Biostable L-DNA-Templated Aptamer-Silver Nanoclusters for Cell-Type-Specific Imaging at Physiological Temperature

DNA-templated fluorescent metal nanoclusters and their illuminating applications

After the discovery of DNA during the mid-20th century, a multitude of novel methodologies have surfaced which exploit DNA for its various properties. One such recently developed application of DNA is as a template in metal nanocluster formation. In the early years of the new millennium, a group of researchers found that DNA can be adopted as a template for the binding of metal nanoparticles that ultimately form nanoclusters. Three metal nanoclusters have been studied so far, including silver, gold, and copper, which have a plethora of biological applications. This review focuses on the synthesis, mechanisms, and novel applications of DNA-templated metal nanoclusters, including the therapies that have employed them for their wide range of fluorescent properties, and the future perspectives related to their development by exploiting machine learning algorithms and molecular dynamics simulation studies.

Rolling Circle Amplification-Based Self-Assembly to Form a "GPS-Nanoconveyor" for In Vitro Targeted Imaging and Enhanced Gene/Chemo (CRISPR/DOX) Synergistic Therapy

The GPS-Nanoconveyor (MA-NV@DOX-Cas13a) is a targeted nanoplatform designed for the imaging and gene/chemotherapy synergistic treatment of melanoma. It utilizes rolling circle amplification (RCA) products as a scaffold to construct a DNA "Nanoconveyor" (NV), which incorporates a multivalent aptamer (MA) as a "GPS", encapsulates doxorubicin (DOX) in the transporter, and equips it with CRISPR/Cas13a ribonucleoproteins (Cas13a RNP). Carrying MA enhances the ability to recognize the overexpressed receptor nucleolin on B16 cells, enabling targeted imaging and precise delivery of MA-NV@DOX-Cas13a through receptor-mediated endocytosis. The activation of signal transducer and activator of transcription 3 (STAT3) in cancer cells triggers cis-cleavage of CRISPR/Cas13a, initiating its trans-cleavage function. Additionally, deoxyribonuclease I (DNase I) degrades MA-NV, releasing DOX for intracellular imaging and as a chemotherapeutic agent. Experiments demonstrate the superior capabilities of this versatile nanoplatform for cellular imaging and co-treatment while highlighting the advantages of these nanodrug delivery systems in mitigating DOX side effects.

DNA-Functionalized Porphyrinic Metal-Organic Framework-Based Drug Delivery System for Targeted Bimodal Cancer Therapy

A DNA-functionalized porphyrinic MOF (porMOF) drug delivery system was successfully constructed. porMOF as a photosensitizer and drug delivery carrier can integrate photodynamic therapy (PDT) and chemotherapy. Via the strong coordination interaction between the zirconium cluster of porMOF and the terminal phosphate group of DNA, the stable modification of the DNA layer on the porMOF surface is achieved. Meanwhile, the introduction of C/G-rich base pairs into the DNA double-stranded structure provides more binding sites of chemotherapeutic drug doxorubicin (DOX). AS1411, an aptamer of nucleolin proteins that are overexpressed by cancer cells, is introduced in the double-stranded terminal, which can endow the nanosystem with the ability to selectively recognize cancer cells. C-rich sequences in DNA double strands form an i-motif structure under acidic conditions to promote the highly efficient release of DOX in cancer cells. In vitro and in vivo experiments demonstrate that the synergistic PDT/chemotherapy modality achieves highly efficient cancer cell killing and tumor ablation without undesirable side effects.

Highly photoluminescent tryptophan-coated copper nanoclusters based turn-off fluorescent probe for determination of tetracyclines

Employing cheap Cu nanoclusters to design a novel fluorescent probe have promising opportunities in the field of optical sensors. Here, we fabricated a highly photoluminescent D-tryptophan (D-Trp)-coated Cu nanoclusters (Trp-Cu NCs) by rapid microwave-assisted method to achieve precise quantification of tetracyclines (TC). Due to protecting groups of Trp, the synthesized Trp-Cu NCs have remarkable fluorescence stability with a quantum yield reached 12.5%. A distinct fluorescence quenching with the incremental addition of TC via the internal filtration effect (IFE). Based on turn-off fluorescence within 1 min, a detection method for detecting TC was constructed with a linear range of 0.3-120 μM and a limit of detection (LOD) of 0.12 μM. Besides, the proposed fluorescent probe has been employed for the determination of practical samples such as water samples, milk and honey, and exhibited satisfactory recoveries of 96.1%-108.2%, with relative standard deviations (RSD) lower than 5.0%. This is a sensitive, rapid and easily recognizable Trp-Cu NCs based sensing platform for the determination of TC, which could offer a powerful tool for ensuring food safety.

