Nucleic acid conjugated nanomaterials for enhanced molecular recognition

DNA-Templated In Situ Synthesis of Highly Dispersed AuNPs on Nitrogen-Doped Graphene for Real-Time Electrochemical Monitoring of Nitric Oxide Released from Live Cancer Cells

Dispersion promotion of nanomaterials can significantly enhance their catalytic activities. With a new DNA-templated in situ synthesis approach, we report the preparation of highly dispersed AuNPs on nitrogen-doped graphene sheets (NGS) with significantly improved electrocatalytic ability for the monitoring of nitric oxide (NO) released from live cancer cells. The template DNA is adsorbed on NGS via π-π stacking, and the Au precursor chelates along the DNA lattice through dative bonding. Subsequent introduction of the reducing agent leads to in situ nucleation and growth of AuNPs, eventually resulting in highly dispersed AuNPs on NGS. Because of the synergistic enhancement of the catalytic activities of AuNPs and NGS, as well as the high dispersion of AuNPs, such a nanocomposite shows significant electro-oxidation capability toward NO, leading to a highly sensitive subnanomolar detection limit for NO in vitro. More importantly, the laminin glycoproteins can be readily adsorbed on the surface of the nanomaterials to render excellent biocompatibility for the adhesion and proliferation of live cells, enabling the biointerface for electrochemical detection of NO released from live cancer cells.

Surface Functionalisation of Upconversion Nanoparticles with Different Moieties for Biomedical Applications

Lanthanide ion-doped upconversion nanoparticles (UCNPs) that can convert low-energy infrared photons into high-energy visible and ultraviolet photons, are becoming highly sought-after for advanced biomedical and biophotonics applications. Their unique luminescent properties enable UCNPs to be applied for diagnosis, including biolabeling, biosensing, bioimaging, and multiple imaging modality, as well as therapeutic treatments including photothermal and photodynamic therapy, bio-reductive chemotherapy and drug delivery. For the employment of the inorganic nanomaterials into biological environments, it is critical to bridge the gap in between nanoparticles and biomolecules via surface modifications and subsequent functionalisation. This work reviews the various ways to surface modify and functionalise UCNPs so as to impart different functional molecular groups to the UCNPs surfaces for a broad range of applications in biomedical areas. We discussed commonly used base functionalities, including carboxyl, amino and thiol moieties that are typically imparted to UCNP surfaces so as to provide further functional capacity.

An engineered one-site aptamer with higher sensitivity for label-free detection of adenosine on graphene oxide

The 27-nucleotide DNA aptamer for adenosine and ATP, originally selected by the Szostak lab in 1995, has been a very popular model system for biosensor development. This unique aptamer has two target binding sites, and we recently showed that it is possible to remove either site while the other one still retains binding. From an analytical perspective, tuning the number of binding sites has important implications in modulating sensitivity of the resulting biosensors. In this work, we report that the engineered one-site aptamer showed excellent signaling properties with a 2.6-fold stronger signal intensity and also a 4.2-fold increased detection limit compared with the wild-type two-site aptamer. The aptamer has a hairpin structure, and the length of the hairpin stem was systematically varied for the one-site aptamers. Isothermal titration calorimetry and a label-free fluorescence signaling method with graphene oxide and SYBR Green I were respectively used to evaluate binding and sensor performance. Although longer stemmed aptamers produced better adenosine binding affinity, the signaling was quite independent of the stem length as long as more than three base pairs were left. This was explained by the higher affinity of binding to GO by the longer aptamers, cancelling out the higher affinity for adenosine binding. This work further confirms the analytical applications of such one-site adenosine aptamers, which are potentially useful for improved ATP imaging and for developing new biosensors.

Pyrophosphate ion-triggered competitive displacement of ssDNA from a metal-organic framework and its application in fluorescent sensing of alkaline phosphatase

Nanomaterial/aptamer assembly has been extensively explored in the detection of various targets, but some limitations still exist in its practical applications, especially time consumption and low-efficient detachment of the aptamer from the nanomaterial surface. In this work, we demonstrated the ligand role of pyrophosphate ion (PPi) in the competitive displacement of ssDNA from the nanoscaffold surface. For this purpose, a fluorescein-labeled ssDNA (F-DNA) and a mixed valence state cerium (Ce³⁺/Ce⁴⁺)-based MOF (MVCM) were employed as the signal response unit and nanoscaffold, respectively. Benefiting from the existence of Ce⁴⁺, the MVCM exhibits an ultrahigh quenching efficiency (more than 90%) to F-DNA fluorescence, which is 3-fold higher than that of the MOF with Ce³⁺ only. However, it was found that PPi can effectively suppress the quenching effect of the MVCM by competitive coordination with the MVCM to displace F-DNA. Different from the conventional target-induced conformational change of aptamers, the PPi-triggered displacement assay is independent of the ssDNA sequence and can be rapidly completed in just 2 min. The displacement assay is also highly sensitive, even at a PPi concentration as low as 55 nM. In contrast to PPi, however, the phosphate ions and other anions cannot displace F-DNA from the MVCM surface to switch on the F-DNA fluorescence. Inspired by this fact, the PPi-triggered displacement assay was further applied in the detection of alkaline phosphatase (ALP). The detection limit toward ALP was obtained at 0.18 mU mL^-1. Moreover, the accurate determination of ALP concentration in serum samples indicates the applicability of this sensing system in detecting real samples.

