Comprehensive Screen of Metal Oxide Nanoparticles for DNA Adsorption, Fluorescence Quenching, and Anion Discrimination

Construction and Application of Nanozyme Sensor Arrays

Compared with traditional "lock-key mode" biosensors, a sensor array consists of a series of sensing elements based on intermolecular interactions (typically hydrogen bonds, van der Waals forces, and electrostatic interactions). At the same time, sensor arrays also have the advantages of fast response, high sensitivity, low energy consumption, low cost, rich output signals, and imageability, which have attracted widespread attention from researchers. Nanozymes are nanomaterials which own enzyme-like properties. Because of the adjustable activity, high stability, and cost effectiveness of nanozymes, they are potential candidates for construction of sensor arrays to output different signals from analytes through the chemoresponse of colorants, which solves the shortcomings of traditional sensors that they cannot support multiple detection and lack universality. Recently, a sensor array based on nanozymes as nonspecific recognition receptors has attracted much more attention from researchers and has been applied to precise recognition of proteins, bacteria, and heavy metals. In this perspective, attention is given to nanozymes and the regulation of their enzyme-like activity. Particularly, the building principles and methods for sensor arrays based on nanozymes are analyzed, and the applications are summarized. Finally, the approaches to overcome the challenges and perspectives are also presented and analyzed for facilitating further research and development of nanozyme sensor arrays. This perspective should be helpful for gaining insight into research ideas within the field of nanozyme sensor arrays.

Equilibrium interactions of biomimetic DNA aptamers produce intrafibrillar calcium phosphate mineralization of collagen

Native and biomimetic DNA structures have been demonstrated to impact materials synthesis under a variety of conditions but have only just begun to be explored in this role compared to other biopolymers such as peptides, proteins, polysaccharides, and glycopolymers. One selected DNA aptamer has been explored in calcium phosphate and calcium carbonate mineralization, demonstrating sequence-dependent control of kinetics, morphology, and crystallinity. This aptamer is here applied to a biologically-relevant bone model system that uses collagen hydrogels. In the presence of the aptamer, intrafibrillar collagen mineralization is observed compared to negative controls and a positive control using well-studied poly-aspartic acid. The mechanism of interaction is explored through affinity measurements, kinetics of calcium uptake, and kinetics of aptamer uptake into the forming mineral. There is a marked difference observed between the selected aptamer containing a G-quadruplex secondary structure compared to a control sequence with no G-quadruplex. It is hypothesized that the equilibrium interaction of the aptamer with calcium-phosphate precursors and with the collagen itself leads to slow kinetic mineral formation and a morphology appropriate to bone. This points to new uses for DNA aptamers in biologically-relevant mineralization systems and the possibility of future biomedical applications. STATEMENT OF SIGNIFICANCE: Collagen is the protein structural component that mineralizes with calcium phosphate to form durable bone. Crystalline calcium phosphate must be infused throughout the collagen fiber structure to produce a strong material. This process is assisted by soluble proteins that interact with both calcium phosphate precursors and the collagen protein and has been proposed to follow a polymer-induce liquid precursor (PILP) model. Further understanding of this model and control of the process through synthetic, biomimetic molecules could have significant advantages in biomedical, restorative procedures. For the first time, synthetic DNA aptamers with specific secondary structures are here shown to influence and direct collagen mineralization. The mechanism of this process has been studied to demonstrate an important equilibrium between the DNA aptamer, calcium phosphate precursors, and collagen.

Dissemination of antibiotic resistance genes is regulated by iron oxides: Insight into the influence on bacterial transformation

The transportation of antibiotic resistance genes (ARGs) in manure-soil-plant continuums poses risks to human health. Horizontal gene transfer, particularly for bacterial transformation, is an important way for ARG dissemination. As crucial components in soils, iron oxides impacted the fates of various abiotic and biotic contaminants due to their active properties. However, whether they can influence the transformation of ARGs is unknown, which waits to be figured out to boost the assessment and control of ARG spread risks. In this study, we have investigated the effects of goethite, hematite, and magnetite (0-250 mg/L, with sizes < 100 nm and > 100 nm) on the transfer of ampicillin resistance genes to Escherichia coli cells. At lower iron oxide concentrations, the transformation of ARGs was first facilitated (transformation frequency reached up to 3.38-fold higher), but the facilitating effects gradually weakened and eventually disappeared as concentrations further increased. Particle size and iron oxide type were not the universal determinants controlling the transformation. At lower concentrations, iron oxides interacted with proteins and phospholipids in E. coli envelope structures, and induced the overgeneration of intracellular reactive oxygen species. Consequently, they led to pore formation and permeability enhancement on the cell membrane, thus promoting the transformation. The facilitation was also associated with the carrier-like effect of iron oxides for antibiotic resistance plasmids. At higher concentrations, the weakened facilitations were attributed to the aggregation of iron oxides. In this study, we highlight the crucial roles of the concentrations (contents) of iron oxides on the dissemination of ARGs in soils; this study may serve as a reference for ARG pollution control in future agricultural production.

Cellular Alterations Due to Direct and Indirect Interaction of Nanomaterials with Nucleic Acids

Deoxyribonucleic acid (DNA) represents the main reservoir of genetic information in the cells, which is why it is protected in the nucleus. Entry into the nucleus is, in general, difficult, as the nuclear membrane is a selective barrier to molecules longer than 40 kDa. However, in some cases, the size of certain nanoparticles (NPs) allows their internalization into the nucleus, thus causing a direct effect on the DNA structure. NPs can also induce indirect effects on DNA through reactive oxygen species (ROS) generation. In this context, nanomaterials are emerging as a disruptive tool for the development of novel therapies in a broad range of biomedical fields; although their effect on cell viability is commonly studied, further interactions with DNA or indirect alterations triggered by the internalization of these materials are not always clarified, since the small size of these materials makes them perfectly suitable for interaction with subcellular structures, such as the nucleus. In this context, and using as a reference the predicted interactions presented in a computational model, we describe and discuss the observed direct and indirect effects of the implicated nanomaterials on DNA.