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.

Nonbiodegradable Spiegelmer-Driven Colorimetric Biosensor for Bisphenol A Detection

Spiegelmers are enantiomers of natural D-oligonucleotides that bind to targets with distinct structures such as aptamers. The high susceptibility of natural D-form aptamers to nucleases greatly hinders their application in biological environments. Here, a nonbiodegradable spiegelmer-based platform for the sensitive detection of bisphenol A (BPA) was developed. Due to the symmetric molecule of BPA, the D-form aptamer can be directly converted into mirror forms via chemical synthesis. Aptamer-target interactions that involve chemically synthesized spiegelmers were characterized by biolayer interferometry, and their stabilities were tested in various biological fluids by exposure to nucleases. We demonstrate for the first time the use of a nuclease-resistant spiegelmer in a simple, label-free gold nanoparticle-based colorimetric assay to detect BPA in a highly sensitive and selective manner. The aptasensor exhibits an LOD of 0.057 ng/mL and dynamic range of 10⁵ (100 pg/mL to 10 mg/mL). With sensing capacity and biological stability, the developed aptasensor shows great potential to utilize in in-field applications such as water quality monitoring.

DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review

Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.

Multibranched Linear DNA-Controlled Assembly of Silver Nanoclusters and Their Applications in Aptamer-Based Cell Recognition

DNA-templated silver nanoclusters (DNA-AgNCs) are promising fluorescent materials and have been used in cancer diagnosis. Although many different DNA-AgNC applications have been realized, most of them rely on individual DNA-AgNCs or assembled DNA-AgNCs with limited recognition abilities, resulting in low detection sensitivity or off-target effects, in turn, hindering the performance of DNA-AgNCs in cancer cell recognition. As a solution, we assembled DNA-AgNCs by a multibranched linear (MBL) DNA structure formed through a trigger-initiated hybridization chain reaction (HCR) regarding the natural compatibility of DNA-AgNCs with DNA programmability and the advantages of DNA assembly in incorporating repetitive and functional moieties into one structure. By the specific modification of the trigger, MBL-AgNCs tethered with the targeting aptamer and partially hybridized duplex, which works as a component of DNA logic platform relying on the combination of cascade strand displacement reaction and specific recognition ability of aptamers, were obtained, respectively. DNA-AgNCs assembled by the aptamer-tethered MBL structure exhibited about 20-fold enhanced detection sensitivity in recognizing cancer cells compared to individual aptamer-tethered DNA-AgNCs. DNA-AgNCs assembled by the duplex-attached MBL exhibited logic performance in analyzing dual cell surface receptors with the assistance of "AND" logic platform, thus identifying cancer cells with high sensitivity and resolution. The facile conjugation of the MBL structure with different functional DNA structures makes it an ideal platform to assemble DNA-AgNCs used for aptamer-based cell recognition, thus broadening the potential applications of DNA-AgNCs.

Multivalent Aptamer Approach: Designs, Strategies, and Applications

Aptamers are short and single-stranded DNA or RNA molecules with highly programmable structures that give them the ability to interact specifically with a large variety of targets, including proteins, cells, and small molecules. Multivalent aptamers refer to molecular constructs that combine two or more identical or different types of aptamers. Multivalency increases the avidity of aptamers, a particularly advantageous feature that allows for significantly increased binding affinities in comparison with aptamer monomers. Another advantage of multivalency is increased aptamer stabilities that confer improved performances under physiological conditions for various applications in clinical settings. The current study aims to review the most recent developments in multivalent aptamer research. The review will first discuss structures of multivalent aptamers. This is followed by detailed discussions on design strategies of multivalent aptamer approaches. Finally, recent developments of the multivalent aptamer approach in biosensing and biomedical applications are highlighted.

