NiO Nanoparticles for Exceptionally Stable DNA Adsorption and Its Extraction from Biological Fluids

A New Phosphorylated Protein Analysis Strategy based on Trypsin Encapsulated in Metal-Organic Frameworks with High Efficiency and a Simplified Workflow

Phosphoproteomics research is crucial for clinical diagnosis. However, due to the self-hydrolysis of natural proteases and the complex typical pretreatment protocol, the traditional bottom-up method is not enough to achieve rapid analysis of phosphorylated proteins. In this work, we encapsulate trypsin (Try) in the ZIF-L(Co) to develop a new strategy that simplifies the phosphorylated protein analysis process and achieves rapid analysis. Try is encapsulated in the mesoporous ZIF-L(Co) to allow the proteins to be accessible to the enzymes. The hydrophobic ZIF-L(Co) can cause the unfolding of proteins and accelerates the digestion process. The Co(II) nodes enhance the affinity toward phosphorylated proteins and capture phosphopeptides selectively. Compared to the traditional denaturation, digestion, and enrichment method, which costs 20 h at least, our strategy simplifies the pretreatment workflow and yields phosphopeptides in just 3.4 h. This strategy is further applied in the analysis of phosphorylated proteins in biosamples such as nonfat milk, egg yolk, and human serum. The results show equivalent performance with the traditional method and exhibit great potential in bioanalysis. This new phosphorylated protein analysis strategy provides a powerful tool for proteomics analysis and promotes research in the field of biomedicine.

A comprehensive adsorption and desorption study on the interaction of DNA oligonucleotides with TiO2 nanolayers

The utilization of TiO2 nanolayers that possess excellent biocompatibility and physical properties in DNA sensing and sequencing remains largely to be explored. To examine their applicability in gene sequencing, a comprehensive study on the interaction of DNA oligonucleotides with TiO2 nanolayers was performed through adsorption and desorption experiments. TiO2 nanolayers with 10 nm thickness were fabricated via magnetron sputtering onto a 6-inch silicon wafer. A simple chip block method, validated via quartz crystal microbalance experiments with dissipation monitoring (QCM-D), was proposed to study the adsorption behaviors and interaction mechanisms under a variety of critical influencing factors, including DNA concentration, length, and type, adsorption time, pH, and metal ions. It is determined that the adsorption takes 2 h to reach saturation in the MES solution and the adsorption capacity is significantly enhanced by lowering the pH due to the isoelectric point being pH = 6 for TiO2. The adsorption percentages of nucleobases are largely similar in the MES solution while following 5T = 5G > 5C > 5A in HEPES buffer for an adsorption duration of 2.5 h. Through pre-adsorption experiments, it is deduced that DNA oligonucleotides are horizontally adsorbed on the nanolayer. This further demonstrates that mono-, di-, and tri-valent metal ions promote the adsorption, whereas Zn2+ has strong adsorption by inducing DNA condensation. Based on the desorption experiments, it is revealed that electrostatic force dominates the adsorption over van der Waals force and hydrogen bonds. The phosphate group is the main functional group for adsorption, and the adsorption strength increases with the length of the oligonucleotide. This study provides comprehensive data on the adsorption of DNA oligonucleotides onto TiO2 nanolayers and clarifies the interaction mechanisms therein, which will be valuable for applications of TiO2 in DNA-related applications.

Novel and Extremely Sensitive NiAl2O4-NiO Nanostructures on an ITO Sensing Electrode for Enhanced Detection of Ascorbic Acid

The current study focused on the design of an extremely sensitive electrochemical sensor of ascorbic acid based on a mixture of NiAl2O4-NiO nanoparticles that, produced in a single step using the sol-gel method, on an ITO electrode. This new sensing platform is useful for the detection of ascorbic acid with a wide range of concentrations extending from the attomolar to the molar. SEM micrographs show the porous structure of the NiAl2O4-NiO sample, with a high specific surface area, which is beneficial for the catalytic performance of the nanocomposite. An XRD diffractogram confirmed the existence of two phases, NiAl2O4 and NiO, both corresponding to the face-centred cubic crystal structure. The performances of the modified electrode, as a biomolecule, in the detection of ascorbic acid was evaluated electrochemically by cyclic voltammetry and chronoamperometry. The sensor exhibited a sensitive electrocatalytic response at a working potential of E = +0.3 V vs. Ag/Ag Cl, reaching a steady-state current within 30 s after each addition of ascorbic acid solution with a wide dynamic range of concentrations extending from attolevels (10-18 M) to molar (10 mM) and limits of detection and quantification of 1.2 × 10-18 M and 3.96 × 10-18 M, respectively. This detection device was tested for the quantification of ascorbic acid in a 500 mg vitamin C commercialized tablet that was not pre-treated.