Bioorthogonal DNA Adsorption on Polydopamine Nanoparticles Mediated by Metal Coordination for Highly Robust Sensing in Serum and Living Cells

DNA-functionalized nanomaterials, such as various 2D materials, metal oxides, and gold nanoparticles, have been extensively explored as biosensors. However, their practical applications for selective sensing and imaging in biological samples remain challenging due to interference from the sample matrix. Bioorthogonal chemistry has allowed specific reactions in cells, and we want to employ this concept to design nanomaterials that can selectively adsorb DNA but not proteins or other abundant biomolecules. In this work, DNA oligonucleotides were found to be adsorbed on polydopamine nanoparticles (PDANs) via polyvalent metal-mediated coordination, and such adsorption bioorthogonally resisted DNA displacement by various biological ligands, showing better performance compared to graphene oxide and metal oxide nanoparticles for DNA detection. Using DNA/PDANs as biosensors, a detection limit of <1 nM target DNA was achieved in serum and other biological samples, and imaging of cancer-related microRNA in cells was demonstrated. The DNA binding mechanism on PDAN was further studied by ligand displacement experiments and X-ray photoelectron spectroscopy characterization, which demonstrated the critical role of polyvalent metal ions to bridge DNA with PDANs. This work provides fundamental insights into the biointerface science of PDANs with DNA, which can benefit applications in biosensor design, directed assembly of nanomaterials, bioimaging, and drug delivery.

Colorimetric determination of mercury(II) via the inhibition by ssDNA of the oxidase-like activity of a mixed valence state cerium-based metal-organic framework

This work demonstrates the inhibition effects of single-stranded (ssDNA) on the oxidase-like activity of a mixed-valence state cerium-based metal-organic framework, denoted as MVC-MOF. The MVC-MOF was synthesized by partial oxidation of cerium(III) which leads to the presence of both Ce(III) and Ce(IV) ions. The latter endows the MVC-MOF with a typical oxidase-like activity. However, on addition of ssDNA, the catalytic activity of the MVC-MOF is inhibited because it binds the MVC-MOF and thereby shield its active sites. This prevents the access of substrates. The inhibition by ssDNA depends on its length but not its sequence. By contrast, negligible changes in the oxidase-mimicking activity are observed if double-stranded DNA (dsDNA) is added. By employing a thymine-rich ssDNA (T-ssDNA) as a model DNA, a colorimetric assay was developed for the determination of Hg(II). This ion binds to T-ssDNA and causes the formation of T-dsDNA. Hence, the oxidase-mimicking activity is compromised. By using the oxidase substrate 3,3',5,5'-tetramethylbenzidine that gives a colored product in the presence of oxygen, the assay has a linear response that covers 0.05 to 6 μM Hg(II) with a detection limit of 10.5 nM, and exhibits high selectivity over other metal ions. The assay was successfully applied to the determination of Hg(II) in environmental water samples. Graphical abstract Schematic of the inhibition effect of ssDNA on the oxidase-like activity of MVC-MOF that converts colorless TMB to oxTMB with blue color in the presence of oxygen, and its application in the construction of a colorimetric assay for Hg(II) determination.

Continuously Tunable Nucleotide/Lanthanide Coordination Nanoparticles for DNA Adsorption and Sensing

Metal-organic coordination polymers (CPs) have attracted great research interest because they are easy to prepare, porous, flexible in composition, and designable in structure. Their applications in biosensor development, drug delivery, and catalysis have been explored. Lanthanides and nucleotides can form interesting CPs, although most previous works have focused on a single type of metal ligand. In this work, we explored mixed nucleotides and studied their DNA adsorption properties using fluorescently labeled oligonucleotides. Adenosine monophosphate (AMP) and guanosine monophosphate (GMP) formed negatively charged CP nanoparticles with most lanthanides, and thus a salt was required to adsorb negatively charged DNA. DNA adsorption was faster and reached a higher capacity with lighter lanthanides. Desorption of pre-adsorbed DNA by inorganic phosphates, urea, proteins, surfactants, and competing DNA was successively carried out. The results suggested the importance of the DNA phosphate backbone, although hydrogen bonding and DNA bases also contributed to adsorption. The AMP CPs adsorbed DNA more strongly than the GMP ones, and using mixtures of AMP and GMP, continuous tuning of DNA adsorption affinity was achieved. Such CPs were also used as a sensor for DNA detection based on the different affinities of single- and double-stranded DNA, and a detection limit of 0.9 nM target DNA was achieved. Instead of tuning DNA adsorption by varying the length and sequence of DNA, the composition of CPs can also be controlled to achieve this goal.

Biomedical applications of carbon nanomaterials: Drug and gene delivery potentials

One of the major components in the development of nanomedicines is the choice of the right biomaterial, which notably determines the subsequent biological responses. The popularity of carbon nanomaterials (CNMs) has been on the rise due to their numerous applications in the fields of drug delivery, bioimaging, tissue engineering, and biosensing. Owing to their considerably high surface area, multifunctional surface chemistry, and excellent optical activity, novel functionalized CNMs possess efficient drug-loading capacity, biocompatibility, and lack of immunogenicity. Over the past few decades, several advances have been made on the functionalization of CNMs to minimize their health concerns and enhance their biosafety. Recent evidence has also implied that CNMs can be functionalized with bioactive peptides, proteins, nucleic acids, and drugs to achieve composites with remarkably low toxicity and high pharmaceutical efficiency. This review focuses on the three main classes of CNMs, including fullerenes, graphenes, and carbon nanotubes, and their recent biomedical applications.

