: Detection, protection and medication

Zoonotic viruses originate from birds or animal sources and responsible for disease transmission from animals to people through zoonotic spill over and presents a significant global health concern due to lack of rapid diagnostics and therapeutics. The Corona viruses (CoV) were known to be transmitted in mammals. Early this year, SARS-CoV-2, a novel strain of corona virus, was identified as the causative pathogen of an outbreak of viral pneumonia in Wuhan, China. The disease later named corona virus disease 2019 (COVID-19), subsequently spread across the globe rapidly. Nano-particles and viruses are comparable in size, which serves to be a major advantage of using nano-material in clinical strategy to combat viruses. Nanotechnology provides novel solutions against zoonotic viruses by providing cheap and efficient detection methods, novel, and new effective rapid diagnostics and therapeutics. The prospective of nanotechnology in COVID 19 is exceptionally high due to their small size, large surface-to-volume ratio, susceptibility to modification, intrinsic viricidal activity. The nano-based strategies address the COVID 19 by extending their role in i) designing nano-materials for drug/vaccine delivery, ii) developing nano-based diagnostic approaches like nano-sensors iii) novel nano-based personal protection equipment to be used in prevention strategies.This review aims to bring attention to the significant contribution of nanotechnology to mitigate against zoonotic viral pandemics by prevention, faster diagnosis and medication point of view.

Activation of the Catalytic Activity of Thrombin for Fibrin Formation by Ultrasound

The regulation of enzyme activity is a method to control biological function. We report two systems enabling the ultrasound-induced activation of thrombin, which is vital for secondary hemostasis. First, we designed polyaptamers, which can specifically bind to thrombin, inhibiting its catalytic activity. With ultrasound generating inertial cavitation and therapeutic medical focused ultrasound, the interactions between polyaptamer and enzyme are cleaved, restoring the activity to catalyze the conversion of fibrinogen into fibrin. Second, we used split aptamers conjugated to the surface of gold nanoparticles (AuNPs). In the presence of thrombin, these assemble into an aptamer tertiary structure, induce AuNP aggregation, and deactivate the enzyme. By ultrasonication, the AuNP aggregates reversibly disassemble releasing and activating the enzyme. We envision that this approach will be a blueprint to control the function of other proteins by mechanical stimuli in the sonogenetics field.

Recent Advances in Nucleic Acid Modulation for Functional Nanozyme

Nanozymes have the potential to replace natural enzymes, so they are widely used in energy conversion technologies such as biosensors and signal transduction (converting biological signals of a target into optical, electrical, or metabolic signals). The participation of nucleic acids leads nanozymes to produce richer interface effects and gives energy conversion events more attractive characteristics, creating what are called “functional nanozymes”. Since different nanozymes have different internal structures and external morphological characteristics, functional modulation needs to be compatible with these properties, and attention needs to be paid to the influence of nucleic acids on nanozyme activity. In this review, “functional nanozymes” are divided into three categories, (nanozyme precursor ion)/ (nucleic acid) self-assembly, nanozyme-nucleic acid irreversible binding, and nanozyme-nucleic acid reversible binding, and the effects of nucleic acids on modulation principles are summarized. Then, the latest developments of nucleic acid-modulated nanozymes are reviewed in terms of their use in energy conversion technology, and their conversion mechanisms are critically discussed. Finally, we outline the advantages and limitations of “functional nanozymes” and discuss the future development prospects and challenges in this field.

Polarity control of DNA adsorption enabling the surface functionalization of CuO nanozymes for targeted tumor therapy

Nanomaterials with intrinsic catalytic activities (nanozyme) have drawn broad attention for various biomedical applications, with peroxidase-mimic nanozymes particularly attractive for cancer therapy due to their capability to catalyze the conversion of tumor-abundant H₂O₂ into more toxic hydroxyl radicals (˙OH) for effective tumor ablation. However, the facile surface modification of nanozymes for tumor-targeted delivery while retaining their catalytic activity remains a challenge. Here, we report an approach to functionalize the CuO nanozyme with DNA to enable targeted delivery and selective tumor destruction. We systematically studied the adsorption of DNA on the CuO surface, with special attention paid to the catalytic activity and DNA adsorption stability in the presence of various biological ligands. After gaining a fundamental understanding, a di-block DNA sequence was designed for adsorption on to the CuO surface, which allowed stable adsorption during in vivo circulation, passive accumulation into the tumor tissue, and the specific recognition of tumor cells, resulting in significant nanocatalytic tumor suppression in tumor xenograft mice models with no noticeable cytotoxicity. This work paves a way for the rational design of DNA-modified nanozymes for catalytic tumor therapy, and fundamentally, provides a new insight into the biointerface chemistry of CuO with DNA.

Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors

The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA-peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide's spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface-liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.

Aptasensor based on a flower-shaped silver magnetic nanocomposite enables the sensitive and label-free detection of troponin I (cTnI) by SERS

Acute myocardial infarction (AMI) is nowadays the leading death cause worldwide. For that reason, the early diagnosis of AMI is of central importance to reduce the risk of death. In this sense, aptamer-based sensors for surface-enhanced Raman spectroscopy (SERS aptasensors) emerged as an interesting alternative for future high-performance diagnostic tools. SERS aptasensors combine the fast, precise, and sensitive nature of SERS measurements with the selectivity of aptamers for specific biological targets. Herein, we report an efficient SERS aptasensor for the detection of cardiac troponin I (cTnI), a gold-standard biomarker for AMI. Our SERS platform comprises a magnetite core with an intermediate silica shell, and a flower-shaped silver layer (Fe₃O₄@SiO₂@Ag) to confer excellent plasmonic properties and ease of collection by magnetism. The branched silver structure combined with magnetic aggregation offers a high near-field amplification to superior SERS performance. Additionally, a tailored DNA aptamer with high specificity for cTnI was anchored to the silver surface to produce the aptasensor with increased sensing capability towards cTnI. With our SERS aptasensor, a cTnI concentration as low as 10 ng ml^-1 (10^-11 mol l^-1) could be detected. This value is ten times lower than the upper threshold of the typical concentration range of cTnI of AMI patients. Hence, our SERS aptasensor holds great promise to be explored in AMI diagnosis.

Dissecting the Effect of Salt for More Sensitive Label-Free Colorimetric Detection of DNA Using Gold Nanoparticles

Taking advantage of the protection effect of single-stranded DNA oligonucleotides, gold nanoparticles (AuNPs) remain dispersed and retain a red color with the addition of a low concentration of salt, while AuNPs would aggregate in the presence of double-stranded DNA. This difference has been used to design label-free colorimetric sensors for DNA detection. NaCl is the most commonly used salt to induce the aggregation of AuNPs. In this work, we aimed to test if other salts can provide even better sensor performance and to understand the effects of the cations and anions in salts. We first studied the effect of anions, including halides (NaF, NaCl, NaBr, and NaI), and other common salts (NaNO₃, NaClO₄, Na₂SO₄, Na₂S₂O₃, sodium phosphate, and sodium citrate). Among them, weakly adsorbing ones such as F^-, citrate, and phosphate appeared to yield better sensitivity than Cl^-. Anions can directly adsorb on the AuNPs and affect DNA adsorption. We then tested cations, and only group 1A metals (LiCl, NaCl, KCl, RbCl, and CsCl) can signal DNA adsorption, while divalent metals (MgCl₂, CaCl₂, MnCl_2, and NiCl₂) barely showed the effect of DNA. CsCl only works for strongly adsorbing DNA, such as A₁₅, but not weakly adsorbing T₁₅. Overall, NaF is a better salt than NaCl by having a 2.3-fold higher sensitivity, which was confirmed in a DNA sensing assay. This work has identified a better salt yielding higher sensitivity, and sensing work relying on the change of the aggregation state of AuNPs can benefit from this study.

