Progress on the development of DNA-mediated metal nanomaterials for environmental and biological analysis

DNA-Encoded Bidirectional Regulation of the Peroxidase Activity of Pt Nanozymes for Bioanalysis

Rational regulation of nanozyme activity can promote biochemical sensing by expanding sensing strategies and improving sensing performance, but the design of effective regulatory strategies remains a challenge. Herein, a rapid DNA-encoded strategy was developed for the efficient regulation of Pt nanozyme activity. Interestingly, we found that the catalytic activity of Pt nanozymes was sequence-dependent, and its peroxidase activity was significantly enhanced only in the presence of T-rich sequences. Thus, different DNA sequences realized bidirectional regulation of Pt nanozyme peroxidase activity. Furthermore, the DNA-encoded strategy can effectively enhance the stability of Pt nanozymes at high temperatures, freezing, and long-term storage. Meanwhile, a series of studies demonstrated that the presence of DNA influenced the reduction degree of H₂PtCl₆ precursors, which in turn affected the peroxidase activity of Pt nanozymes. As a proof of application, the sensor array based on the Pt nanozyme system showed superior performance in the accurate discrimination of antioxidants. This study obtained the regulation rules of DNA on Pt nanozymes, which provided theoretical guidance for the development of new sensing platforms and new ideas for the regulation of other nanozyme activities.

DNA-Guided Metallization of Nanomaterials and Their Biomedical Applications

Precise control of the structure of metallic nanomaterials is critical for the advancement of nanobiotechnology. As DNA (deoxyribonucleic acid) can readily modify various moieties, such as sulfhydryl, carboxyl, and amino groups, using DNA as a directing ligand to modulate the morphology of nanomaterials is a promising strategy. In this review, we focus on the use of DNA as a template to control the morphology of metallic nanoparticles and their biomedical applications, discuss the use of DNA for the metallization of gold and silver, explore the factors that influence the process, and outline its biomedical applications. This review aims to provide valuable insights into the DNA-guided growth of nanomaterials. The challenges and future directions are also discussed.

Constructing DNA logic circuits based on the toehold preemption mechanism

Strand displacement technology and ribozyme digestion technology have enriched the intelligent toolbox of molecular computing and provided more methods for the construction of DNA logic circuits. In recent years, DNA logic circuits have developed rapidly, and their scalability and accuracy in molecular computing and information processing have been fully demonstrated. However, existing DNA logic circuits still have some problems such as high complexity of DNA strands (number of DNA strands) hindering the expansion of practical computing tasks. In view of the above problems, we presented a toehold preemption mechanism and applied it to construct DNA logic circuits using E6-type DNAzymes, such as half adder circuit, half subtractor circuit, and 4-bit square root logic circuit. Different from the dual-track logic expressions, all the signals in the circuits of this study were monorail which substantially reduced the number of DNA strands in the DNA logic circuits. The presented preemption mechanism provides a way to simplify the implementation of large and complex DNA integrated circuits.

Highly Sensitive Fluorescence Detection of Global 5-Hydroxymethylcytosine from Nanogram Input with Strongly Emitting Copper Nanotags

Quantitative analysis of 5-hydroxymethylcytosine (5hmC) has remarkable clinical significance to early cancer diagnosis; however, it is limited by the requirement in current assays for large amounts of starting material and expensive instruments requring expertise. Herein, we present a highly sensitive fluorescence method, termed hmC-TACN, for global 5hmC quantification from several nanogram inputs based on terminal deoxynucleotide transferase (TdT)-assisted formation of fluorescent copper (Cu) nanotags. In this method, 5hmC is labeled with click tags by T4 phage β-glucosyltransferase (β-GT) and cross-linked with a random DNA primer via click chemistry. TdT initiates the template-free extension along the primer at the modified 5hmC site and then generates a long polythymine (T) tail, which can template the production of strongly emitting Cu nanoparticles (CuNPs). Consequently, an intensely fluorescent tag containing numerous CuNPs can be labeled onto the 5hmC site, providing the sensitive quantification of 5hmC with a limit of detection (LOD) as low as 0.021% of total nucleotides (S/N = 3). With only a 5 ng input (∼1000 cells) of genomic DNA, global 5hmC levels were accurately determined in mouse tissues, human cell lines (including normal and cancer cells of breast, lung, and liver), and urines of a bladder cancer patient and healthy control. Moreover, as few as 100 cells can also be distinguished between normal and cancer cells. The hmC-TACN method has great promise of being cost effective and easily mastered, with low-input clinical utility, and even for the microzone analysis of tumor models.