Nucleoside Analogue-Based Supramolecular Nanodrugs Driven by Molecular Recognition for Synergistic Cancer Therapy

The utilization of nanotechnology for the delivery of a wide range of anticancer drugs has the potential to reduce adverse effects of free drugs and improve the anticancer efficacy. However, carrier materials and/or chemical modifications associated with drug delivery make it difficult for nanodrugs to achieve clinical translation and final Food and Drug Administration (FDA) approvals. We have discovered a molecular recognition strategy to directly assemble two FDA-approved small-molecule hydrophobic and hydrophilic anticancer drugs into well-defined, stable nanostructures with high and quantitative drug loading. Molecular dynamics simulations demonstrate that purine nucleoside analogue clofarabine and folate analogue raltitrexed can self-assemble into stable nanoparticles through molecular recognition. In vitro studies exemplify how the clofarabine:raltitrexed nanoparticles could greatly improve synergistic combination effects by arresting more G1 phase of the cell cycle and reducing intracellular deoxynucleotide pools. More importantly, the nanodrugs increase the blood retention half-life of the free drugs, improve accumulation of drugs in tumor sites, and promote the synergistic tumor suppression property in vivo.

Adsorption of Phosphate and Polyphosphate on Nanoceria Probed by DNA Oligonucleotides

Phosphate-containing molecules exist in many forms in biology and the environment, and their interaction with metal oxides is an important aspect of their chemistry and biochemistry. In this work, phosphates with different degrees of polymerization (e.g., orthophosphate, pyrophosphate (PPi), sodium triphosphate (STPP), sodium trimetaphosphate (STMP), and polyphosphate with 25 phosphate units) and phosphates with one or two capping groups were studied. CeO₂ nanoparticles (nanoceria) were used as a model metal oxide. DNA is also a polyphosphate, and a fluorescently labeled DNA oligonucleotide was mixed with nanoceria. These phosphate species were individually added to displace the adsorbed DNA. Longer phosphate chains were more efficient when each molecule was used at the same molar concentration, whereas PPi and STPP were most efficient at the same total phosphorus atom concentration. By capping the phosphate with organic groups, the affinity was significantly decreased. Isothermal titration calorimetry (ITC) was also performed to quantitatively measure thermodynamic parameters. Although STMP was very slow at displacing DNA, it was still adsorbed very strongly by nanoceria from ITC, indicating kinetic effects likely due to its ring structure. This observation allowed us to use the DNA as a probe to study the hydrolysis of STMP to form STPP. In summary, this study provides a systematic understanding of phosphate species interacting with metal oxides, and interestingly, it demonstrates an analytical application as well.

Biochemistry and biomedicine of quantum dots: from biodetection to bioimaging, drug discovery, diagnostics, and therapy

According to recent research, nanotechnology based on quantum dots (QDs) has been widely applied in the field of bioimaging, drug delivery, and drug analysis. Therefore, it has become one of the major forces driving basic and applied research. The application of nanotechnology in bioimaging has been of concern. Through in vitro labeling, it was found that luminescent QDs possess many properties such as narrow emission, broad UV excitation, bright fluorescence, and high photostability. The QDs also show great potential in whole-body imaging. The QDs can be combined with biomolecules, and hence, they can be used for targeted drug delivery and diagnosis. The characteristics of QDs make them useful for application in pharmacy and pharmacology. This review focuses on various applications of QDs, especially in imaging, drug delivery, pharmaceutical analysis, photothermal therapy, biochips, and targeted surgery. Finally, conclusions are made by providing some critical challenges and a perspective of how this field can be expected to develop in the future.

STATEMENT OF SIGNIFICANCE

Quantum dots (QDs) is an emerging field of interdisciplinary subject that involves physics, chemistry, materialogy, biology, medicine, and so on. In addition, nanotechnology based on QDs has been applied in depth in biochemistry and biomedicine. Some forward-looking fields emphatically reflected in some extremely vital areas that possess inspiring potential applicable prospects, such as immunoassay, DNA analysis, biological monitoring, drug discovery, in vitro labelling, in vivo imaging, and tumor target are closely connected to human life and health and has been the top and forefront in science and technology to date. Furthermore, this review has not only involved the traditional biochemical detection but also particularly emphasized its potential applications in life science and biomedicine.

Nanoplasmonic sensors for biointerfacial science

In recent years, nanoplasmonic sensors have become widely used for the label-free detection of biomolecules across medical, biotechnology, and environmental science applications. To date, many nanoplasmonic sensing strategies have been developed with outstanding measurement capabilities, enabling detection down to the single-molecule level. One of the most promising directions has been surface-based nanoplasmonic sensors, and the potential of such technologies is still emerging. Going beyond detection, surface-based nanoplasmonic sensors open the door to enhanced, quantitative measurement capabilities across the biointerfacial sciences by taking advantage of high surface sensitivity that pairs well with the size of medically important biomacromolecules and biological particulates such as viruses and exosomes. The goal of this review is to introduce the latest advances in nanoplasmonic sensors for the biointerfacial sciences, including ongoing development of nanoparticle and nanohole arrays for exploring different classes of biomacromolecules interacting at solid-liquid interfaces. The measurement principles for nanoplasmonic sensors based on utilizing the localized surface plasmon resonance (LSPR) and extraordinary optical transmission (EOT) phenomena are first introduced. The following sections are then categorized around different themes within the biointerfacial sciences, specifically protein binding and conformational changes, lipid membrane fabrication, membrane-protein interactions, exosome and virus detection and analysis, and probing nucleic acid conformations and binding interactions. Across these themes, we discuss the growing trend to utilize nanoplasmonic sensors for advanced measurement capabilities, including positional sensing, biomacromolecular conformation analysis, and real-time kinetic monitoring of complex biological interactions. Altogether, these advances highlight the rich potential of nanoplasmonic sensors and the future growth prospects of the community as a whole. With ongoing development of commercial nanoplasmonic sensors and analytical models to interpret corresponding measurement data in the context of biologically relevant interactions, there is significant opportunity to utilize nanoplasmonic sensing strategies for not only fundamental biointerfacial science, but also translational science applications related to clinical medicine and pharmaceutical drug development among countless possibilities.