Nucleic Acid Aptamers for Molecular Diagnostics and Therapeutics: Advances and Perspectives

The advent of SELEX (systematic evolution of ligands by exponential enrichment) technology has shown the ability to evolve artificial ligands with affinity and specificity able to meet growing clinical demand for probes that can, for example, distinguish between the target leukemia cells and other cancer cells within the matrix of heterogeneity, which characterizes cancer cells. Though antibodies are the conventional and ideal choice as a molecular recognition tool for many applications, aptamers complement the use of antibodies due to many unique advantages, such as small size, low cost, and facile chemical modification. This Minireview will focus on the novel applications of aptamers and SELEX, as well as opportunities to develop molecular tools able to meet future clinical needs in biomedicine.

NIR-cleavable drug adducts of gold nanostars for overcoming multidrug-resistant tumors

An aptamer-conjugated gold nanostar (dsDDA-AuNS) has been developed for targeting nucleolin present in both tumor cells and tumor vasculature for conducting a drug-resistant cancer therapy. AuNS with its strong absorption in the near-infrared (NIR) region was assembled with a layer of the anti-nucleolin aptamer AS1411. An anticancer drug, namely doxorubicin (DOX), was specifically conjugated on deoxyguanosine residues employing heat and acid labile methylene linkages. In response to NIR irradiation, dsDDA-AuNS allowed on-demand therapeutics. AS1411 played an active role in drug cargo-nucleus interactions, enhancing drug accumulation in the nuclei of drug-resistant breast cancer cells. The intravenous injection of dsDDA-AuNS allowed higher drug accumulation in drug-resistant tumors over naked drugs, leading to greater therapeutic efficacy even at a 54-fold less equivalent drug dose. The in vivo triggered release of DOX from dsDDA-AuNS was achieved by NIR irradiation, resulting in simultaneous photothermal and chemotherapeutic actions, yielding superior tumor growth inhibition than those obtained from either type of monotherapy for overcoming drug resistance in cancers.

Yttrium Oxide as a Strongly Adsorbing but Nonquenching Surface for DNA Oligonucleotides

A large number of nanomaterials can strongly adsorb DNA and quench fluorescence, such as graphene oxide, gold nanoparticles, and most metal oxides. On the other hand, noncationic nanomaterials that adsorb DNA but cannot quench fluorescence are less known. These materials are attractive for studying the mechanism of DNA-based surface reactions. Y₂O₃ was found to have this property. Herein, we used fluorescently labeled oligonucleotides as probes to study the mechanism of DNA adsorption. The fluorescence was quenched at low concentrations of Y₂O₃ and then recovered and even enhanced with higher Y₂O₃ concentrations. The reason was attributed to the intermolecular quenching by the DNA bases of the neighboring strands. The fluorescence enhancement was due to breaking of the intramolecular fluorophore/DNA interactions, and the most enhancement was observed with a Cy3-labeled DNA. DNA adsorption followed the Langmuir isotherm on Y₂O₃. Desorption experiments suggested that DNA was adsorbed through the phosphate backbone, with FAM-G₁₅ and FAM-C₁₅ adsorbed more strongly than the other two DNA homopolymers. With a high salt concentration, no fluorescence change was observed, suggesting that the DNA adsorbed in a folded state reducing intermolecular quenching. Overall, Y₂O₃ might be useful as a model surface for investigating DNA hybridization on a surface.

Poly[N-(2-hydroxypropyl)methacrylamide]-Modified Magnetic γ-F2 O3 Nanoparticles Conjugated with Doxorubicin for Glioblastoma Treatment

With the aim to develop a new anticancer agent, we prepared poly[N-(2-hydroxypropyl)methacrylamide-co-methyl 2-methacrylamidoacetate] [P(HP-MMAA)], which was reacted with hydrazine to poly[N-(2-hydroxypropyl)methacrylamide-co-N-(2-hydrazinyl-2-oxoethyl)methacrylamide] [P(HP-MAH)] to conjugate doxorubicin (Dox) via hydrazone bond. The resulting P(HP-MAH)-Dox conjugate was used as a coating of magnetic γ-Fe₂ O₃ nanoparticles obtained by the coprecipitation method. In vitro toxicity of various concentrations of Dox, P(HP-MAH)-Dox, and γ-Fe₂ O₃ @P(HP-MAH)-Dox nanoparticles was determined on somatic healthy cells (human bone marrow stromal cells hMSC), human glioblastoma line (GaMG), and primary human glioblastoma (GBM) cells isolated from GBM patients both at a short and prolonged exposition time (up to 7 days). Due to hydrolysis of the hydrazone bond in acid milieu of tumor cells and Dox release, the γ-Fe₂ O₃ @P(HP-MAH)-Dox nanoparticles significantly decreased the GaMG and GBM cell growth compared to free Dox and P(HP-MAH)-Dox in low concentration (10 nM), whereas in hMSCs it remained without effect. γ-F₂ O₃ @PHP nanoparticles alone did not affect the viability of any of the tested cells.