Copper nanocluster composites for analytical (bio)-sensing and imaging: a review

As an ideal substitute for traditional organic fluorescent dyes or up-conversion nanomaterials, copper nanoclusters (CuNCs) have developed rapidly and have been involved in exciting achievements in versatile applications. The emergence of novel CuNCs composites improves the poor stability and fluorescence intensity of CuNCs. With this in mind, great efforts have been made to develop a wide variety of CuNCs composites, and impressive progress has been made in the past few years. In this review, we systematically summarize absorption, fluorescence, electrochemiluminescence, and catalytic properties and focus on the multiple factors that affect the fluorescence properties of CuNCs. The fluorescence properties of CuNCs are discussed from the point of view of core size, surface ligands, self-assembly, metal defects, pH, solvent, ions, metal doping, and confinement effect. Especially, we illustrate the research progress and representative applications of CuNCs composites in bio-related fields, which have received considerable interests in the past years. Additionally, the sensing mechanism of CuNCs composites is highlighted. Finally, we summarize current challenges and look forward to the future development of CuNCs composites. Schematic diagram of the categories, possible sensing mechanisms, and bio-related applications of copper nanoclusters composites.

Biosynthesis and Cytotoxic Properties of Ag, Au, and Bimetallic Nanoparticles Synthesized Using Lithospermum erythrorhizon Callus Culture Extract

The present study reports a green chemistry approach for the rapid and easy biological synthesis of silver (Ag), gold (Au), and bimetallic Ag/Au nanoparticles using the callus extract of Lithospermum erythrorhizon as a reducing and capping agent. The biosynthesized nanoparticles were characterized with ultraviolet-visible (UV-Vis) spectroscopy, X-ray diffraction (XRD) analysis, and transmission electron microscopy (TEM). Our results showed the formation of crystalline metal nanostructures of both spherical and non-spherical shape. Energy dispersive X-ray (EDX) spectroscopy showed the characteristic peaks in the silver and gold regions, confirming the presence of the corresponding elements in the monometallic particles and both elements in the bimetallic particles. Fourier-transform infrared (FTIR) spectroscopy affirmed the role of polysaccharides and polyphenols of the L. erythrorhizon extract as the major reducing and capping agents for metal ions. In addition, our results showed that the polysaccharide sample and the fraction containing secondary metabolites isolated from L. erythrorhizon were both able to produce large amounts of metallic nanoparticles. The biosynthesized nanoparticles demonstrated cytotoxicity against mouse neuroblastoma and embryonic fibroblast cells, which was considerably higher for Ag nanoparticles and for bimetallic Ag/Au nanoparticles containing a higher molar ratio of silver. However, fibroblast migration was not significantly affected by any of the nanoparticles tested. The obtained results provide a new example of the safe biological production of metallic nanoparticles, but further study is required to uncover the mechanism of their toxicity so that the biomedical potency can be assessed.

Bi2S3/rGO Composite Based Electrochemical Sensor for Ascorbic Acid Detection

The engineering of an efficient electrochemical sensor based on a bismuth sulfide/reduced graphene oxide (Bi2S3/rGO) composite to detect ascorbic acid (AA) is reported. The Bi2S3 nanorods/rGO composite was synthesized using a facile hydrothermal method. By varying the amount of graphene oxide (GO) added to the synthesis, the morphology and size of Bi2S3 nanorods anchored on the surface of rGO can be tuned. Compared to a bare glassy carbon electrode (GCE), the GCE modified with Bi2S3/rGO composite presented enhanced electrochemical performance, which was attributed to the optimal electron transport between the rGO support and the loaded Bi2S3 as well as to an increase in the number of active catalytic sites. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) analysis of Bi2S3/rGO/GCE demonstrate that the active Bi2S3/rGO layer on GCE plays an important role in the electrochemical behavior of the sensor. In particular, the Bi2S3/rGO/GCE sensor shows a wide detecting range (5.0–1200 μM), low detection limit (2.9 µM), good sensitivity (268.8 μA mM−1 cm−2), and sufficient recovery values (97.1–101.6%) for the detection of ascorbic acid.

Fluorescent DNA-templated silver nanoclusters for highly sensitive detection of D-penicillamine

Herein, fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) with red emission were synthesized and utilized as novel probe to detect D-penicillamine (D-Pen) for the first time. D-Pen molecules contain a thiol which can combine with Ag to form a non-fluorescent ground state complex, inducing the aggregation of DNA-AgNCs followed by the fluorescence quenching. The quenching mechanism is well-studied and found to be a static quenching process. This method can detect D-Pen in the range of 0.025-0.7 μM with the detection limit as low as 8 nM, which is 1-3 orders of magnitude more sensitive than those based on other fluorescent nanoprobes. More importantly, the preparation procedure for DNA-AgNCs is fast and without the requirement of heavy metal ions. Thus, this detection strategy is time-saving and eco-friendly. Satisfactory recoveries have been acquired for monitoring D-Pen in human serum samples and pharmaceutical samples owing to the high sensitivity.