A label-free cyclic amplification strategy for microRNA detection by coupling graphene oxide-controlled adsorption with superlong poly(thymine)-hosted fluorescent copper nanoparticles

Herein, based on a terminal deoxynucleotidyl transferase (TdT)-mediated superlong poly-T-templated-copper nanoparticles (poly T-CuNPs) strategy, a simple, universal and label-free fluorescent biosensor for the detection of miRNA was constructed by employing graphene oxide (GO) and DNase I. In this strategy, GO and DNase I were used as a switch and amplifier of the signal generation pathway, respectively, and the fluorescence of poly T-CuNPs was used as the signal output. In the presence of target miRNA, the DNA dissociated from the GO surface by forming a miRNA/DNA duplex and was degraded by DNase I. The short oligos with 3'-OH, the product of DNase I degradation, could be recognized by the TdT and added to a long poly-T tail. Finally, the fluorescence signal was output through the synthesis of poly T-CuNPs. As a proof of concept, let-7a was analyzed. The method showed good sensitivity and selectivity with a linear response in the 50 pM-10,000 pM let-7a concentration range and a 30 pM limit of detection (LOD = 30 pM, R² = 0.9954, the relative standard deviation were 2.79%-5.30%). It was also successfully applied to the determination of miRNA in spiked human serum samples. It showed good linearity in the range of 500-10000 pM (R² = 0.9969, the relative standard deviation were 1.61%-3.85%). Moreover, both the adsorption of GO and the degradation of DNase I are DNA sequence-independent; thus, this method can be applied to the detection of any miRNA simply by changing the assisted-DNA sequence.

Recent advances in constructing high-order DNA structures

Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.

DNA Nanotechnology-Enabled Fabrication of Metal Nanomorphology

In recent decades, DNA nanotechnology has grown into a highly innovative and widely established field. DNA nanostructures have extraordinary structural programmability and can accurately organize nanoscale materials, especially in guiding the synthesis of metal nanomaterials, which have unique advantages in controlling the growth morphology of metal nanomaterials. This review started with the evolution in DNA nanotechnology and the types of DNA nanostructures. Next, a DNA-based nanofabrication technology, DNA metallization, was introduced. In this section, we systematically summarized the DNA-oriented synthesis of metal nanostructures with different morphologies and structures. Furthermore, the applications of metal nanostructures constructed from DNA templates in various fields including electronics, catalysis, sensing, and bioimaging were figured out. Finally, the development prospects and challenges of metal nanostructures formed under the morphology control by DNA nanotechnology were discussed.

Fluorescent AgNCs Formed on Bifunctional DNA Template for Potassium Ion Detection

In this study, we examined properties of silver nanoclusters, which are AgNCs stabilized by DNA oligonucleotide scaffold containing G-quadruplex-forming sequences: human telomeric (Tel22) or thrombin-binding aptamer (TBA). Thus, we obtained two fluorescent probes abbreviated as Tel22C12-AgNCs and TBAC12-AgNCs, which were characterized using absorption, circular dichroism and fluorescence spectroscopy. Both probes emit green and red fluorescence. The presence of silver nanoclusters did not destabilize the formed G-quadruplexes. The structural changes of probes upon binding K+ or Na+ ions cause quenching in their red emission. Green emission was slightly quenched only in the case of Tel22C12-AgNCs; on the contrary, for TBAC12-AgNC’s green emission, we observed an increasing fluorescence signal. Moreover, the Tel22C12-AgNCs system shows not only a higher binding preference for K+ over Na+, but it was able to monitor small changes in K+ concentrations in the buffer mimicking extracellular conditions (high content of Na+ ions). These results suggest that Tel22C12-AgNCs exhibit the potential to monitor transmembrane potassium transport.

Microenvironment-responsive DNA-conjugated albumin nanocarriers for targeted therapy

Drug delivery with accurate targeting and efficient treatment has become an essential strategy for cancer therapy. Two nanocarriers based on bovine serum albumin (BSA) and DNA were synthesized via click chemistry and DNA hybridization reactions (DNA-BSA1 and DNA-BSA2). One of the hybridized oligonucleotides, Linker1, in DNA-BSA1 included a pH-sensitive i-motif sequence and a cancer cell-targeted guanine-quadruplex-structured AS1411 aptamer sequence, and the other, Linker2, in DNA-BSA2 had only the same pH-sensitive i-motif sequence. Doxorubicin (DOX) molecules could be quickly and preferentially intercalated into double-stranded DNA via non-covalent interactions, and the encapsulation efficiency of DNA-BSA1 and DNA-BSA2 was almost 100% and 87.5%, respectively. As a mimic of the cancer cell microenvironment, a pH-trigger and a deoxyribonuclease I (DNase I)-trigger release mechanism was individually proposed to explain the dynamic release of the DNA-BSA@DOX under acidic conditions and the presence of DNase I in vitro. Intracellular uptake and cytotoxicity experiments confirmed that the nanocarrier DNA-BSA1@DOX had accurate targeting and efficient treatment towards cancer cells due to the high affinity and specificity of AS1411 to nucleolin, which is overexpressed in cancer cells. Furthermore, in vivo studies showed that the nanocarrier system could efficiently inhibit tumor growth. Therefore, the entire bio-based nanocarrier DNA-BSA is a promising candidate for the loading and release of anti-cancer drugs for accurate delivery and efficient treatment.