DNA-functionalized metal or metal-containing nanoparticles for biological applications

The conjugation of DNA molecules with metal or metal-containing nanoparticles (M/MC NPs) has resulted in a number of new hybrid materials, enabling a diverse range of novel biological applications in nanomaterial assembly, biosensor development, and drug/gene delivery. In such materials, the molecular recognition, gene therapeutic, and structure-directing functions of DNA molecules are coupled with M/MC NPs. In turn, the M/MC NPs have optical, catalytic, pore structure, or photodynamic/photothermal properties, which are beneficial for sensing, theranostic, and drug loading applications. This review focuses on the different DNA functionalization protocols available for M/MC NPs, including gold NPs, upconversion NPs, metal-organic frameworks, metal oxide NPs and quantum dots. The biological applications of DNA-functionalized M/MC NPs in the treatment or diagnosis of cancers are discussed in detail.

Ce-based solid-phase catalysts for phosphate hydrolysis as new tools for next-generation nanoarchitectonics

This review comprehensively covers synthetic catalysts for the hydrolysis of biorelevant phosphates and pyrophosphates, which bridge between nanoarchitectonics and biology to construct their interdisciplinary hybrids. In the early 1980s, remarkable catalytic activity of Ce4+ ion for phosphate hydrolysis was found. More recently, this finding has been extended to Ce-based solid catalysts (CeO2 and Ce-based metal-organic frameworks (MOFs)), which are directly compatible with nanoarchitectonics. Monoesters and triesters of phosphates, as well as pyrophosphates, were effectively cleaved by these catalysts. With the use of either CeO2 nanoparticles or elegantly designed Ce-based MOF, highly stable phosphodiester linkages were also hydrolyzed. On the surfaces of all these solid catalysts, Ce4+ and Ce3+ coexist and cooperate for the catalysis. The Ce4+ activates phosphate substrates as a strong acid, whereas the Ce3+ provides metal-bound hydroxide as an eminent nucleophile. Applications of these Ce-based catalysts to practical purposes are also discussed.

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.

Adsorption of antibiotic, heavy metal and antibiotic plasmid by a wet-state silicon-rich biochar/ferrihydrite composite to inhibit antibiotic resistance gene proliferation/transformation

Decreasing bioaccessible antibiotics, heavy metals, and antibiotic resistance genes (ARGs) in soil by adsorption is an attractive, but unrealized, approach for ARG risk reduction. This approach has the potential to reduce the (co)selection pressure from antibiotics and heavy metals on bacteria and ARG horizontal gene transformation to pathogens. Here, a wet-state silicon-rich biochar/ferrihydrite composite (SiC-Fe(W)) synthesized by loading ferrihydrite onto rice straw-derived biochar was examined for i) adsorption of oxytetracycline and Cu²⁺ to reduce (co)selection pressure and ii) adsorption of extracellular antibiotic resistance plasmid pBR322 (containing tetA and bla_TEM-1) to inhibit ARG transformation. SiC-Fe(W) gained the adsorption priority of biochar (for Cu²⁺) and wet-state ferrihydrite (for oxytetracycline and pBR322) and showed adsorptive enhancement (for Cu²⁺ and oxytetracycline) from a more wrinkled and exposed surface from biochar silica-dispersed ferrihydrite and a more negatively charged biochar, and the adsorption capacity for SiC-Fe(W) was 17-135 times that of soil. Correspondingly, 10 g/kg SiC-Fe(W) amendment increased the soil adsorption coefficient K_d by 31%-1417% and reduced the selection pressure from dissolved oxytetracycline, co-selection pressure from dissolved Cu²⁺, and transformation frequency of pBR322 (assessed with Escherichia coli). The development of Fe-O-Si bonds on silicon-rich biochar in alkaline enhanced ferrihydrite stability and adsorption capacity (for oxytetracycline), presenting a new potential strategy of biochar/ferrihydrite composite synthesis for adsorptive inhibition of ARG proliferation and transformation in ARG pollution control.

Confinement of defect-rich bimetallic In2O3/CeO2 nanocrystals in mesoporous nitrogen-doped carbon as a sensitive platform for photoelectrochemical aptasensing of Escherichia coli

The sensitive determination of food-borne pathogens from food products is essential to ensure food safety and to protect people's health. Herein, a novel photoelectrochemical (PEC) aptasensor was manufactured based on defect-rich bimetallic cerium/indium oxide nanocrystals confined in mesoporous nitrogen-doped carbon (denoted as In₂O₃/CeO₂@mNC) for sensitively detecting Escherichia coli (E. coli) from real samples. A new cerium-based polymer-metal-organic framework [polyMOF(Ce)] was synthesized using polyether polymer containing 1,4-benzenedicarboxylic acid unit (L8) as ligand, trimesic acid as co-ligand, and cerium ions as coordination centers. After adsorbing trace indium ions (In³⁺), the gained polyMOF(Ce)/In³⁺ complex was calcined at high temperature under nitrogen atmosphere, resulting in the production of a series of defect-rich In₂O₃/CeO₂@mNC hybrids. Benefitting from the advantages of high specific surface area, large pore size, and multiple functionality of polyMOF(Ce), In₂O₃/CeO₂@mNC hybrids showed enhanced visible light absorption ability, separation performance of the photo-generated electrons and holes, promoted electron transfer, as well as the strong bioaffinity toward E. coli-targeted aptamer. Accordingly, the constructed PEC aptasensor illustrated an ultralow detection limit of 1.12 CFU mL^-1, remarkably lower than most of the reported E. coli biosensors, along with high stability and selectivity, excellent reproducibility, and expected regeneration ability. The present work provides insight into the construction of a general PEC biosensing strategy based on MOF-based derivatives for the sensitive analysis of food-borne pathogens.