Gold Nanoparticles Adsorb DNA and Aptamer Probes Too Strongly and a Comparison with Graphene Oxide for Biosensing

Using fluorescently labeled DNA oligonucleotides and nanomaterials for developing biosensors has been extensively reported for gold nanoparticles (AuNPs) and graphene oxide (GO) among others. These materials have vastly different affinities and mechanisms for interacting with DNA, and their analytical performance is likely to be different. In this work, we used several DNA sequences and, respectively, adsorbed them on AuNPs and GO to quench fluorescence. Different from previous work, we used KCN to fully dissolve the AuNPs to calculate the percentage of the desorbed DNA due to the complementary DNA (cDNA) and aptamer target. The desorbed probe DNA from the AuNPs was less than 5% for all of the targets including DNA, adenosine, Hg²⁺, and lysozyme, indicating a very strong DNA adsorption affinity. Desorption of DNA was achieved by adding HEPES buffer, NaCl, and As(III), but such desorption was attributed to the adsorption of these molecules or ions by the AuNPs instead of their interaction with the adsorbed DNA. For GO, more probes desorbed with addition of target analytes but so did nonspecific desorption by random DNA and proteins. In summary, AuNPs are unlikely to be a good surface for developing biosensors relying solely on the desorption of probe DNA, while for GO the main problem is nonspecific desorption.

Biominerals Formed by DNA and Calcium Oxalate or Hydroxyapatite: A Comparative Study

Biominerals formed by DNA and calcium oxalate (CaOx) or hydroxyapatite (HAp), the most important and stable phase of calcium phosphate) have been examined and compared using a synergistic combination of computer simulation and experimental studies. The interest of this comparison stems from the medical observation that HAp- and CaOx-based microcalcifications are frequently observed in breast cancer tissues, and some of their features are used as part of the diagnosis. Molecular dynamics simulations show that (1) the DNA double helix remains stable when it is adsorbed onto the most stable facet of HAp, whereas it undergoes significant structural distortions when it is adsorbed onto CaOx; (2) DNA acts as a template for the nucleation and growth of HAp but not for the mineralization of CaOx; and (3) the DNA double helix remains stable when it is encapsulated inside HAp nanopores, but it becomes destabilized when the encapsulation occurs into CaOx nanopores. Furthermore, CaOx and HAp minerals containing DNA molecules inside and/or adsorbed on the surface have been prepared in the lab by mixing solutions containing the corresponding ions with fish sperm DNA. Characterization of the formed minerals, which has been focused on the identification of DNA using UV-vis spectroscopy, indicates that the tendency to adsorb and, especially, encapsulate DNA is much smaller for CaOx than for HAp, which is in perfect agreement with results from molecular dynamics simulations. Finally, quantum mechanical calculations have been performed to rationalize these results in terms of molecular interactions, evidencing the high affinity of Ca²⁺ toward oxalate anions in an aqueous environment.

Analysis of circulating non-coding RNAs in a non-invasive and cost-effective manner

Non-coding RNAs (ncRNAs) participate in regulation of gene expression, and are highly relevant to pathological development. They are found to be stably present in diverse body fluids, including those in the circulatory system, which can be sampled non-invasively for clinical tests. Thus, circulating ncRNAs have great potential to be disease biomarkers. However, tremendous efforts are desired to discover and utilize ncRNAs as biomarkers in clinical diagnosis, calling for technological advancement in analysis of circulating ncRNAs in biospecimens. Hence, this review summarizes the recent developments in this area, highlighting the works devoted to cancer diagnosis and prognosis. Three main directions are focused: 1) Extraction and purification of ncRNAs from body fluids; 2) Quantification of the purified circulating ncRNAs; and 3) Microfluidic platforms for integration of both steps to enable point-of-care diagnostics. These technologies have laid a solid foundation to move forward the applications of circulating ncRNAs in disease diagnosis and cure.