Self-Assembled Growing DNA Tree Mediated by Exosomes for Amplified Imaging of Messenger RNA in Living Cells

Sensitive, accurate, and nondestructive probing of endogenous messenger RNA (mRNA) in living cells places extremely high demands on nanocarriers and probes and is still a challenge. In the present study, we describe a target-triggered self-assembled DNA tree for amplified analysis of mRNA in intact living cells. The probes assembled into a DNA tree are transported into cells by exosomes, which is beneficial for reducing cell damage and realizing nondestructive analysis. The probes are l-configured single-stranded DNAs (LDNAs) that can resist the degradation of exonuclease and endonuclease, thus laying the foundation for accurate analysis. Under the induction of the target mRNA, the probes in the cells assemble into a small plantlet and eventually grow into a tree after a few rounds of self-cycling, achieving the exponential amplification of fluorescence signals. Compared with the signal amplification based on one-dimensional DNA trunk self-assembly, the three-dimensional DNA tree shows an excellent sensitivity both ex situ and in situ. In this way, favorable sensitivity, accuracy, and nondestructive analysis are integrated into one system. This DNA tree expands the analysis platform for analyzing more biomarkers on a genetic level in an intracellular, nondestructive, and hypersensitive manner and holds great potential in clinical diagnostic and research applications.

Development of General Methods for Detection of Virus by Engineering Fluorescent Silver Nanoclusters

Viruses have caused significant damage to the world. Effective detection is required to relieve the impact of viral infections. A biomolecule can be used as a template such as deoxyribonucleic acid (DNA), peptide, or protein, for the growth of silver nanoclusters (AgNCs) and for recognizing a virus. Both the AgNCs and the recognition elements are tunable, which is promising for the analysis of new viruses. Considering that a new virus such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently requires a facile sensing strategy, various virus detection strategies based on AgNCs including fluorescence enhancement, color change, quenching, and recovery are summarized. Particular emphasis is placed on the molecular analysis of viruses using DNA stabilized AgNCs (DNA-AgNCs), which detect the virus's genetic material. The more widespread applications of AgNCs for general virus detection are also discussed. Further development of these technologies may address the challenge for facile detection of SARS-CoV-2.

Recent advances in templated synthesis of metal nanoclusters and their applications in biosensing, bioimaging and theranostics

As a kind of promising nanomaterials, metal nanoclusters (MNCs) generally composed of several to hundreds of metal atoms have received increasing interest owing to their unique properties, such as ultrasmall size (<2 nm), fascinating physical and chemical properties, and so on. Recently, template-assisted synthesis of MNCs (e.g., Au, Ag, Cu, Pt and Cd) has attracted extensive attention in biological fields. Up to now, various templates (e.g., dendrimers, polymers, DNAs, proteins and peptides) with different configurations and spaces have been applied to prepare MNCs with the advantages of facile preparation, controllable size, good water-solubility and biocompatibility. Herein, we focus on the recent advances in the template-assisted synthesis of MNCs, including the templates used to synthesize MNCs, and their applications in biosensing, bioimaging, and disease theranostics. Finally, the challenges and future perspectives of template-assisted synthesized MNCs are highlighted. We believe that this review could not only arouse more interest in MNCs but also promote their further development and applications by presenting the recent advances in this area to researchers from various fields, such as chemistry, material science, physiology, biomedicine, and so on.

The Fluorescent Palette of DNA-Templated Silver Nanoclusters for Biological Applications

Recently years have witnessed a surge in application of DNA-AgNCs in optics, catalysis, sensing, and biomedicine. DNA-templated silver nanoclusters (DNA-AgNCs), as emerging fluorophores, display superior optical performance since their size is close to the Fermi wavelength. DNA-AgNCs possess unique features, including high fluorescence quantum yields and stability, biocompatibility, facile synthesis, and low toxicity, which are requisite for fluorescent probes. The fluorescent emission of DNA-AgNCs can cover the violet to near-infrared (NIR) region by varying the DNA sequences, lengths, and structures or by modifying the environmental factors (such as buffer, pH, metal ions, macromolecular polymers, and small molecules). In view of the above excellent properties, we overview the DNA-AgNCs from the viewpoints of synthesis and fluorescence properties, and summarized its biological applications of fluorescence sensing and imaging.