Secondary Structure of DNA Aptamer Influences Biomimetic Mineralization of Calcium Carbonate

Calcium materials, such as calcium carbonate, are produced in natural and industrial settings that range from oceanic to biomedical. An array of biological and biomimetic template molecules have been employed in controlling and understanding the mineralization reaction but have largely focused on small molecule additives or disordered polyelectrolytes. DNA aptamers are synthetic and programmable biomolecules with polyelectrolyte characteristics but with predictable and controllable secondary structure akin to native extracellular moieties. This work demonstrates for the first time the influence of DNA aptamers with known G-quadruplex structures on calcium carbonate mineralization. Aptamers demonstrate kinetic inhibition of mineral formation, sequence and pH-dependent uptake into the mineral, and morphological control of the primarily calcite material in controlled solution conditions. In reactions initiated from the complex matrix of ocean water, DNA aptamers demonstrated enhancement of mineralization kinetics and resulting amorphous material. This work provides new biomimetic tools to employ in controlled mineralization and demonstrates the influence that template secondary structure can have in material formation.

Nano-bio interaction: An overview on the biochemical binding of DNA to inorganic nanoparticles for the development of anticancer and antibacterial nano-platforms

It has long been known that inorganic nanoparticles (NPs) can interact with biological macromolecules and show a wider range of biomedical characteristics, including antibacterial, anticancer and antioxidant effects, which cannot be mimicked by their bulky counterparts. It is of great importance in their biomedical applications to study DNA damage in bacterial and cancer cells to develop biocompatible therapeutic nano-platforms derived from inorganic NPs. Therefore, to determine how DNA interacts with inorganic NPs serving as therapeutic agents, thermodynamic and structural studies are essential for an understanding of those mechanisms, thereby allowing for their modulation and manipulation of nano-bio interface. In this paper, we aimed to overview the biophysical techniques typically employ to study DNA-NP interactions as well as the mechanistic aspects of the interaction between different inorganic NPs and calf thymus DNA (CT-DNA), a well-known laboratory model, followed by a survey of different parameters affecting the interaction of NPs and DNA. The molecular interactions between inorganic NPs and DNA were then discussed in relation to their anticancer and antibacterial properties. As a final point, we discussed challenges and future perspectives to put forward the possible applications of the field. In conclusion, the interaction between NPs and DNA needs to be studied more deeply in order to develop potential NP-based anticancer and antibacterial platforms for future clinical applications.

Degradation and adsorption of synthetic DNA water tracers in environmental matrices

Synthetic DNA tracers are gaining interest as tools for tracking contamination pathways and hydraulic connections in surface water and groundwater systems. However, few quantitative data exist that describe DNA tracer degradation and adsorption in environmental matrices. We undertook laboratory experiments to quantify the degradation of multiple double-stranded DNA tracers in stream water, groundwater, and domestic and dairy-shed effluent, and adsorption to stream sediments, soils, coastal sand aquifer media and alluvial sandy gravel aquifer media. Faster DNA tracer degradation seemed to be associated with high bacterial concentrations in the liquid phase. Overall, the degradation of the 352 base pair (bp) DNA tracers in the aqueous phase was significantly (P = 0.018) slower than that of the 302 bp DNA tracers. Although the tracers' internal amplicon lengths were similar, the longer non-amplified flanking regions of the 352 bp tracers may better protect them from environmental degradation. Thermodynamic analysis suggests that longer flanking regions contribute to greater tracer stability. This finding may explain our previous field observations that 352 bp tracer mass reductions were often lower than 302 bp tracer mass reductions. The 2 sets of DNA tracers did not differ significantly regarding their adsorption to stream sediment-stream water or aquifer media-groundwater mixtures (P > 0.067), but the 352 bp tracers showed significantly less adsorption to soil-effluent mixtures than the 302 bp tracers (P = 0.005). The DNA tracers' adsorption to soil-effluent mixtures was comparatively less than their adsorption to the aquifer media-groundwater and stream sediment-stream water mixtures, suggesting that DNA tracers may compete with like-charged organic matter for adsorption sites. These findings provide insights into the fate of DNA tracers in the environment. The DNA tracers' degradation rate constants determined in this study for a range of environmental conditions could assist the design of future field investigations.

A Label-Free Colorimetric Assay Based on Gold Nanoparticles for the Detection of H2O2 and Glucose

The significance of sensing hydrogen peroxide (H2O2) is due to its ubiquity, being a potential biomarker as well as an end-product of several oxidation reactions. Herein, based on gold nanoparticles (AuNPs) and coupled with single-stranded DNA (ssDNA) and ceria nanoparticles (CeO2), we developed a novel colorimetric method to detect H2O2 and glucose in NaCl solutions. In the presence of H2O2, ssDNA adsorbed on the surface of CeO2 could be released and subsequently decorated AuNPs, resulting in a distinct color change of the aqueous solution from purple to red, which could be observed by the naked eye. Since H2O2 can be produced in the process of glucose oxidation by glucose oxidase (GOx), this approach can also be employed to detect glucose. By employing this sensing system, the detection limits for H2O2 and glucose are about 0.21 μM and 3.01 µM, respectively. Additionally, monitoring the content of glucose in blood serum samples was successfully achieved by the proposed strategy. This work opens a potential avenue for the quantitative detection of H2O2 and glucose in clinical diagnostics.