Fluorescence Polarization for Probing DNA Adsorption by Nanomaterials and Fluorophore/DNA Interactions

Fluorescence polarization (FP) is attractive for measuring binding interactions and has been recently used to study DNA adsorption on nanomaterials. Since most nanomaterials are strong fluorescence quenchers, correlations among adsorption efficiency, quenching efficiency, and FP need to be interpreted carefully. In this work, carboxyfluorescein (FAM)-labeled DNA oligonucleotides were studied under various quenching conditions. First, quenching was induced by lowering the pH, taking advantage of the fact that FAM is almost nonfluorescent at a pH below 4. Strong interactions were observed between the FAM label and polyadenine DNA, as judged by the increased FP at low pH, while FAM-labeled polythymine DNA was less affected by the pH. Comparisons were also performed with FAM-labeled poly(ethylene glycol) and bovine serum albumin. An equation was derived to calculate the effect of fluorescence quenching and DNA adsorption by nanomaterials. For strongly quenching nanomaterials, such as graphene oxide, DNA adsorption alone does not change the measured FP. Light scattering and weak fluorescence from graphene oxide increase FP in these cases. For comparison, a strongly adsorbing but weak quenching material, Y₂O₃, was also studied and the result was consistent with a normal binding reaction. Overall, FP is a powerful technique for binding and adsorption assays, but quenched samples need to be interpreted with care.

Mn2+-Assisted DNA Oligonucleotide Adsorption on Ti2C MXene Nanosheets

As a new type of 2D nanomaterial, MXene (transition metal carbide/nitride) nanosheets are already widely used in catalysis, sensing, and energy research. DNA is a popular sensing molecule. Compared to other 2D materials such as graphene oxide, MoS₂, and WS₂, few fundamental studies were carried out on DNA adsorption by MXene. Due to its exfoliation and delamination process, the surface of MXene is abundant in -F, -OH, and -O- groups, rendering the surface negatively charged and repelling DNA. In previous studies, surface modification of MXene was performed to promote DNA adsorption. Herein, Mn²⁺ was discovered to promote DNA adsorption on unmodified Ti₂C MXene. Different from Ca²⁺ and Mg²⁺, Mn²⁺ can inverse the ζ-potential of the Ti₂C MXene to positive. DNA mainly uses its phosphate backbone for adsorption, while its bases contribute significantly less. In addition, delayed DNA desorption was observed through the addition of inorganic phosphate due to the formation of manganese phosphate to gradually extract Mn²⁺ from the DNA/MXene complex. Finally, DNA-induced DNA desorption from the Ti₂C MXene can hardly distinguish the complementary DNA from a random DNA, which is very different from that for graphene oxide. This difference is likely due to the distinct surface chemistry between the MXene and graphene oxide.

Adsorption of Arsenite on Gold Nanoparticles Studied with DNA Oligonucleotide Probes

Gold nanoparticles (AuNPs) have been extensively used for detecting arsenite, As(III). Many methods rely on a DNA aptamer that claimed to bind specifically to inorganic arsenic. In these cases, the focus was on arsenic binding to the aptamer, while the potential interactions between As(III) and the AuNP surface were ignored. Herein, a set of spectroscopic and isothermal titration calorimetry (ITC) experiments were conducted to measure the adsorption of As(III) by AuNPs and its competition with DNA adsorption. With 10 mM As(III), 18% of adsorbed DNA was displaced from AuNPs, while preadsorption of only 20 μM As(III) inhibited DNA adsorption by around 50%. The affinity of As(III) on AuNPs is comparable to Br^- and guanosine. ITC and Raman spectroscopy both indicated that only As(III) can be adsorbed, while As(V) had no measurable interactions with the AuNPs. Based on this understanding, a random DNA sequence was used and a similar colorimetric response in the presence of As(III) was observed. This study confirmed the affinity between As(III) and the gold surface. The As(III)/gold interaction is strong enough to affect DNA adsorption, and care should be taken to interpret the observations based on the color change of AuNPs for the detection of As(III).