Fluorescent DNA Probing Nanoscale MnO2: Adsorption, Dissolution by Thiol, and Nanozyme Activity

Manganese dioxide (MnO₂) is an interesting material due to its excellent biocompatibility and magnetic properties. Adsorption of DNA to MnO₂ is potentially of interest for drug delivery and sensing applications. However, little fundamental understanding is known about their interactions. In this work, carboxyfluorescein (FAM)-labeled DNA oligonucleotides were used to explore the effect of salt concentration, pH, and DNA sequence and length for adsorption by MnO₂, and comparisons were made with graphene oxide (GO). The DNA desorbs from MnO₂ by free inorganic phosphate, while it desorbs from GO by adenosine and urea. Therefore, DNA is mainly adsorbed on MnO₂ through its phosphate backbone, and DNA has a stronger affinity on MnO₂ than on GO based on a salt-shock assay. At the same time, DNA was used to study the effect of thiol containing compounds on the dissolution of MnO₂. Adsorbed DNA was released from MnO₂ after its dissolution by thiol, but not from other metal oxides with lower solubility such as CeO₂, TiO₂, and Fe₃O₄. DNA-functionalized MnO₂ was then used for detecting glutathione (GSH) with a detection limit of 383 nM. Finally, DNA was found to inhibit the peroxidase-like activity of MnO₂. This study has offered many fundamental insights into the interaction between MnO₂ and two important biomolecules: DNA and thiol-containing compounds.

Length-Dependent Diblock DNA with Poly-cytosine (Poly-C) as High-Affinity Anchors on Graphene Oxide

DNA-functionalized graphene oxide (GO) is a popular system for biosensor development and directed materials assembly. Compared to covalent attachment, simple physisorption of DNA has been more popular, and a DNA sequence with a strong affinity on GO is highly desirable. Recently, we found that poly-cytosine (poly-C) DNA can strongly adsorb on many common nanomaterials, including GO. To identify an optimal length of poly-C DNA, we herein designed a series of diblock DNA sequences containing between 0 and 30 cytosines. The displacement of a random sequenced DNA by poly-C DNA was demonstrated, confirming the desired diblock structure on GO with the poly-C block anchoring on the surface and the other block available for hybridization. The adsorption density of poly-C containing DNA did not vary much as the length of the poly-C block increased, suggesting the conformation of the anchoring DNA on the GO was quite independent of the DNA length. With a longer poly-C block, the efficiency of surface hybridization of the other block increased, while nonspecific adsorption of noncomplementary DNA was inhibited more. Compared to poly-adenine (poly-A)-containing DNAs, which were previously used for the same purpose, poly-C DNA adsorption is more stable. Using four types of 15-mer DNA homopolymers as the intended anchoring sequences, the C₁₅ DNA had the best hybridization efficiency. This work has suggested the optimal length for the poly-C block to be 15-mer or longer, and it has provided interesting insights into the DNA/GO biointerface.

Nanotechnology-based recent approaches for sensing and remediation of pesticides

Pesticides are meant to control and destroy the pests and weeds. They are classified into different categories on the basis their origin and type of pest they target. Chemical pesticides such as insecticides, herbicides and fungicides are commonly used in agricultural fields. However, the excessive use of these agrochemicals have adverse effects on environment such as reduced population of insect pollinators, threat to endangered species and habitat of birds. Upon consumption; chemical pesticides also cause various health issues such as skin, eye and nervous system related problems and cancer upon prolonged exposure. Various techniques in the past have been developed on the basis of surface adsorption, membrane filtration and biological degradation to reduce the content of pesticides. However, slow response, less specificity and sensitivity are some of the drawbacks of such techniques. In recent times, Nanotechnology has emerged as a helping tool for the sensing and remediation of pesticides. This review focuses on the use of this technology for the detection, degradation and removal of pesticides. Nanomaterials have been classified into nanoparticles, nanotubes and nanocomposites that are commonly used for detection, degradation and removal of pesticides. The review also focuses on the chemistry behind the sensing and remediation of pesticides using nanomaterials. Different types of nanoparticles, viz. metal nanoparticles, bimetallic nanoparticles and metal oxide nanoparticles; nanotubes such as carbon nanotubes and halloysite nanotubes have been used for the detection, degradation and removal of pesticides. Further, various enzyme-based biosensors for detection of pesticides have also been summarized.