Delivery of antibacterial silver nanoclusters to Pseudomonas aeruginosa using species-specific DNA aptamers

Introduction. The use of silver as an antimicrobial therapeutic is limited by its toxicity to host cells compared with that required to kill bacterial pathogens.Aim. To use aptamer targeting of DNA scaffolded silver nanoclusters as an antimicrobial agent for treating Pseudomonas aeruginosa infections.Methodology. Antimicrobial activity was assessed in planktonic cultures and in vivo using an invertebrate model of infection.Results. The aptamer conjugates that we call aptabiotics have potent antimicrobial activity. Targeted silver nanoclusters were more effective at killing P. aeruginosa than the equivalent quantity of untargeted silver nanoclusters. The aptabiotics have an IC₅₀ of 1.3-2.6 µM against planktonically grown bacteria. Propidium iodide staining showed that they rapidly depolarize bacterial cells to kill approximately 50 % of the population within 10 min following treatment. In vivo testing in the Galleria mellonella model of infection prolonged survival from an otherwise lethal infection.Conclusion. Using P. aeruginosa as a model, we show that targeting of DNA-scaffolded silver nanoclusters with an aptamer has effective fast-acting antimicrobial activity in vitro and in an in vivo animal model.

Chiral Interaction Is a Decisive Factor To Replace d-DNA with l-DNA Aptamers

Nucleic acid aptamers have been widely used in various fields such as biosensing, DNA chip, and medical diagnosis. However, the high susceptibility of nucleic acids to ubiquitous nucleases reduces the biostability of aptamers and limits their applications in biological contexts. Therefore, improving the biostability of aptamers becomes an urgent need. Herein, we present a simple strategy to resolve this problem by directly replacing the d-DNA-based aptamers with left-handed l-DNA. By testing several reported aptamers against respective targets, we found that our proposed strategy stood up well for nonchiral small molecule targets (e.g., Hemin and cationic porphyrin) and chiral targets whose interactions with aptamers are chirality-independent (e.g., ATP). We also found that the l-DNA aptamers were indeed endowed with greatly improved biostability due to the extraordinary resistance of l-DNA to nuclease digestion. With respect to other small-molecule targets whose interactions with aptamers are chirality-dependent (e.g., kanamycin) and biomacromolecules (e.g., tyrosine kinase-7), however, the proposed strategy was not entirely effective likely due to the participation of the DNA backbone chirality into the target recognition. In spite of this limitation, this strategy indeed paves an easy way to screen highly biostable aptamers important for the applications in many fields.

Green Layer-by-Layer Assembly of Porphyrin/G-Quadruplex-Based Near-Infrared Nanocomposite Photosensitizer with High Biocompatibility and Bioavailability

A simple and green layer-by-layer assembly strategy is developed for the preparation of a highly bioavailable nanocomposite photosensitizer by assembling near-infrared (NIR) light-sensitive porphyrin/G-quadruplex complexes on the surface of a highly biocompatible nanoparticle that is prepared via Zn²⁺-assisted coordination self-assembly of an amphiphilic amino acid. After being efficiently delivered to the target site and internalized into tumor cells via enhanced permeability and retention effect and interactions between aptamers and tumor markers, the as-prepared nanoassembly can be directly used as an NIR light-responsive photosensitizer for tumor photodynamic therapy (PDT) since the porphyrin/G-quadruplex complexes are exposed on the nanoassembly surface and kept in an active state. It can also disassemble under the synergistic stimuli of an acidic pH environment and overexpressed glutathione, leasing more efficient porphyrin/G-quadruplex composite photosensitizers while reducing the interference caused by glutathione-dependent ¹O₂ consumption. Since the nanoassembly can work no matter if it is disassembled or not, the compulsory requirement for in vivo photosensitizer release is eliminated, thus resulting in the great improvement of the bioavailability of the photosensitizer. The PDT applications of the nanoassembly were well demonstrated in both in vitro cell and in vivo animal experiments.