Three-Dimensional Molecular Transfer from DNA Nanocages to Inner Gold Nanoparticle Surfaces

It is of great interest to construct DNA-functionalized gold nanoparticles (DNA-AuNPs) with a controllable number of DNA strands and relative orientations. Herein, we describe a three-dimensional (3D) molecular transfer strategy, in which a pattern of DNA strands can be transferred from a DNA icosahedron cage (I-Cage) to the wrapped AuNP surface. The results show that DNA-AuNPs produced by this method inherit DNA pattern information encoded in the transient I-Cage template with high fidelity. Controllable numbers and positions of DNA on the surface of AuNPs can be simultaneously realized by direct "printing" of a DNA pattern from the nanoshell (I-Cage) to the nanocore (AuNP), further expanding the applications of DNA nanotechnology to nanolithography. Prospectively, the customized DNA-printed nanoparticles possess great potential for constructing programmable architectures for optoelectronic devices as well as smart biosensors for biomedical applications.

Revealing transient events of molecular recognition via super-localization imaging of single-particle motion

Molecular recognition plays an important role in biological systems and relates to a wide range of applications in disease diagnostics and therapeutics. Studies based on steady state or ensemble analysis may mask critical dynamic information of single recognition events. Here we report a study of monitoring the transient molecular recognition via single particle motion. We utilized a super-localization imaging methodology, to comprehensively evaluate the rotational Brownian motion of a single nanoparticle in spatial-temporal-frequential domain, with a spatial accuracy ~20 nm and a temporal resolution of ~10 ms. The transient moment of molecular encountering was captured and different binding modes were discriminated. We observed that the transient recognition events were not static states of on or off, but stochastically undergoes dynamical transformation between different binding modes. This study improves our understanding about the dynamic nature of molecular recognition events beyond the ensemble characterization via binding constant.

Boron-Carbon-Nitride Sheet as a Novel Surface for Biological Applications: Insights from Density Functional Theory

Understanding the interaction between nanoscale materials and nucleobases is essential for their use in nanobiotechnology and nanomedicine. Our ab initio calculations indicate that the interaction of nucleobases [adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)] with boron-carbon-nitride (BCN) is mainly governed by van der Waals interactions. The adsorption energies, ranging from -0.560 to -0.879 eV, decrease in the order of G > A > T > C > U, which can be attributed to π-π interactions and different side groups of the nucleobases. We found that anions (N and O atoms) of nucleobases prefer to stay on top of cation (B) of the substrate. The results also showed that BCN exhibits superior binding strength than graphene and boron-nitride-based materials. We also found that upon adsorption, the fundamental properties of BCN and nucleobases remains unaltered, which suggests that BCN is a promising template for self-assembly of nucleobases.

Universal DNA biosensing based on instantaneously electrostatic attraction between hexaammineruthenium (III) and DNA molecules

Despite rapid progress in DNA biosensors by employing various materials as well as techniques, most of the reported sensors are based on specific recognition of a DNA fragment, however can not perform universal measurement of DNA molecules (i.e. genomic DNA). In this work, we proposed a novel DNA biosensing method based on instantaneously electrostatic attraction (IEA) between hexaammineruthenium (III) and DNA molecules. The current variation of freely diffused Ru(NH₃)₆³⁺ caused by its quick and strong static interaction with phosphate backbones was employed as a universal probe to detect DNA molecules in solution, with no need for immobilization of capture probes on the electrode. After optimization, 30 μL of 300 μM Ru(NH₃)₆³⁺ solution was added onto the gold electrode with a working electrode diameter of 2 mm, and a detection limit of 3.8 ng/μL was achieved, which is equivalent to NanoDrop™ One spectrometer, the commonly used instrument for DNA quantification. Using reusable and inexpensive gold electrode, the approach provided an easy-operated sequence-independent DNA detection method, and was proved to be able to detect genomic and plasmid DNA directly.