One-Step in Situ Detection of miRNA-21 Expression in Single Cancer Cells Based on Biofunctionalized MoS2 Nanosheets

Here, we report the one-step in situ detection of targeted miRNAs expression in single living cancer cells via MoS₂ nanosheet-based fluorescence on/off probes. The strategy is based on the folic acid (FA)-poly(ethylene glycol)-functionalized MoS₂ nanosheets with adsorbed dye-labeled single-stranded DNA (ssDNA). Once the nanoprobes are internalized into cancer cells, the hybridization between the probes and target miRNA results in the detachment of dye-labeled ssDNA from MoS₂ nanosheets surface, leading to the green fluorescence recovery. In this nanoprobe, MoS₂ nanosheets offer advantages of high fluorescence quenching efficiency and extremely low toxicity. The FA conjugation could protect the probes and improve cancer cell transfection efficiency. The ability of this nanoprobe for endogenous miRNA detection in single living cancer cells is demonstrated for two types of cancer cells with different miRNA-21 expressions (MCF-7 and Hela cells). This functionalized MoS₂ nanosheet-based nanoprobes could provide a sensitive and real-time detection of intracellular miRNA detection platform.

Synergistic molecular assembly of an aptamer and surfactant on gold nanoparticles for the colorimetric detection of trace levels of As3+ ions in real samples

A facile and selective aptasensor was developed by the synergistic molecular assembly of the Ars-3 aptamer on AuNPs for the detection of As³⁺ ions using CTAB as a binder.

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials

Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈10¹⁴ random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions. This leads to a very high background binding making aptamer selection difficult. Screening, on the other hand, can be designed to compare relative binding affinities of different DNA sequences and could be more appropriate for inorganic surfaces. The resulting sequences have been used for DNA-directed assembly, sorting of carbon nanotubes, and DNA-controlled growth of inorganic nanomaterials. It was recently discovered that poly-cytosine (C) DNA can strongly bind to a diverse range of nanomaterials including nanocarbons (graphene oxide and carbon nanotubes), various metal oxides and transition-metal dichalcogenides. In this Concept article, we articulate the need for screening and potential artifacts associated with traditional aptamer selection methods for inorganic surfaces. Representative examples of application are discussed, and a few future research opportunities are proposed towards the end of this article.

Interfacing DNA Oligonucleotides with Calcium Phosphate and Other Metal Phosphates

Calcium phosphate (CaP) has long been used for DNA delivery, although its fundamental interaction with DNA, especially with single-stranded DNA oligonucleotides, remains to be fully understood. Using fluorescently labeled oligonucleotides, we herein studied DNA adsorption isotherm and the effect of DNA length and sequence. Longer DNAs are adsorbed more strongly, and at neutral pH, poly-C DNAs are adsorbed more than the other three DNA homopolymers. However, at near pH 11, the pH of CaP synthesis, T₃₀ DNA is adsorbed more strongly than C₃₀ or A₃₀. This can explain why T₃₀ and G₃₀ can fully inhibit the growth of CaP, while A₃₀ and C₃₀ only retarded its growth kinetics. DNA adsorption also reduces aggregation of CaP. DNA desorption experiments were carried out using concentrated urea, thymidine, or inorganic phosphate as competitors, and desorption was observed only in the presence of phosphate, suggesting that DNA uses its phosphate backbone to interact with the CaP surface. Desorption was also promoted by raising the NaCl concentration suggesting the electrostatic nature of interaction. Finally, ten different metal phosphate materials were synthesized by co-precipitating each metal ion (Ce³⁺, Fe³⁺, Ca²⁺, Ni²⁺, Zn²⁺, Mn²⁺, Ba²⁺, Cu²⁺, Sr²⁺, Co²⁺), and DNA adsorption by these phosphate precipitants was found to be related to their surface charge and metal chemistry. This work has revealed fundamental surface science of DNA adsorption by CaP and other metal phosphate salts, and this knowledge might be useful for gene delivery, biomineralization, and DNA-directed assembly of metal phosphate materials.

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study

Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (T_m) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (T_a) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA T_m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T_a increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.

A Molecular Recognition Approach To Synthesize Nucleoside Analogue Based Multifunctional Nanoparticles for Targeted Cancer Therapy

Tumor-targeted drug delivery with simultaneous cancer imaging is highly desirable for personalized medicine. Herein, we report a supramolecular approach to design a promising class of multifunctional nanoparticles based on molecular recognition of nucleobases, which combine excellent tumor-targeting capability via aptamer, controlled drug release, and efficient fluorescent imaging for cancer-specific therapy. First, an amphiphilic prodrug dioleoyl clofarabine was self-assembled into micellar nanoparticles with hydrophilic nucleoside analogue clofarabine on their surface. Thereafter, two types of single-stranded DNAs that contain the aptamer motif and fluorescent probe Cy5.5, respectively, were introduced onto the surface of the nanoparticles via molecular recognition between the clofarabine and the thymine on DNA. These drug-containing multifunctional nanoparticles exhibit good capabilities of targeted clofarabine delivery to the tumor site and intracellular controlled drug release, leading to a robust and effective antitumor effect in vivo.

Multifunctional Nanotechnology-Enabled Sensors for Rapid Capture and Detection of Pathogens

Nanomaterial-based sensing approaches that incorporate different types of nanoparticles (NPs) and nanostructures in conjunction with natural or synthetic receptors as molecular recognition elements provide opportunities for the design of sensitive and selective assays for rapid detection of contaminants. This review summarizes recent advancements over the past ten years in the development of nanotechnology-enabled sensors and systems for capture and detection of pathogens. The most common types of nanostructures and NPs, their modification with receptor molecules and integration to produce viable sensing systems with biorecognition, amplification and signal readout are discussed. Examples of all-in-one systems that combine multifunctional properties for capture, separation, inactivation and detection are also provided. Current trends in the development of low-cost instrumentation for rapid assessment of food contamination are discussed as well as challenges for practical implementation and directions for future research.