Terminal Deoxynucleotidyl Transferase-Catalyzed Preparation of pH-Responsive DNA Nanocarriers for Tumor-Targeted Drug Delivery and Therapy

Developing a highly efficient carrier for tumor-targeted delivery and site-specific release of anticancer drugs is a good way to overcome the side effects of traditional cancer chemotherapy. Benefiting from the nontoxic and biocompatible characteristics, DNA-based drug carriers have attracted increasing attention. Herein, we reported a novel and readily manipulated strategy to construct spherical DNA nanocarriers. In this strategy, terminal deoxynucleotidyl transferase (TdT)-catalyzed DNA extension reaction is used to prepare a thick DNA layer on a gold nanoparticle (AuNP) surface by extending long poly(C) sequences from DNA primers immobilized on AuNPs. The poly(C) extension products can then hybridize with G-rich oligonucleotides to give CG-rich DNA duplexes (for loading anticancer drug doxorubicin, Dox) and multiple AS1411 aptamers. Via synergic recognition of multiple aptamer units to nucleolin proteins, biomarker of malignant tumors, Dox-loaded DNA carrier can be efficiently internalized in cancer cells and achieve burst release of drugs in acidic organelles because of i-motif formation-induced DNA duplex destruction. An as-prepared pH-responsive drug carrier was demonstrated to be promising for highly efficient delivery of Dox and selective killing of cancer cells in both in vitro and in vivo experiments, thus showing a huge potential in anticancer therapy.

G-Quadruplex/Porphyrin Composite Photosensitizer: A Facile Way to Promote Absorption Redshift and Photodynamic Therapy Efficacy

Photosensitizer is one of the most important elements of photodynamic therapy (PDT). Herein, we reported a novel strategy to prepare a new series of composite photosensitizers. The composite photosensitizer was prepared by simply mixing DNA G-quadruplexes with a hydrophilic porphyrin (TMPipEOPP)⁴⁺·4I^-. Compared with the conventional porphyrin photosensitizers, the excitation wavelength of the composite one has been ∼50 nm redshifted (from 650 to 700 nm), which is beneficial to the penetration of the light. Moreover, the composite photosensitizer showed an about 7.4-fold increase of light absorption efficiency, thus greatly enhancing the singlet oxygen (¹O₂) generation capacity and PDT efficacy. What is more, the introduction of nucleic acids in the composite photosensitizer could also provide some extra charming properties, such as the targeted recognition ability conferred by aptamer and high capability to assemble with various drug carriers. We demonstrated that the composite photosensitizer could be easily assembled with MnO₂ nanosheet. The obtained nanodevice integrated the merits of a composite photosensitizer and MnO₂ nanosheet, thus showing strong near-infrared absorption, high ¹O₂ generation efficiency, avoidance of nonideal ¹O₂ consumption by glutathione, and in situ O₂ generation to relieve tumor hypoxia. This nanodevice showed greatly improved PDT efficacy both in vitro and in vivo, presenting a huge potential for applications in clinical therapy for tumors.

Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications

Recent advances in nanotechnology and engineering have generated many nanomaterials with unique physical and chemical properties. Over the past decade, numerous nanomaterials are introduced into many research areas, such as sensors for environmental monitoring, food safety, point-of-care diagnostics, and as transducers for solar energy transfer. Meanwhile, functional nucleic acids (FNAs), including nucleic acid enzymes, aptamers, and aptazymes, have attracted major attention from the biomedical community due to their unique target recognition and catalytic properties. Benefiting from the recent progress of molecular engineering strategies, the physicochemical properties of nanomaterials are endowed by the target recognition and catalytic activity of FNAs in the presence of a target analyte, resulting in numerous smart nanoprobes for diverse applications including intracellular imaging, drug delivery, in vivo imaging, and tumor therapy. This progress report focuses on the recent advances in designing and engineering FNA-based nanomaterials, highlighting the functional outcomes toward in vivo applications. The challenges and opportunities for the future translation of FNA-based nanomaterials into clinical applications are also discussed.

Aptamer chemistry

Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.