Magnetic composite microspheres with a controlled mesoporous shell for highly efficient DNA extraction and fragment screening

Rapid extraction and screening of high-purity DNA fragments is an indispensable technology in advanced molecular biology. In this article, mesoporous magnetic composite microspheres (MSP@mTiO2) with tunable pore sizes were successfully fabricated for high-purity DNA extraction and fragment screening. Owing to the strong complexation ability of Ti ions with DNA phosphate groups and the high specific surface area of mesoporous microspheres, the MSP@mTiO2 microspheres possess excellent adsorption performance, where the saturated loading capacity of MSP@mTiO2 with a specific surface area of 122 m2 g-1 is as high as 575 μg mg-1 for a salmon sperm specimen. ITC experiments demonstrated that DNA adsorption on MSP@mTiO2 microspheres is mainly driven by entropy, which gives us more potential ways to regulate the balance of adsorption and desorption. Meanwhile, the mesoporous MSP@mTiO2 microspheres exhibit a much higher extraction efficiency compared with non-porous MSP@TiO2 for whole genome DNA from Arabidopsis thaliana plants. Interestingly, DNA fragments with different lengths could be screened by simply regulating the pore size of MSP@mTiO2 or the concentration of Na3PO4 in the eluent. A small pore size and low phosphate concentration are advantageous for the extraction of short-stranded DNA fragments, and DNA fragments (≤1000 bp) can be efficiently extracted when the mesopore size of MSP@mTiO2 is lower than 7.6 nm. The extraction results from the mesoporous composite microspheres provide new promising insights into the purification and screening of DNA from complex biological samples.

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.

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.

Small DNAs that Bind Nickel(II) Specifically and Tightly

Metal recognition by nucleic acids provides an intriguing route for biosensing of metal. Toward this goal, a key prerequisite is the acquisition of nucleic acids that can selectively respond to specific metals. Herein, we report for the first time the discovery of two small DNAs that can specifically bind Ni²⁺ and discriminate against similar ions, particularly, Co²⁺. Their minimal effective constructs are 60-70 nucleotides (nt) in length with Ni²⁺ binding even at harsh denaturing conditions of 8 M urea and 50 mM EDTA. Using isothermal titration calorimetry (ITC), we estimated the dissociation constant (K_D) of a representative DNA to be 24.0 ± 4.5 μM, with a 9:1 stoichiometry of Ni²⁺ bound to DNA. As being engineered into nanosized particles, these DNAs can act like nanosponges to specifically adsorb Ni²⁺ from artificial wastewater, demonstrating their potential as a novel molecular tool for high-quality nickel enrichment and detection.

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.

Metal-Doped Polydopamine Nanoparticles for Highly Robust and Efficient DNA Adsorption and Sensing

Controlling DNA adsorption on nanomaterials is crucial for a wide range of applications in analytical and biomedical sciences. Polydopamine (PDA) is a versatile material that can be coated on nearly any surface, and thus adsorbing DNA onto PDA can be a general method for indirect DNA functionalization of surfaces. Polyvalent metal ions were reported to promote DNA adsorption on PDA nanoparticles (NPs), but previous works added the metal ions after the formation of PDA. Herein, we compared the effect of polyvalent metal ions added during the synthesis of PDA NPs (called metal-doped) with the effect of polyvalent metal ions added after the synthesis (metal-adsorbed). A series of metal ions including Ca²⁺, Zn²⁺, Ni²⁺, Fe³⁺, and Gd³⁺ were tested, and Zn²⁺ was studied in detail due to its excellent ability for promoting DNA adsorption. With 100 μM Zn²⁺, metal-doped NPs were ∼30% more efficient than metal-adsorbed NPs for DNA adsorption in buffer attributable to a higher metal loading on the surface of the metal-doped NPs. Metal leaching was negligible from the metal-doped NPs, and they showed a remarkably higher robustness than the metal-adsorbed NPs, resulting in a 20-fold higher DNA extraction efficiency from serum. Based on the desorption studies, a higher adsorption affinity for the metal-doped NPs was confirmed. Finally, the Zn²⁺-doped PDA NPs were used for sensitive DNA detection with a limit of detection of 0.45 nM, and the sensor was highly resistant to nonspecific protein and phosphate displacement.