Nucleic acid-functionalized transition metal nanosheets for biosensing applications

In clinical diagnostics, as well as food and environmental safety practices, biosensors are powerful tools for monitoring biological or biochemical processes. Two-dimensional (2D) transition metal nanomaterials, including transition metal chalcogenides (TMCs) and transition metal oxides (TMOs), are receiving growing interest for their use in biosensing applications based on such unique properties as high surface area and fluorescence quenching abilities. Meanwhile, nucleic acid probes based on Watson-Crick base-pairing rules are also being widely applied in biosensing based on their excellent recognition capability. In particular, the emergence of functional nucleic acids in the 1980s, especially aptamers, has substantially extended the recognition capability of nucleic acids to various targets, ranging from small organic molecules and metal ions to proteins and cells. Based on π-π stacking interaction between transition metal nanosheets and nucleic acids, biosensing systems can be easily assembled. Therefore, the combination of 2D transition metal nanomaterials and nucleic acids brings intriguing opportunities in bioanalysis and biomedicine. In this review, we summarize recent advances of nucleic acid-functionalized transition metal nanosheets in biosensing applications. The structure and properties of 2D transition metal nanomaterials are first discussed, emphasizing the interaction between transition metal nanosheets and nucleic acids. Then, the applications of nucleic acid-functionalized transition metal nanosheet-based biosensors are discussed in the context of different signal transducing mechanisms, including optical and electrochemical approaches. Finally, we provide our perspectives on the current challenges and opportunities in this promising field.

Comparison of MoS2, WS2, and Graphene Oxide for DNA Adsorption and Sensing

Interfacing DNA with two-dimensional (2D) materials has been intensely researched for various analytical and biomedical applications. Most of these studies have been performed on graphene oxide (GO) and two metal dichalcogenides, molybdenum disulfide (MoS₂) and tungsten disulfide (WS₂); all of them can all adsorb single-stranded DNA. However, they use different surface forces for adsorption based on their chemical structures. In this work, fluorescently labeled DNA oligonucleotides were used and their adsorption capacities and kinetics were studied as a function of ionic strength, DNA length, and sequence. Desorption of DNA from these surfaces was also measured. DNA is more easily desorbed from GO by various denaturing agents, whereas surfactants yield more desorption from MoS₂ and WS₂. Our results are consistent with the fact that DNA can be adsorbed by GO via π-π stacking and hydrogen bonding, and MoS₂ and WS₂ mainly use van der Waals force for adsorption. Finally, fluorescent DNA probes were adsorbed by these 2D materials for detecting complementary DNA. For this assay, GO gave the highest sensitivity, whereas they all showed a similar detection limit. This study has enhanced our fundamental understanding of DNA adsorption by two important types of 2D materials and is useful for further rational optimization of their analytical and biomedical applications.

Tuning DNA adsorption affinity and density on metal oxide and phosphate for improved arsenate detection

Arsenic (As) contamination in groundwater presents a major health and environmental concern in developing countries. Typically, As is found in two oxidation states. Most chemical tests for inorganic arsenic are focused on As(III), and few have been developed for As(V). We are interested in developing biosensors for As(V) based on its similarity with phosphate. Building upon previous work involving DNA-capped Fe₃O₄ nanoparticles for As(V) detection, we investigated two other nanomaterials: CeO₂ and CePO₄ in terms of DNA adsorption and As(V) induced DNA desorption. Fluorescently labeled DNA is physically adsorbed to the surface sites on the nanoparticle surface via its phosphate backbone. In the cases of CeO₂ and Fe₃O₄, the fluorescence was quenched due to electron transfer, whereas for the insulating CePO₄, no quenching was observed. Arsenate, being similar to phosphate, can also bind to the surface of the nanoparticles and displace the DNA, increasing the fluorescence signal. The length and sequence of DNA were systematically studied. Using this method, CeO₂ performed significantly better than Fe₃O₄, lowering the detection limit by almost 10-fold. In addition, for CeO₂ and CePO₄, using shorter DNA was more effective for As(V) detection than using the longer DNA since they both adsorb DNA more tightly than Fe₃O₄ does. Overall, CeO₂ has the best performance since it has an intermediate adsorption affinity of DNA, while CePO₄ adsorbs DNA too strongly.

Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

DNA-functionalized gold nanoparticles (AuNPs) have been extensively used in sensing, drug delivery, and materials science. A key step is to attach DNA to AuNPs, forming a stable and functional conjugate. Although the traditional salt-aging method takes a full day or longer, a recent low-pH method allows DNA conjugation in a few minutes. The effect of low pH was attributed to the protonation of adenine (A) and cytosine (C), resulting in an overall lower negative charge density on DNA. In this work, the effect of DNA conformation at low pH is studied. Using circular dichroism (CD) spectroscopy, the parallel poly-A duplex (A-motif) is detected when a poly-A segment is linked to a random DNA, a design typically used for DNA conjugation. A DNA staining dye, thiazole orange, is identified for detecting such A-motifs. The A-motif structure is ideal for DNA conjugation because it exposes the thiol group to directly react with the gold surface while minimizing nonspecific DNA base adsorption. For nonthiolated DNA, the optimal procedure is to incubate DNA and AuNPs followed by lowering the pH. The i-motif formed by poly-C DNA at low pH is less favorable to the conjugation reaction because of its unique way of folding. The stability of poly-A and poly-G DNA at low pH is examined. An excellent stability of poly-A DNA is confirmed, but poly-G has lower stability. This study provides new fundamental insights into a practically useful technique of conjugating DNA to AuNPs.