Highly Selective Photoelectrochemical Assay of Arsenate Based on Magnetic Co3O4-Fe3O4 Cubes and the Negative-Background Signal Strategy

Water pollution presents a significant environmental concern on earth. Herein, due to the serious environmental harmfulness of arsenate [As(V)], an iron phthalocyanine (FePc)-induced switchable photocurrent-polarity platform was developed for highly selective assay of As(V). First, magnetic Co₃O₄-Fe₃O₄ cubes were obtained by calcination of the CoFe Prussian blue analogue and then functionalized with oligonucleotide (S1). In the presence of As(V), S1 could be released based on the stronger affinity between As(V) and Co₃O₄-Fe₃O₄ cubes. After magnetic separation by Co₃O₄-Fe₃O₄ cubes, the released S1 was used to trigger the catalytic hairpin assembly (CHA) and hybridization chain reaction, resulting in the formation of lots of G-quadruplex structures on the AgInS₂/ITO electrode. Then, the capture of FePc by the G-quadruplex led to the switch of the photocurrent polarity of the AgInS₂/ITO electrode from the anode to the cathode. Thus, As(V) was sensitively assayed with a low detection limit of 1.0 nM and a wide linear response range from 10 nM to 200 μM. This meets the detection requirement of the World Health Organization for the arsenic concentration in drinking water [less than 10 μg L^-1 (130 nM)]. In addition, whether it was cationic or anionic interferents except phosphate (PO₄^3-), only As(V) could generate the cathodic photocurrent, effectively avoiding the false-positive or false-negative results during As(V) assay. Interestingly, As(V) was also simultaneously separated from the detection system by Co₃O₄-Fe₃O₄ magnetic cubes. The proposed photoelectrochemical platform may have a great potential application for the selective detection of As(V) in environmental fields.

Binding Force and Site-Determined Desorption and Fragmentation of Antibiotic Resistance Genes from Metallic Nanomaterials

Interfacial interactions between antibiotic resistance genes (ARGs) and metallic nanomaterials (NMs) lead to adsorption and fragmentation of ARGs, which can provide new avenues for selecting NMs to control ARGs. This study compared the adsorptive interactions of ARGs (tetM-carrying plasmids) with two metallic NMs (ca. 20 nm), i.e., titanium dioxide (nTiO₂) and zero-valent iron (nZVI). nZVI had a higher adsorption rate (0.06 min^-1) and capacity (4.29 mg/g) for ARGs than nTiO₂ (0.05 min^-1 and 2.15 mg/g, respectively). No desorption of ARGs from either NMs was observed in the adsorptive background solution, isopropanol or urea solutions, but nZVI- and nTiO₂-adsorbed ARGs were effectively desorbed in NaOH and NaH₂PO₄ solutions, respectively. Molecular dynamics simulation revealed that nTiO₂ mainly bound with ARGs through electrostatic attraction, while nZVI bound with PO₄^3- of the ARG phosphate backbones through Fe-O-P coordination. The ARGs desorbed from nTiO₂ remained intact, while the desorbed ARGs from nZVI were splintered into small fragments irrelevant to DNA base composition or sequence location. The ARG removal by nZVI remained effective in the presence of PO₄^3-, natural organic matter, or protein at environmentally relevant concentrations and in surface water samples. These findings indicate that nZVI can be a promising nanomaterial to treat ARG pollution.

Iron oxide nanoparticles conjugated with organic optical probes for in vivo diagnostic and therapeutic applications

The role and scope of functional inorganic nanoparticles in biomedical research is well established. Among these, iron oxide nanoparticles (IONPs) have gained maximum attention as they can provide targeting, imaging and therapeutic capabilities. Furthermore, incorporation of organic optical probes with IONPs can significantly enhance the scope and viability of their biomedical applications. Combination of two or more such applications renders multimodality in nanoparticles, which can be exploited to obtain synergistic benefits in disease detection and therapy viz theranostics, which is a key trait of nanoparticles for advanced biomedical applications. This review focuses on the use of IONPs conjugated with organic optical probe/s for multimodal diagnostic and therapeutic applications in vivo.

Bio-nano interactions: binding proteins, polysaccharides, lipids and nucleic acids onto magnetic nanoparticles

The major interest in nanoparticles as an application platform for biotechnology arises from their high surface-to-volume ratio. Iron oxide nanoparticles (IONPs) are particularly appealing due to their superparamagnetic behavior, which enables bioseparation using external magnetic fields. In order to design advanced biomaterials, improve binding capacities and develop innovative processing solutions, a thorough understanding of the factors governing organic-inorganic binding in solution is critical but has not yet been achieved, given the wide variety of chemical and physical influences. This paper offers a critical review of experimental studies of the interactions between low cost IONPs (bare iron oxides, silica-coated or easily-functionalized surfaces) and the main groups of biomolecules: proteins, lipids, nucleic acids and carbohydrates. Special attention is devoted to the driving forces and interdependencies responsible of interactions at the solid-liquid interface, to the unique structural characteristics of each biomolecular class, and to environmental conditions influencing adsorption. Furthermore, studies focusing on mixtures, which are still rare, but absolutely necessary to understand the biocorona, are also included. This review concludes with a discussion of future work needed to fill the gaps in knowledge of bio-nano interactions, seeking to improve nanoparticles' targeting capabilities in complex systems, and to open the door for multipurpose recognition and bioseparation processes.

A Turn-ON fluorometric biosensor based on ssDNA immobilized with a metal phenolic nanomaterial for the sequential detection of Pb(ii) and epirubicin cancer drug

In this paper, we propose a fluorescent biosensor for the sequential detection of Pb2+ ions and the cancer drug epirubicin (Epn) using the interactions between label-free guanine-rich ssDNA (LFGr-ssDNA), acridine orange (AO), and a metal-phenolic nanomaterial (i.e., nano-monoclinic copper-tannic acid (NMc-CuTA)). An exploration of the sensing mechanism shows that LFGr-ssDNA and AO strongly adsorb on NMc-CuTA through π-π stacking and electrostatic interactions, and this results in the fluorescence quenching of AO. In order to sense the target Pb2+, initially, LFGr-ssDNA specifically binds with Pb2+ ions to form a G4 complex (G-Pb2+-G base pair), which was released from the surface of NMc-CuTA with strong AO fluorescence enhancement (Turn-ON). The subsequent addition of a biothiol, like cysteine (Cys), to the G4 complex decreases the fluorescence, as the Pb2+ ions released from the G4 complex have a higher interaction affinity with the sulfur atoms of Cys; this further induces the unwinding of the G4 complex to form LFGr-ssDNA. Finally, Epn was added to this, which intercalates with LFGr-ssDNA to form a G4 complex via G-Epn-G, resulting in fluorescence recovery (Turn-ON). Accordingly, the Turn-ON fluorescent probe had subsequent limits of detection of 1.5 and 5.6 nM for Pb2+ and Epn, respectively. Hence, the reported NMc-CuTA-based sensing platform has potential applications for the detection of Pb2+ and Epn in real samples with good sensitivity and selectivity.