Oligonucleotide-Functionalized Enzymes Chemisorbing on Magnetic Layered Double Hydroxides: A Multimodal Catalytic Platform with Boosted Activity for Ultrasensitive Glucose Detection

A reasonable design of multifarious chemo- and biocatalytic functions within individual nano/microunits is urgently desired for high-performance cascade reactions but has heretofore remained elusive. Herein, glucose oxidase was functionalized with oligonucleotides and steadily chemisorbed on magnetic layered double hydroxides (mLDHs) to construct a multimodal catalytic platform for realizing divergent reactions with heterogeneous and biocatalytic steps. The flowerlike mLDHs served both as an enzyme support and a peroxidase mimic cooperating with enzymes for tandem catalysis. Oligo-DNA connected the enzymes to mLDHs like a bridge, and a stepwise ligand-exchange-assisted coordination mechanism was proposed to explain the robust interaction between DNA and mLDHs. More importantly, DNA significantly improved the bioactivity of the whole system. The acceleration mechanism was attributed to the diffusion tunnels for the substrate/product and enhanced substrates binding on mLDHs. The multimodal catalytic platform was applied for colorimetric and electrochemical sensing of glucose with a low limit of detection and high selectivity. The practical analysis capability of the ultrasensitive sensor was evaluated by detecting glucose in human serum and sweat, showing reliable results, satisfactory recovery, and excellent stability. The strategy of combining mLDHs and enzymes for cascade catalysis provides a universal approach to prepare chemo-enzyme hybrids with high performance, which holds great promise for applications in biosensors and industrial catalysis.

Transition Metal-Mediated DNA Adsorption on Polydopamine Nanoparticles

Polydopamine (PDA) is a widely used universal coating for a broad range of materials. Interfacing PDA with various biomolecules, such as DNA, is critical for applications such as sensing, intracellular delivery, and material fabrication. Because of the negative surface charge of PDA at neutral pH, electrostatic repulsion exists between PDA and DNA. In previous studies, modified DNA or low pH was used to overcome this repulsion for DNA adsorption. More recently, divalent Ca²⁺ was found to bridge DNA and PDA. Herein, we studied four transition metals (Mn²⁺, Co²⁺, Zn²⁺, and Ni²⁺) and compared their efficiencies with Ca²⁺ for promoting DNA adsorption. These transition metals induced a more efficient and tighter DNA binding compared to Ca²⁺. In all these cases, the DNA phosphate backbone played a dominant role in adsorption, although DNA bases might also interact with strong binding metals such as Ni²⁺. Moreover, when the adsorption affinity was stronger, sensing was more selective to complementary DNA. Finally, aging of PDA appeared to be detrimental for DNA adsorption, which could be due to further oxidation of PDA. We showed that using Zn²⁺ or Ni²⁺ could considerably relieve the aging effect, while storing PDA at 4 °C could slow down aging.

Interaction of single- and double-stranded DNA with multilayer MXene by fluorescence spectroscopy and molecular dynamics simulations

The integration of nucleic acids with nanomaterials has attracted great attention from various research communities in search of new nanoscale tools for a range of applications, from electronics to biomedical uses. MXenes are a new class of multielement 2D materials baring exciting properties mostly directed to energy-related fields. These advanced materials are now beginning to enter the biomedical field given their biocompatibility, hydrophilicity and near-infrared absorption. Herein, we elucidate the interaction of MXene Ti3C2T x with fluorophore-tagged DNA by fluorescence measurements and molecular dynamics simulations. The system showed potential for biosensing with unequivocal detection at picomole levels and single-base discrimination. We found that this material possesses a kinetically unique entrapment/release behavior, with potential implications in time-controlled biomolecule delivery. Our findings present MXenes as platforms for binding nucleic acids, contributing to their potential for hybridization-based biosensing and related bio-applications.

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.

DNA-Functionalized Nanoceria for Probing Oxidation of Phosphorus Compounds

Chemical reactions without an obvious optical signal change, such as fluorescence or color, are difficult to monitor. Often, more advanced analytical techniques such as high-performance liquid chromatography and mass spectroscopy are needed. It would be useful to convert such reactions to those with changes in optical signals. In this work, we demonstrate that fluorescently labeled DNA oligonucleotides adsorbed on nanomaterials can probe such reactions, and oxidation of phosphorus-containing species was used as an example. Various metal oxides were tested, and CeO2 nanoparticles were found to be the most efficient for this purpose. Among phosphate, phosphite, and hypophosphite, only phosphate produced a large signal, indicating its strongest adsorption on CeO2 to displace the DNA. This was further used to screen oxidation agents to convert lower oxidation-state compounds to phosphate, and bleach was found to be able to oxidize phosphite. Canonical discriminant analysis was performed to discriminate various phosphorus species using a sensor array containing different metal oxides. On the basis of this, glyphosate was studied for its adsorption and oxidation. Although this method is not specific enough for selective biosensors, it is useful as a tool to produce sensitive optical signals to follow important chemical transformations.

Highly active fluorogenic oxidase-mimicking NiO nanozymes

NiO nanoparticles can quickly catalyze oxidation of Amplex red to produce fluorescent products for intracellular imaging, much more efficiently than other types of tested nanozymes.