Comparison of Graphene Oxide and Reduced Graphene Oxide for DNA Adsorption and Sensing

Fluorescently labeled DNA adsorbed on graphene oxide (GO) is a well-established sensing platform for detecting a diverse range of analytes. GO is a loosely defined material and its oxygen content may vary depending on the condition of preparation. Sometimes, a further reduction step is intentionally performed to decrease the oxygen content, and the resulting material is called reduced GO (rGO). In this study, DNA adsorption and desorption from GO and rGO is systematically compared. Under the same salt concentration, DNA adsorbs slightly faster with a 2.6-fold higher capacity on rGO. At the same time, DNA adsorbed on rGO is more resistant to desorption induced by temperature, pH, urea, and organic solvents. Various lengths and sequences of DNA probes have been tested. When its complementary DNA is added as a model target analyte, the rGO sample has a higher signal-to-background and signal-to-noise ratio, whereas the GO sample has a slightly higher absolute signal increase and faster signaling kinetics. DNAs adsorbed on GO or rGO are still susceptible to nonspecific displacement by other DNA and proteins. Overall, although rGO adsorbs DNA more tightly, it allows efficient DNA sensing with an extremely low background fluorescence signal.

Label-Free Ag⁺ Detection by Enhancing DNA Sensitized Tb(3+) Luminescence

In this work, the effect of Ag⁺ on DNA sensitized Tb³⁺ luminescence was studied initially using the Ag⁺-specific RNA-cleaving DNAzyme, Ag10c. While we expected to observe luminescence quenching by Ag⁺, a significant enhancement was produced. Based on this observation, simple DNA oligonucleotide homopolymers were used with systematically varied sequence and length. We discovered that both poly-G and poly-T DNA have a significant emission enhancement by Ag⁺, while the absolute intensity is stronger with the poly-G DNA, indicating that a G-quadruplex DNA is not required for this enhancement. Using the optimized length of the G7 DNA (an oligo constituted with seven guanines), Ag⁺ was measured with a detection limit of 57.6 nM. The signaling kinetics, G7 DNA conformation, and the binding affinity of Tb³⁺ to the DNA in the presence or absence of Ag⁺ are also studied to reveal the mechanism of emission enhancement. This observation is useful not only for label-free detection of Ag⁺, but also interesting for the rational design of new biosensors using Tb³⁺ luminescence.

A competitive coordination-based CeO2 nanowire-DNA nanosensor: fast and selective detection of hydrogen peroxide in living cells and in vivo

A competitive coordination-based hydrogen peroxide (H2O2) nanosensor is constructed by the assembly of FAM-tagged single-strand (ss) DNA on cerium oxide nanowires (CeO2 NWs). This fluorescent nanosensor is capable of rapidly and selectively tracking H2O2 within living cells, as well as directly visualizing H2O2 generated by wound-induced oxidative damage in zebrafish larvae.

2-Aminopurine-modified DNA homopolymers for robust and sensitive detection of mercury and silver

Heavy metal detection is a key topic in analytical chemistry. DNA-based metal recognition has advanced significantly producing many specific metal ligands, such as thymine for Hg²⁺ and cytosine for Ag⁺. For practical applications, however, robust sensors that can work in a diverse range of salt concentrations need to be developed, while most current sensing strategies cannot meet this requirement. In this work, 2-aminopurine (2AP) is used as a fluorescence label embedded in the middle of four 10-mer DNA homopolymers. 2AP can be quenched up to 98% in these DNA without an external quencher. The interaction between 2AP and all common metal ions is studied systematically for both free 2AP base and 2AP embedded DNA homopolymers. With such low background, Hg²⁺ induces up to 14-fold signal enhancement for the poly-T DNA, and Ag⁺ enhances up to 10-fold for the poly-C DNA. A detection limit of 3nM is achieved for both metals. With these four probes, silver and mercury can be readily discriminated from the rest. A comparison with other signaling methods was made using fluorescence resonance energy transfer, graphene oxide, and SYBR Green I staining, respectively, confirming the robustness of the 2AP label. Detection of Hg²⁺ in Lake Huron water was also achieved with a similar sensitivity. This work has provided a comprehensive fundamental understanding of using 2AP as a label for metal detection, and has achieved the highest fluorescence enhancement for non-protein targets.

Magnetic Iron Oxide Nanoparticle Seeded Growth of Nucleotide Coordinated Polymers

The introduction of functional molecules to the surface of magnetic iron oxide nanoparticles (NPs) is of critical importance. Most previously reported methods were focused on surface ligand attachment either by physisorption or covalent conjugation, resulting in limited ligand loading capacity. In this work, we report the seeded growth of a nucleotide coordinated polymer shell, which can be considered as a special form of adsorption by forming a complete shell. Among all of the tested metal ions, Fe(3+) is the most efficient for this seeded growth. A diverse range of guest molecules, including small organic dyes, proteins, DNA, and gold NPs, can be encapsulated in the shell. All of these molecules were loaded at a much higher capacity compared to that on the naked iron oxide NP core, confirming the advantage of the coordination polymer (CP) shell. In addition, the CP shell provides better guest protein stability compared to that of simple physisorption while retaining guest activity as confirmed by the entrapped glucose oxidase assay. Use of this system as a peroxidase nanozyme and glucose biosensor was demonstrated, detecting glucose as low as 1.4 μM with excellent stability. This work describes a new way to functionalize inorganic materials with a biocompatible shell.