Spherical Nucleic Acid Mediated Functionalization of Polydopamine-Coated Nanoparticles for Selective DNA Extraction and Detection

Magnetic nanoparticles have been widely used for the separation of biomolecules for biological applications due to the mild and efficient separation process. In previous studies, core-shell magnetic nanoparticles (NPs) were designed for DNA extraction without much sequence specificity. In this work, to achieve highly selective DNA extraction, we designed a core-shell magnetic structure by coating polydopamine (PDA) on Fe₃O₄ NPs. Without divalent metal ions, PDA does not adsorb DNA at neutral pH. The Fe₃O₄@PDA NPs were then functionalized with spherical nucleic acids (SNA) to provide a high density of probe DNA. Fe₃O₄@PDA@SNA was also compared with when a linear SH-DNA was covalently attached to the NPs surface, showing a higher density of the probe SNA than SH-DNA can be loaded on the NPs in a remarkably shorter time. Nonspecific DNA extraction was thoroughly inhibited by both probes. DNA extraction by the Fe₃O₄@PDA@SNA was more effective as well as 5-fold faster than by the Fe₃O₄@PDA@SH-DNA, probably due to the favorable standing conformation of DNA strands in SNA. Moreover, extraction by Fe₃O₄@PDA@SNA showed high robustness in fetal bovine serum, and the same design can be used for selective detection of DNA. Finally, the method was also demonstrated on silica NPs and WS₂ nanosheets for coating with PDA and SNA. Altogether, our findings revealed an interesting and general surface modification strategy using PDA@SNA conjugates for sequence-specific DNA extraction.

Nanomaterial and Aptamer-Based Sensing: Target Binding versus Target Adsorption Illustrated by the Detection of Adenosine and ATP on Metal Oxides and Graphene Oxide

Target molecule-induced desorption of aptamer probes from nanomaterials has been a very popular sensing method, taking advantage of the fluorescence quenching or catalytic activity of nanomaterials for signal generation. While it is generally conceived that aptamers desorb due to binding to target molecules, in this work, we examined the effect of competitive target adsorption. From five metal oxide nanoparticles including CeO₂, ZnO, NiO, Fe₃O₄, and TiO₂, only ATP was able to induce desorption of its aptamer. Adenosine could not, even though it had an even higher affinity than ATP to the aptamer. The same conclusion was also observed with a random DNA that cannot bind ATP, indicating that the desorption of DNA was due to competitive adsorption of ATP instead of aptamer binding. On graphene oxide, however, adenosine produced slightly more aptamer desorption than ATP under most of the conditions, and this can be partially attributed to the weaker interaction of negatively charged ATP with negatively charged graphene oxide. For such surface-based biosensors, it is recommended that a nonaptamer control DNA be tested side-by-side to ensure the sensing mechanism to be related to aptamer binding instead of target adsorption.

Polyvalent Metal Ion Promoted Adsorption of DNA Oligonucleotides by Montmorillonite

Montmorillonite (MMT) is a two-dimensional (2D) clay material. Its abundance on the early earth has attracted studies for its role in prebiotic reactions, and adsorption of DNA to MMT is potentially important for understanding the origin of life. Although several possible models of DNA adsorption on MMT have been established, a consensus on the adsorption mechanism has yet to be formed, thereby a fundamental adsorption study is performed here. Adding up to 300 mM NaCl failed to promote DNA adsorption on MMT, Al₂O₃, or SiO₂ nanoparticles. For polyvalent metals, DNA adsorption was achieved following the order Ce³⁺ > Cu²⁺ > Ni²⁺ > Zn²⁺. Among them, Ce³⁺ and Cu²⁺ inverted the surface charge of MMT to positive. In addition, using washing experiments, Cu²⁺- and Ce³⁺-mediated adsorption mainly depended on the DNA phosphate backbone, while Ni²⁺ and Zn²⁺ interacted with the backbone phosphate groups and adenine bases of DNA. Overall, these polyvalent metal ions promoted DNA adsorption via a cation bridge model. This research provides new insights into the surface interactions of MMT and DNA, which is conducive to future work on the interaction between clays and biopolymers.

DNA interfaces with dimensional materials for biomedical applications

DNA interfaces with nano, micro, and macro materials have gained widespread attention for various applications. Such interfaces exhibit distinct functions and properties not only due to the unique properties of interfacing materials but also sequence- and conformation-dependent characteristics of the DNA. Therefore, DNA interfaces with diverse dimensional materials have advanced our understanding of the interaction mechanisms and the properties of such interfaces. The unique interfacial properties of such novel materials have applications in nanotechnology, biophysics, cell biology, biosensing, and bioelectronics. The field is growing rapidly with the frequent emergence of new interfaces carrying remarkable interfacial character. In this review article, we have classified the DNA interfaces into 0D, 1D, 2D, and 3D categories based on the types of dimensional materials. We review the key efforts made in the last five years and focus on types of interfaces, interfacing mechanisms, and their state-of-the-art applications. This review will draw a general interest because of the diversity in the DNA materials science but also the unique applications that will play a cutting-edge role in biomedical and biosensing research.

DNA interfaces with 0–3 dimensional materials through physisorption and chemisorption mechanisms acquire unique interfacial character for novel biomedical applications.

Effect of proteins on the oxidase-like activity of CeO2 nanozymes for immunoassays

Protein adsorption inhibits the oxidase-like activity of CeO₂ nanoparticles. Coating a partial shell of silica on CeO₂ and subsequent conjugation of antibodies allow highly sensitive and selective detection of fenitrothion.