A ratiometric fluorescence assay for bleomycin based on dual-emissive chameleon DNA-templated silver nanoclusters

The authors design dual-emissive DNA-templated silver nanoclusters (DNA-AgNCs) for ratiometric fluorescence sensing bleomycin (BLM) for the first time. A hairpin probe containing two different C-rich DNA templates at two terminals is used to synthesize chameleon DNA-AgNCs, which possess two emission peaks when they are in close proximity. A strong emission is founded at 622 nm (λex = 570 nm) while a weak one is located at 572 nm (λex = 504 nm). Meanwhile, the loop of this probe contains the scission site (5'-GC-3') of BLM. The loop can be cleaved into two parts by BLM-Fe(II) complex, inducing the two DNA-AgNCs away from each other. The fluorescence intensity at 572 nm and 622 nm increases and decreases, respectively. Such chameleon DNA-AgNCs exhibit an obvious fluorescence discoloration from orange to yellow. Therefore, a sensitive ratiometric fluorescent strategy for BLM detection has been proposed with the detection limit of 67 pM. Finally, this ratiometric method is used to detect BLM in serum samples.

Synthesis of FeO@SiO2-DNA core-shell engineered nanostructures for rapid adsorption of heavy metals in aqueous solutions

Creating novel and innovative nanostructures is a challenge, aiming to discover nanomaterials with promising properties for environmental remediation. In this study, the physicochemical and adsorption properties of a heterogeneous nanostructure are evaluated for the rapid removal of heavy metal ions from aqueous solutions. Core–shell nanostructures are prepared using iron oxide cores and silica dioxide shells. The core is synthesized via the co-precipitation method and modified in situ with citric acid to grow a carboxyl layer. The shell was hydrolyzed/condensed and then functionalized with amine groups for ds-DNA condensation via electrostatic interaction. The characterization techniques revealed functional FeO@SiO₂–DNA nanostructures with good crystallinity and superparamagnetic response (31.5 emu g⁻¹). The predominant superparamagnetic nature is attributed to the citric acid coating. This improves the dispersion and stability of the magnetic cores through the reduction of the dipolar–dipolar interaction and the enhancement of the spin coordination. The rapid adsorption mechanism of FeO@SiO₂–DNA was evaluated through the removal of Pb(ii), As(iii), and Hg(ii). A rapid adsorption rate is observed in the first 15 min, attributed to a heterogeneous chemisorption mechanism based on electrostatic interactions. FeO@SiO₂–DNA shows higher adsorption efficiency of 69% for Pb(ii) removal compared to As(iii) (51%) and Hg(ii) (41%). The selectivity towards Pb(ii) is attributed to the similar acid nature to ds-DNA, where the ionic strength interaction provides good affinity and stability. The facile synthesis and rapid adsorption suggest a promising nanostructure for the remediation of water sources contaminated with heavy metal ions and can be extended to other complex molecules.

Facile synthesis of well-dispersed and magnetic FeO@SiO₂–DNA nanostructures with electrostatic active sites for interaction and rapid adsorption of heavy metals.

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

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

Freezing-Driven DNA Adsorption on Gold Nanoparticles: Tolerating Extremely Low Salt Concentration but Requiring High DNA Concentration

Attaching thiolated DNA to gold nanoparticles (AuNPs) is a highly important and useful reaction for many applications. Various methods such as adding salts, acids, polymers, and surfactants have been developed to facilitate the reaction. Recently, it was reported that a very high DNA density can be achieved simply by freezing AuNPs with the DNA without any other reagents. DNA oligonucleotides are also known to stretch and align upon freezing. In this work, a set of experiments were performed with a fluorophore and thiol dual-labeled DNA, and the DNA loading density and colloidal stability of AuNPs were measured. The initial salt concentration was unimportant, and even 0.1 mM Na⁺ allowed around 100 DNA attached to each 13 nm AuNPs. On the other hand, a high DNA concentration of 3 μM was needed to achieve the high DNA density and good colloidal stability of AuNPs. When the thiolated DNA was forced in stable secondary structures, the attachment was low, and preadsorbed DNA also inhibited the DNA attachment by the freezing method. Overall, nonstructured thiolated DNA strands need to align by freezing and quickly attached through the ends of the DNA. This work illustrates practical experiment design conditions and offers fundamental surface science insights for the DNA attachment by freezing.