Programmable Regulation of DNA Conjugation to Gold Nanoparticles via Strand Displacement

Catalytic Gold Nanoparticle Assembly Programmed by DNAzyme Circuits

Assembled gold nanoparticle (AuNP) superstructures can generate unique physicochemical characteristics and be used in various applications, thus becoming an attractive research field. Recently, several DNA-assisted gold nanoparticle assembly methods have been rigorously developed that typically require a non-catalytic equimolar molecular assembly to guarantee the designed assembly. Although efficient and accurate, exploring such non-catalytic nanoparticle assemblies in the complex cellular milieu under low trigger concentrations remains challenging. Therefore, developing a catalytic method that facilitates gold nanoparticle assemblies with relatively low DNA trigger concentrations is desirable. In this report, a catalytic method to program gold nanoparticle assemblies by DNAzyme circuits is presented, where only a small number of DNA triggers are able to induce the production of a large number of the desired nanoparticle assemblies. The feasibility of using logic DNAzyme circuits to control catalytic nanoparticle assemblies is experimentally verified. Additionally, catalytic AuNP assembly systems are established with cascading and feedback functions. The work provides an alternative research direction to enrich the tool library of nanoparticle assembly and their application in biosensing and nanomedicine.

Bifunctional Calix[4]arene-Coated Gold Nanoparticles for Orthogonal Conjugation

Gold nanoparticles (AuNPs) are currently intensively exploited in the biomedical field as they possess interesting chemical and optical properties. Although their synthesis is well-known, their controlled surface modification with defined densities of ligands such as peptides, DNA, or antibodies remains challenging and has generally to be optimized case by case. This is particularly true for applications like in vivo drug delivery that require AuNPs with multiple ligands, for example a targeting ligand and a drug in well-defined proportions. In this context, we aimed to develop a calixarene-modification strategy that would allow the controlled orthogonal conjugation of AuNPs, respectively, via amide bond formation and copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). To do this, we synthesized a calix[4]arene-tetradiazonium salt bearing four PEG chains ended by an alkyne group (C1) and, after optimization of its grafting on 20 nm AuNPs, we demonstrated that CuAAC can be used to conjugate an azide containing dye (N₃-cya7.5). It was observed that AuNPs coated with C1 (AuNPs-C1) can be conjugated to approximately 600 N₃-cya7.5 that is much higher than the value obtained for AuNPs decorated with traditional thiolated PEG ligands terminated by an alkyne group. The control over the number of molecules conjugated via CuAAC was even possible by incorporating a non-functional calixarene (C2) into the coating layer. We then combined C1 with a calix[4]arene-tetradiazonium salt bearing four carboxyl groups (C3) that allows conjugation of an amine (NH₂-cya7.5) containing dye. The conjugation potential of these bifunctional AuNPs-C1/C3 was quantified by UV-vis spectroscopy: AuNPs decorated with equal amount of C1 and C3 could be conjugated to approximately 350 NH₂-dyes and 300 N₃-dyes using successively amide bond formation and CuAAC, demonstrating the control over the orthogonal conjugation. Such nanoconstructs could benefit to anyone in the need of a controlled modification of AuNPs with two different molecules via two different chemistries.

DNA Nanotweezers for Biosensing Applications: Recent Advances and Future Prospects

DNA nanotweezers (DTs) are reversible DNA nanodevices that can optionally switch between opened and closed states. Due to their excellent flexibility and high programmability, they have been recognized as a promising platform for constructing a diversity of biosensors and logic gates, as well as a versatile tool for molecular biology studies. In this review, we provide an overview of biosensing applications using DTs. First, the design and working principle of DTs are introduced. Next, the signal producing principles of DTs are summarized. Furthermore, biosensing applications of DTs for varying targets and purposes, both in buffers and complex biological environments, are highlighted. Finally, we provide potential opportunities and challenges for the further development of DTs.

Ultrastable PEGylated Calixarene-Coated Gold Nanoparticles with a Tunable Bioconjugation Density for Biosensing Applications

Many in vivo and in vitro applications using gold nanoparticles (AuNPs) require (i) their PEGylation, as it increases their stability and prevents nonspecific protein adsorption, and (ii) their conjugation to biomolecules, that provides them with specific recognition properties. Currently, the functionalization of AuNPs is based on thiol chemistry that suffers from two major drawbacks: (i) the Au-S bond is labile and confers limited chemical robustness to the organic layer, and (ii) control over the bioconjugation density is highly challenging. We report here a novel functionalization strategy based on calix[4]arene-tetradiazonium platforms for the coating of AuNPs with a robust PEG layer and their controlled bioconjugation. AuNPs were first modified with a functional calix[4]arene-diazonium salt bearing three PEG chains ended by a methoxy group and one by a carboxyl group. The resulting particles showed excellent chemical and colloidal stabilities, compared to similar systems obtained via a classical thiol chemistry, and could even be dispersed in human serum without degrading or aggregating. In addition to that, the carboxyl groups protruding from the PEG layer allowed their conjugation via amide bond formation with amine-containing biomolecules such as peptides. The control of the bioconjugation was obtained by grafting mixed layers of functional and nonfunctional PEGylated calix[4]arenes, that allowed varying the number of functional groups carried by the AuNPs and subsequently their bioconjugation capacity while preserving their dense protective PEG shell. Finally, we used these nanomaterials, modified with peptide aptamers, for the in vitro biosensing of a cancer biomarker, Mdm2.

An Artificial Intelligent Signal Amplification System for in vivo Detection of miRNA

MicroRNAs (miRNA) have been identified as oncogenic drivers and tumor suppressors in every major cancer type. In this work, we design an artificial intelligent signal amplification (AISA) system including double-stranded SQ (S, signal strand; Q, quencher strand) and FP (F, fuel strand; P, protect strand) according to thermodynamics principle for sensitive detection of miRNA in vitro and in vivo. In this AISA system for miRNA detection, strand S carries a quenched imaging marker inside the SQ. Target miRNA is constantly replaced by a reaction intermediate and circulatively participates in the reaction, similar to enzyme. Therefore, abundant fluorescent substances from S and SP are dissociated from excessive SQ for in vitro and in vivo visualization. The versatility and feasibility for disease diagnosis using this system were demonstrated by constructing two types of AISA system to detect Hsa-miR-484 and Hsa-miR-100, respectively. The minimum target concentration detected by the system in vitro (10 min after mixing) was 1/10th that of the control group. The precancerous lesions of liver cancer were diagnosed, and the detection accuracy were larger than 94% both in terms of location and concentration. The ability to establish this design framework for AISA system with high specificity provides a new way to monitor tumor progression and to assess therapeutic responses.

Cold-swappable DNA gels

We report an experimental investigation of an all-DNA gel composed by tetra-functional DNA nanoparticles acting as network nodes and bi-functional ones acting as links. The DNA binding sequence is designed to generate at room and lower temperatures a persistent long-lived network. Exploiting ideas from DNA-nanotechnology, we implement in the binding base sequences an appropriate exchange reaction which allows links to swap, constantly retaining the total number of network links. The DNA gel is thus able to rearrange its topology at low temperature while preserving its fully-bonded configuration.