Sol-Gel Synthesis of Spherical Mesoporous High-Entropy Oxides

High-entropy oxides (HEOs) have attracted increasing interest owing to their unique structures and fascinating physicochemical properties. Spherical mesoporous HEOs further inherit the advantages of spherical mesoporous materials including high surface area and tunable pore size. However, it is still a huge challenge to construct HEOs with uniform spheres and a mesoporous framework. Herein, a wet-chemistry sol-gel strategy is demonstrated for the synthesis of spherical mesoporous HEOs (e.g., Ni-Co-Cr-Fe-Mn oxide) with high specific surface area (42-143 m²/g), large pore size (5.5-8.3 nm), unique spherical morphology (∼55 nm), and spinel structure without any impure crystal phase using polyphenol as a polymerizable ligand. The metal/polyphenol-formaldehyde resin colloidal spheres are first synthesized via a sol-gel process. Because of their abundant catechol groups and strong chelating ability with different metal species, polyphenols can not only accommodate five different metal ions in their networks but also be well polymerized by formaldehyde to form colloidal spheres. After calcination, the metal species aggregate together to form HEOs, while the organic resin is fully decomposed to produce mesopores. Because of the open framework with accessible mesopores, they could be used as a peroxymonosulfate catalyst for degradation of organic pollutants and a nanoplatform for efficient detection of DNA. This work demonstrates a straightforward sol-gel strategy for design and synthesis of spherical mesoporous high-entropy materials, which would promote the exploration of new properties of high-entropy materials and extend their application.

Promoting DNA Adsorption by Acids and Polyvalent Cations: Beyond Charge Screening

Adsorbing DNA oligonucleotides onto nanoparticles is the first step in developing DNA-based biosensors, drug delivery systems, and smart materials. Since DNA is a polyanion, it is repelled by negatively charged nanoparticles, which constitute the majority of commonly used nanomaterials. Adding salt such as NaCl to screen charge repulsion is a standard method of promoting DNA adsorption. However, Na⁺ does not supply additional attractive forces. In addition, adding a high concentration of NaCl can cause the aggregation of nanomaterials. In this feature article, we mainly summarize the methods developed in our laboratory to promote DNA adsorption by lowering the pH and by adding polyvalent metal ions, especially transition-metal ions. Various materials including noble metals (gold, silver, and platinum), 2D materials (graphene oxide, MoS₂, WS₂, and MXene), polydopamine, and several metal oxides are discussed. In general, low pH can protonate DNA bases and nanoparticle surfaces, reducing charge repulsion and even leading to attraction, although DNA folding at low pH can sometimes be detrimental to adsorption. Polyvalent metal ions can bridge additional interactions to achieve otherwise impossible adsorption. On the basis of the current understanding, a few future research directions are proposed to further improve DNA adsorption.

Catalytic hairpin assembly indirectly covalent on Fe3O4@C nanoparticles with signal amplification for intracellular detection of miRNA

Fluorescence resonance energy transfer, a promising method for in situ imaging of miRNA in living cells, has intrinsic limitation on sensitivity and selectivity. Herein, a fluorescent amplification strategy based on catalyzed hairpin assembly indirectly covalent on Fe₃O₄@C nanoparticles via short single-stranded DNA was investigated for cellular miRNA detection in living cells, integrating non-enzyme target-active releasing for amplifying the signal output, highly quenching efficiency of Fe₃O₄@C nanoparticles with low background, ssDNA assisted fluorescent group-fueled chain releasing from Fe₃O₄@C nanoparticles with enhanced fluorescence response. The designed platform exhibits highly sensitive in a wide linear concentration range of 0.450 pM-190 pM and is highly specific for miRNA-20a detection with the ability of discriminating one mistake base. Additionally, the CHA-Fe₃O₄@C was successfully applied in imaging visualization of miRNA-20a in the living cell. The strategy provides a promising bioassay approach for clinical research.

A Multichannel Pattern-Recognition-Based Protein Sensor with a Fluorophore-Conjugated Single-Stranded DNA Set

Recently, pattern-recognition-based protein sensing has received considerable attention because it offers unique opportunities that complement more conventional antibody-based detection methods. Here, we report a multichannel pattern-recognition-based sensor using a set of fluorophore-conjugated single-stranded DNAs (ssDNAs), which can detect various proteins. Three different fluorophore-conjugated ssDNAs were placed into a single microplate well together with a target protein, and the generated optical response pattern that corresponds to each environment-sensitive fluorophore was read via multiple detection channels. Multivariate analysis of the resulting optical response patterns allowed an accurate detection of eight different proteases, indicating that fluorescence signal acquisition from a single compartment containing a mixture of ssDNAs is an effective strategy for the characterization of the target proteins. Additionally, the sensor could identify proteins, which are potential targets for disease diagnosis, in a protease and inhibitor mixture of different composition ratios. As our sensor benefits from simple construction and measurement procedures, and uses accessible materials, it offers a rapid and simple platform for the detection of proteins.

Physical and chemical template-blocking strategies in the exponential amplification reaction of circulating microRNAs

The detection of circulating miRNA through isothermal amplification wields many attractive advantages over traditional methods, such as reverse transcription RT-qPCR. However, it is challenging to control the background signal produced in the absence of target, which severely hampers applications of such methods for detecting low abundance targets in complex biological samples. In the present work, we employed both the cobalt oxyhydroxide (CoOOH) nanoflakes and the chemical modification of hexanediol to block non-specific template elongation in exponential amplification reaction (EXPAR). Adsorption by the CoOOH nanoflakes and the hexanediol modification at the 3' end effectively prevented no-target polymerization on the template itself and thus greatly improved the performance of EXPAR, detecting as low as 10 aM of several miRNA targets, including miR-16, miR-21, and miR-122, with the fluorescent DNA staining dye of SYBR Gold™. Little to no cross-reactivity was observed from the interfering strands present in 10-fold excess. Besides contributing to background reduction, the CoOOH nanoflakes strongly adsorbed nucleic acids and isolated them from a complex sample matrix, thus permitting successful detection of the target miRNA in the serum. We expect that simple but sensitive template-blocking EXPAR could be a valuable tool to help with the discovery and validation of miRNA markers in biospecimens. Graphical abstract.