Highly Hybridizable Spherical Nucleic Acids by Tandem Glutathione Treatment and Polythymine Spacing

Gold nanoparticle (AuNP)-templated spherical nucleic acids (SNAs) have been demonstrated as an important functional material in bionanotechnology. Fabrication of SNAs having high hybridization capacity to their complementary sequences is critical to ensure their applicability in areas such as antisense gene therapy and cellular sensing. The traditional salt-aging procedure is effective but tedious, requiring 1-3 days to complete. The rapid low-pH assisted protocol is efficient, but causes concerns related to nonspecific DNA adsorption to the AuNP core. To address these issues, we systematically compared the SNAs prepared by these two methods (salt-aging method and low-pH protocol). In terms of the number of complementary DNA that each SNA can bind and the average binding affinity of each thiolated DNA probe to its complementary strand, both methods yielded comparable hybridizability, although higher loading capacity was witnessed with SNAs made using the low-pH method. Additionally, it was found that nonspecific DNA binding could be eliminated almost completely by a simple glutathione (GSH) treatment of SNAs. Compared to conventional methods using toxic mercapto-hexanol or alkanethiols to remove nonspecific DNA adsorption, GSH is mild, cost-effective, and technically easy to use. In addition, GSH-passivated SNAs minimize the toxicity concerns related to AuNP-induced GSH depletion and therefore offer a more biocompatible alternative to previously reported SNAs. Moreover, rational design of probe sequences through inclusion of a polythymine spacer into the DNA sequences resulted in enhanced DNA loading capacity and stability against salt-induced aggregation. This work provides not only efficient and simple technical solutions to the issue of nonspecific DNA adsorption, but also new insights into the hybridizability of SNAs.

Aptamer-nanoparticle complexes as powerful diagnostic and therapeutic tools

Correct diagnosis and successful therapy are extremely important to enjoy a healthy life when suffering from a disease. To achieve these aims, various cutting-edge technologies have been designed and fabricated to diagnose and treat specific diseases. Among these technologies, aptamer-nanomaterial hybrids have received considerable attention from scientists and doctors because they have numerous advantages over other methods, such as good biocompatibility, low immunogenicity and controllable selectivity. In particular, aptamers, oligonucleic acids or peptides that bind to a specific target molecule, are regarded as outstanding biomolecules. In this review, several screening techniques for aptamers, also called systematic evolution of ligands by exponential enrichment (SELEX) methods, are introduced, and diagnostic and therapeutic aptamer applications are also presented. Furthermore, we describe diverse aptamer-nanomaterial conjugate designs and their applications for diagnosis and therapy.

Silver nanoparticles anchored on nitrogen-doped graphene as a novel electrochemical biosensing platform with enhanced sensitivity for aptamer-based pesticide assay

Silver nanoparticles (NPs) decorated nitrogen doped graphene (NG) nanocomposites were prepared through a one-step thermal-treatment route using arginine as the nitrogen source. By integrating the excellent electrical properties and large surface area of Ag NPs and NG, the obtained Ag/NG nanocomposites show more effective electron transfer and high loading capacity than Ag-graphene and pure NG. In the presence of a target, the stronger interaction between the aptamer and the target promotes the formation of a target-aptamer complex on the electrode surface which blocks the electron transfer. Based on this sensing mechanism, a novel and highly sensitive biosensing platform by the use of Ag/NG as enhancing materials is demonstrated for detection of the model target, acetamiprid. The presented aptasensor exhibited a wide linear response for acetamiprid in the range of 1 × 10(-13) M to 5 × 10(-9) M with a low detection limit of 3.3 × 10(-14) M (S/N = 3). Moreover, this electrochemical aptasensor avoided complicated labeling procedures and showed magnificent sensitivity, high selectivity and low cost, which made it not only convenient but also time-saving and applicable. Furthermore, the proposed design may offer a promising way to develop a new electrochemical aptasensor for sensitive and specific detection of a wide spectrum of analytes in food, medical and environmental fields.

ssDNA-Functionalized Nanoceria: A Redox-Active Aptaswitch for Biomolecular Recognition

Quantification of biomolecular binding events is a critical step for the development of biorecognition assays for diagnostics and therapeutic applications. This paper reports the design of redox-active switches based on aptamer conjugated nanoceria for detection and quantification of biomolecular recognition. It is shown that the conformational transition state of the aptamer on nanoceria, combined with the redox properties of these particles can be used to create surface based structure switchable aptasensing platforms. Changes in the redox properties at the nanoceria surface upon binding of the ssDNA and its target analyte enables rapid and highly sensitive measurement of biomolecular interactions. This concept is demonstrated as a general applicable method to the colorimetric detection of DNA binding events. An example of a nanoceria aptaswitch for the colorimetric sensing of Ochratoxin A (OTA) and applicability to other targets is provided. The system can sensitively and selectivity detect as low as 0.15 × 10(-9) m OTA. This novel assay is simple in design and does not involve oligonucleotide labeling or elaborate nanoparticle modification steps. The proposed mechanism discovered here opens up a new way of designing optical sensing methods based on aptamer recognition. This approach can be broadly applicable to many bimolecular recognition processes and related applications.