Exploring the conformational behaviour and aggregation properties of lipid-conjugated AS1411 aptamers

AS1411 is a nucleolin-binding aptamer which attracted great interest as active targeting ligand for the selective delivery of therapeutic agents to tumour cells. In this work we selected three AS1411 derivatives 5'-conjugated with lipophilic tails and studied their properties in view of their application in liposomial formulations and/or lipid coated-nanoparticles for targeted therapies. The conformational behaviour of these AS1411 analogs has been investigated in comparison with the unmodified aptamer by CD, UV, PAGE, SEC-HPLC, DLS and thioflavin T (ThT) fluorescence assays to get insight in their secondary structure and aggregation properties. This study has been performed in pseudo-physiological buffers mimicking the extra- and intracellular environments, and at different concentrations in the μM range, paying special attention to the effects of the lipophilic tail on the overall aptamer conformation. The 5'-lipidated AS1411 derivatives proved to fold into stable, parallel unimolecular G-quadruplex structures, forming large aggregates, mainly micelles, at conc. >10 μM. Preliminary bioscreenings on selected cancer cells showed that these derivatives are less cytotoxic than AS1411, but maintain a similar biological behaviour. This study demonstrated that lipophilic tails dramatically favour the formation of AS1411 aggregates, however not impairing the formation and thermal stability of its peculiar G4 motifs.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

A ZnO-gated porphyrinic metal–organic framework-based drug delivery system for targeted bimodal cancer therapy

A ZnO-gated porMOF-AS1411 nanosystem was prepared and successfully used for drug delivery and synergistic bimodal cancer therapy.

Fluorescence enhancement for noble metal nanoclusters

Noble metal nanoclusters have attracted great attentions in the area of fluorescence related applications due to their special properties such as low toxicity, excellent photostability and bio-compatibility. However, they still describe disadvantages for low quantum yield compared to quantum dots and organic dyes though the brightness of the fluorescence play an important role for the efficiency of the applications. Attentions have been attracted for exploring strategies to enhance the fluorescence based on the optical fundamentals through various protocols. Some methods have already been successfully proposed for obtaining relative highly fluorescent nanoclusters, which will potentially describe advantages for the application. In this review, we summarize the approach for enhancement of the fluorescence of the nanoclusters based on the modification of the properties, improvement of the synthesis process and optimization of the environment. The limitation and directions for future development of the fabrication of highly fluorescent metal nanoclusters are demonstrated.

Mirror-image aptamer kissing complex for arginine-vasopressin sensing

The recently reported aptamer kissing complex (AKC) strategy has allowed for the development of a new kind of sandwich-like sensing tools. Currently AKC assays have been only applied to low molecular weight molecules and their functionality in complex matrices remains challenging. The objective of the present study broken down into two sub-aims; exploring the propensity to broaden the scope of detectable analytes and designing a more robust system for potential applications to realistic samples. An all L-configuration aptaswitch module derived from a hairpin spiegelmer specific to a larger target, i.e. the arginine-vasopressin (AVP) hormone, was elaborated. The target-induced AKC formation in presence of a specific mirror-image RNA hairpin (L-aptakiss) probe were analyzed by using fluorescence anisotropy. The mirror-image kissing complex was successfully formed when the L-AVP target bound to the engineered L-aptaswitch element. It was also established that the use of methanol as cosolvent significantly improved the assay sensitivity through the stabilization of the ternary complex. Finally, the capability of the mirror-image method to operate in 10-fold diluted, untreated human serum was illustrated. The current work revealed that the AKC concept can be expanded to a wider range of targets and converted to a L-configuration sensing platform especially suitable for bioanalysis purposes.

Ratiometric Catalyzed-Assembly of NanoCluster Beacons: A Nonenzymatic Approach for Amplified DNA Detection

In this work, a novel fluorescent transformation phenomenon of oligonucleotide-encapsulated silver nanoclusters (AgNCs) was demonstrated, in which green-emissive AgNCs effectively transformed to red-emissive AgNCs when placed in close proximity to a special DNA fragment (denoted as convertor here). Taking advantage of a catalyzed-hairpin-assembly (CHA) amplification strategy, we rationally and compatibly engineered a simple and sensitive AgNC-based fluorescent signal amplification strategy through the ratiometric catalyzed-assembly (RCA) of green-emissive NanoCluster Beacon (NCB) with a convertor modified DNA hairpin to induce the template transformation circularly. The proposed ratiometric fluorescent biosensing platform based on RCA-amplified NCB (RCA-NCB) emits intense green fluorescence in the absence of target DNA and will undergo consecutively fluorescent signal transformation from green emission to red emission upon exposure to its target DNA. The ratiometric adaptation of the NCB to CHA circuit advances their general usability as biosensing platform with great improvements in detection sensitivity. By measuring the fluorescence intensity ratio of the red emission and green emission, the proposed RCA-NCB platform exhibits sensitive and accurate analytical performance toward Werner Syndrome-relevant gene, the proof-of-concept target in this work. A low detection limit down to the pM level was achieved, which is lower than most of the reported AgNC-based fluorescent DNA biosensors, making the proposed RCA-NCB biosensing strategy appealing in amplifying the ratiometric fluorescent signal for sensitive DNA detection. Moreover, our proposed RCA-NCB platform shows good recovery toward the target DNA in real human serum samples, illustrating their potential promise for clinical and imaging applications in the future.