Spinel Cobalt Ferrite Nanoparticles for Sensing Phosphate Ions in Aqueous Media and Biological Samples

Phosphate ions perform a variety of functions in metabolic processes and are essential for all living organisms. The determination of the concentration of phosphate ions is useful in clinical diagnosis of various diseases as an inadequate phosphate level could lead to many health problems. In the search for a cost-effective method of fast monitoring, we investigated the use of cobalt ferrite nanoparticles (CoFeNPs) in the selective recognition of phosphate ions dissolved in aqueous media and more complex samples, such as human blood serum. We prepared these NPs by a chemical coprecipitation route and subjected them to annealing at 600 °C for 1 h. The successful formation of the NPs was confirmed by Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, and hysteresis loop measurements. The NPs exhibited a ferrimagnetic behavior, a spinel-type crystalline structure, and hexagonal shape in the nanoscale range. We demonstrated that CoFeNPs containing immobilized fluorescent-labeled single-chain DNA (ssDNA*) probes can be applied for the fast selective detection of phosphate ions dissolved in a liquid medium. We have explored the fact that phosphate groups can displace ssDNA* probes attached to the nanoparticles, therefore causing a perceptible change in the fluorescence signal of the supernatant liquid. This detection method has been tested for the sensing of phosphate ions present both in aqueous solutions and in biological samples, with excellent selectivity and a low limit of detection (∼1.75 nM).

Selected DNA aptamers as hydroxyapatite affinity reagents

DNA aptamers were selected for their ability to bind specifically and quickly to crystalline hydroxyapatite (Ca₁₀(PO₄)₆(OH)₂; HAP), the primary mineral component of enamel and bone. Aptamers were found to have an enhanced percent of G-nucleotides and a propensity for forming a G-quadruplex secondary structure. One aptamer was studied in comparison to control sequences and was found to bind with high affinity and at high loading capacity, with enhanced binding kinetics, and with specificity for crystalline HAP material over amorphous calcium phosphate (ACP) and β-tricalcium phosphate (TCP). The fluorescently-functionalized aptamer was demonstrated to specifically label HAP in a surface binding experiment and suggests the usefulness of this selected aptamer in biomedical or biotechnology fields where the labeling of specific calcium phosphate materials is required.

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.

Thermo-responsive Fluorescent Nanoparticles for Multimodal Imaging and Treatment of Cancers

Theranostic systems capable of delivering imaging and therapeutic agents at a specific target are the focus of intense research efforts in drug delivery. To overcome non-degradability and toxicity concerns of conventional theranostic systems, we formulated a novel thermo-responsive fluorescent polymer (TFP) and conjugated it on the surface of iron oxide magnetic nanoparticles (MNPs) for imaging and therapeutic applications in solid tumors. Methods: TFP-MNPs were synthesized by copolymerizing poly(N-isopropylacrylamide), allylamine and a biodegradable photoluminescent polymer, and conjugating it on MNPs via a free radical polymerization reaction. Physicochemical properties of the nanoparticles were characterized using Fourier transform infrared spectroscopy, dynamic light scattering, and vibrational sample magnetometry. Nanoparticle cytocompatibility, cellular uptake and cytotoxicity were evaluated using in vitro cell assays. Finally, in vivo imaging and therapeutic efficacy studies were performed in subcutaneous tumor xenograft mouse models. Results: TFP-MNPs of ~135 nm diameter and -31 mV ζ potential maintained colloidal stability and superparamagnetic properties. The TFP shell was thermo-responsive, fluorescent, degradable, and released doxorubicin in response to temperature changes. In vitro cell studies showed that TFP-MNPs were compatible to human dermal fibroblasts and prostate epithelial cells. These nanoparticles were also taken up by prostate and skin cancer cells in a dose-dependent manner and exhibited enhanced killing of tumor cells at 41°C. Preliminary in vivo studies showed theranostic capabilities of the nanoparticles with bright fluorescence, MRI signal, and therapeutic efficacy under magnetic targeting after systemic administration in tumor bearing mice. Conclusion: These results indicate the potential of TFP-MNPs as multifunctional theranostic nanoparticles for various biological applications, including solid cancer management.

Nanoceria as a DNase I mimicking nanozyme

We herein communicate the DNase I like activity of nanoceria (CeO2 nanoparticles). Both CeO2 and DNase I cleave polyadenine (poly-A) DNA down to ∼5-mer fragments as the major products, although further cleavage to even shorter fragments was observed with CeO2. Mass spectrometry indicates a hydrolytic cleavage mechanism instead of oxidative cleavage.

A colorimetric sensor array for detection and discrimination of antioxidants based on Ag nanoshell deposition on gold nanoparticle surfaces

There is growing interest in developing a high-performance sensor array for detection and discrimination of antioxidants owing to their widespread use and essential role in the human body. The present work unveils a novel colorimetric sensor array for colorimetric discrimination of antioxidants based on the red, green, and blue alteration (ΔRGB) pattern recognition. In this sensor array, three concentrations of AgNO3 were used as sensing elements, and gold nanoparticles (AuNPs) were employed as a colorimetric probe. In the presence of antioxidants, the sensor array produces unique colorimetric response patterns for the discrimination of these antioxidants due to different reactivities between three different concentrations of AgNO3 and each antioxidant, leading to deposition of different quantities of Ag nanoshells on the surface of AuNPs, enabling an excellent discrimination of six antioxidants (catechin, epigallocatechin 3-gallate, epicatechin, epigallocatechin, epicatechin 3-gallate, and gallocatechin) at a 20 nM level, when linear discriminant analysis (LDA), hierarchical cluster analysis (HCA), centroid diagram, spidergram, and color contour profiles were smartly combined. Furthermore, different concentrations of antioxidants and binary antioxidant mixtures, even ternary mixtures, could also be discriminated with this sensor array. Finally, the sensor array was successfully used for the discrimination of antioxidants in serum samples, demonstrating its potential applications in the diagnosis of antioxidant-related diseases.

Adsorption of DNA Oligonucleotides by Boronic Acid-Functionalized Hydrogel Nanoparticles

Boronic acid-functionalized hydrogels were commonly used for covalent binding of cis-diol-contained molecules such as glucose, but noncovalent adsorption by boronic acids was less studied. DNA as an important polymer has been used to enhance the function of hydrogels including boronic acid-containing gels. In this work, noncovalent interactions between DNA oligonucleotides and boronic acid-containing hydrogel nanoparticles were studied in detail. The gels were composed of either poly(N-isopropylacrylamide) or with additional 5.6 mol % of 3-acrylamidophenylboronic acid (AAPBA). DNA adsorption on the AAPBA-containing gels was achieved with a high salt concentration, which can be explained by electrostatic repulsion between DNA and boronic acid. The critical role of boronic acid was confirmed by adding competing cis-diol-containing molecules such as glucose, fructose, and cytidine. Hydrogen bonding and hydrophobic interactions are important for DNA adsorption based on inhibited adsorption by urea and dimethyl sulfoxide. Polycytosine DNA showed a higher adsorption capacity compared to the other three types of DNA homopolymers. When T₁₅ and T₁₄-rU were compared, no covalent binding was detected for T₁₄-rU, suggesting that a single terminal diol was insufficient to support covalent binding at the low concentration of DNA used. Finally, the boronic acid-containing gels were able to adsorb an aptamer and inhibit its binding function. Binding was rescued by adding glucose to block the boronic acids. This study demonstrates noncovalent boronic acid interactions with DNA, and this information could be useful for designing and optimization of related biosensors and materials.

Fluorescein-Stabilized i-Motif DNA and Its Unfolding Leading to a Stronger Adsorption Affinity

Several previous studies have indicated that polydeoxycytidine (poly-C) DNA has an anomalously high affinity for different types of surfaces. It was hypothesized that the formation of an i-motif structure could be a factor responsible for this enhanced affinity, but this is against the notion that a folded molecule should have fewer interactions with a surface. Herein, the properties of poly-C DNA were examined in detail, focusing on the presence or absence of a FAM (carboxyfluorescein) label and its subsequent adsorption on graphene oxide. Fluorescence and CD spectroscopy studies indicated that FAM can stabilize an i-motif structure in C15 DNA. In particular, the fluorescence of FAM is drastically quenched when the DNA is folded. This structure is irreversibly unfolded upon heating. Furthermore, the unfolded structure has an even higher affinity for graphene oxide than the folded structure. Finally, a large portion of the folded C15 unfolds upon desorption from graphene oxide, and unfolding could happen upon adsorption or desorption of the DNA. This study provides a method to further enhance the adsorption stability of poly-C DNA and calls for care when investigating the potential effects of dye labels on DNA.

Fluorescence Characteristics of Aqueous Synthesized Tin Oxide Quantum Dots for the Detection of Heavy Metal Ions in Contaminated Water

Tin oxide quantum dots were synthesized in aqueous solution via a simple hydrolysis and oxidation process. The morphology observation showed that the quantum dots had an average grain size of 2.23 nm. The rutile phase SnO₂ was confirmed by the structural and compositional characterization. The fluorescence spectroscopy of quantum dots was used to detect the heavy metal ions of Cd²⁺, Fe³⁺, Ni²⁺ and Pb²⁺, which caused the quenching effect of photoluminescence. The quantum dots showed the response of 2.48 to 100 ppm Ni²⁺. The prepared SnO₂ quantum dots exhibited prospective in the detection of heavy metal ions in contaminated water, including deionized water, deionized water with Fe³⁺, reclaimed water and sea water. The limit of detection was as low as 0.01 ppm for Ni²⁺ detection. The first principle calculation based on the density function theory demonstrated the dependence of fluorescence response on the adsorption energy of heavy metal ions as well as ion radius. The mechanism of fluorescence response was discussed based on the interaction between Sn vacancies and Ni²⁺ ions. A linear correlation of fluorescence emission intensity against Ni²⁺ concentration was obtained in the logarithmic coordinates. The density of active Sn vacancies was the crucial factor that determined fluorescence response of SnO₂ QDs to heavy metal ions.

Ligands dissociation induced gold nanoparticles aggregation for colorimetric Al3+ detection

Aluminum is a very important analyte, and developing biosensors for aluminum is an important analytical task. In this work, we report a novel mechanism to design colorimetric sensor based on gold nanoparticles (AuNPs). The AuNPs were prepared by reducing HAuCl₄ using catechols, and the resulting AuNPs can be directly adapted for Al³⁺ detection without any post-modifications, showing high sensitivity and selectivity against other metal ions. Interestingly, our mechanistic studies revealed that Al³⁺-induced AuNPs aggregation was not due to the formation of interparticle crosslinks that refers to the design principle of most AuNPs-based colorimetric sensors reported before. But rather, Al³⁺ competitively coordinated with the capping ligands on AuNPs surface through the formation of stable Al-O bond, which dissociated these ligands from AuNPs surface. As a result, the AuNPs aggregated due to the loss of surface stabilizers. Based on this mechanism, several catechols, including pyrocatechol (PC), 3-(3,4-dihydroxyphenyl) propionic acid (DHCA), levodopa (LDA) and dopamine (DA), were used as reductant to prepare AuNPs for Al³⁺ sensing, and the AuNPs prepared by DA (AuNPs/DA) displayed the highest sensitivity, with detection limit of 0.81 μM. The sensor was then tested for Al content analysis in river water and food samples, and the results supported its practical applications. Importantly, this work expands the design principles for colorimetric sensors by using AuNPs.

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.