A rapid evaluation of acute hydrogen sulfide poisoning in blood based on DNA-Cu/Ag nanocluster fluorescence probe

Hydrogen sulfide (H₂S) is a highly toxic gas as a cause of inhalational death. Accurate detection of H₂S poisoning concentration is valuable and vital for forensic workers to estimate the cause of death. But so far, it is no uniform and reliable standard method to measure sulfide concentrations in H₂S poisoning blood for forensic identification. This study introduces a fluorescence sensing technique into forensic research, in which a DNA-templated copper/silver nanocluster (DNA-Cu/AgNCs) fluorescence probe has been proposed to selective detection of S^2-. Under an optimized condition, the proposed method can allow for determination of S^2- in the concentration range of 10 pM to 1 mM with a linear equation: y = -0.432 lg[S^2-] + 0.675 (R² = 0.9844), with the limit of detection of 3.75 pM. Moreover, acute H₂S poisoning mouse models were established by intraperitoneally injected different doses of Na₂S, and the practical feasibility of the proposed fluorescence sensor has been demonstrated by 35 poisoning blood samples. This proposed method is proved to be quite simple and straightforward for the detection of H₂S poisoning blood. Also it may provide a basis for sulfide metabolizing study in body, and it would be meaningful to further push forensic toxicology identification and clinical laboratory research.

Luminescent turn-on detection of Hg(II) via the quenching of an iridium(III) complex by Hg(II)-mediated silver nanoparticles

A novel luminescent turn-on detection method for Hg(II) was developed. The method was based on the silver nanoparticle (AgNP)-mediated quenching of Ir(III) complex 1. The addition of Hg(II) ions causes the luminescence of complex 1 to be recovered due to the oxidation of AgNPs by Hg(II) ions to form Ag(I) and Ag/Hg amalgam. The luminescence intensity of 1 increased in accord with an increased Hg(II) concentration ranging from 0 nM to 180 nM, with the detection limit of 5 nM. This approach offers an innovative method for the quantification of Hg(II).

DNA Dendrimer-Streptavidin Nanocomplex: an Efficient Signal Amplifier for Construction of Biosensing Platforms

We develop a DNA dendrimer-streptavidin (SA) nanocomplex as a novel signal amplifier to create biosensing platforms for disease-related species. The DNA dendrimer-SA nanocomplex is fabricated by cross-linking the nonlinear hybridization chain reaction based DNA dendrimer with the SA-coupled linker DNA and possesses multiple sticky ends, a high molecular weight, and a hyperbranched nanostructure with large numbers of DNA duplexes. Taking advantage of the DNA dendrimer-SA nanocomplex and a label-free quartz crystal microbalance (QCM) technology, we first construct a mass-sensitive QCM biosensing platform for nucleic acids, which displays high selectivity and sensitivity, with a detection limit of 0.062 nM KRAS gene fragment. Then we present a fluorescent sensing strategy toward HeLa cells by functionalizing the DNA dendrimer-SA nanocomplex using the sgc8 aptamer and the SYBR Green I intercalating dye. The spiked recoveries of targets in physiological media are greater than 90%, demonstrating potential application of created biosensing platforms in clinical diagnosis. This work expands the rule set of designing DNA nanomaterials for development of biosensing strategies, and provides universal platforms for detecting disease-related species through simply altering the related capture and reporter DNA sequences.

Stable, polyvalent aptamer-conjugated near-infrared fluorescent nanocomposite for high-performance cancer cell-targeted imaging and therapy

A novel nanocomposite with improved biostability has been designed and used for cancer cell-specific imaging and targeted therapy.

Fluorescent metal quantum clusters: an updated overview of the synthesis, properties, and biological applications

A brief history of metal quantum clusters, their synthesis methods, physical properties, and an updated overview of their applications is provided.