The discovery and elucidation of genetic codes has profoundly changed not only biology but also many fields of science and engineering. The fundamental building blocks of life comprises of four ...simple deoxyribonucleotides and yet their combinations serve as the carrier of genetic information that encodes for proteins that can carry out many biological functions due to their unique functionalities. Inspired by nature, the functionalities of DNA molecules have been used as a capping ligand for controlling morphology of nanomaterials, and such a control is sequence dependent, which translates into distinct physical and chemical properties of resulting nanoparticles. Herein, an overview on the use of DNA as engineered codes for controlling the morphology of metal nanoparticles, such as gold, silver, and Pd‐Au bimetallic nanoparticles is provided. Fundamental insights into rules governing DNA controlled growth mechanisms are also summarized, based on understanding of the affinity of the DNA nucleobases to various metals, the effect of combination of nucleobases, functional modification of DNA, the secondary structures of DNA, and the properties of the seed employed. The resulting physical and chemical properties of these DNA encoded nanomaterials are also reviewed, while perspectives into the future directions of DNA‐mediated nanoparticle synthesis are provided.
This Review summarizes the use of sequence‐specific DNA molecules as engineered “codes” for controlling the morphology of metal nanoparticles. Insights into rules governing DNA‐controlled growth mechanisms and the properties of these DNA‐coded nanoparticles are described. Furthermore, a look into what the future holds for DNA‐mediated nanoparticle synthesis is discussed.
Recent reports have shown that different DNA sequences can mediate the control of shapes and surface properties of nanoparticles. However, all previous studies have involved only monometallic ...particles, most of which were gold nanoparticles. Controlling the shape of bimetallic nanoparticles is more challenging, and there is little research into the use of DNA-based ligands for their morphological control. We report the DNA-templated synthesis of Pd–Au bimetallic nanoparticles starting from palladium nanocube seeds. The presence of different homo-oligomer DNA sequences containing 10 deoxy-ribonucleotides of thymine, adenine, cytosine, or guanine results in the growth of four distinct morphologies. Through detailed kinetic studies by absorption spectroscopy, scanning electron microscopy (SEM) and scanning transmission electron microscopy (STEM), we have determined the role of DNA in controlling Pd–Au nanoparticle growth morphologies. One major function of DNA is affecting various properties of the incoming metal atoms, including their diffusion and deposition on the Pd nanocube seed. Interestingly, nanoparticle growth in the presence of A10 follows an aggregative growth mechanism that is unique when compared to the other base oligomers. These findings demonstrate that DNA can allow for programmable control of bimetallic nanoparticle morphologies, resulting in more complex hybrid materials with different plasmonic properties. The capability to finely tune multimetallic nanoparticle morphology stems from the versatile structure that is unique to DNA in comparison to conventionally used capping agents in colloidal nanomaterial synthesis.
DNA aptamers are a powerful class of molecules for sensing targets, but have been limited when applied to imaging in living animals because most aptamer probes are fluorescence-based, which limits ...imaging penetration depth. Photoacoustic (PA) imaging emerged as an alternative to MRI and X-ray tomography in biomedical imaging, due to its ability to afford high-resolution images at depths in the cm range. Despite its promise, PA imaging is limited by a lack of strategies to design selective and activatable probes for targets. To overcome this limitation, we report design and demonstration of PA probes based on DNA aptamers that can hybridize to DNA strands conjugated to a near-infrared fluorophore/quencher pair (IRDye 800CW/IRDye QC-1) with efficient contact quenching. Binding of the target triggered a release of the DNA strand with the quencher and thus relief of the contact quenching, resulting in a change of the PA signal ratio at 780/725 nm. Using thrombin as a model, a relationship was established between the thrombin concentrations and the PA ratio, with a dynamic range of 0–1000 nM and a limit of detection of 112 nM. Finally, in vivo PA imaging studies showed that the PA ratio increased significantly 45 min after injection of thrombin but not with injection of PBS as a vehicle control, demonstrating the first aptamer-based activatable PA probe for advanced molecular imaging in living mice. Since in vitro selection can obtain aptamers selective for many targets, the design demonstrated can be applied for PA imaging of a number of targets.
Spatial and temporal distributions of metal ions in vitro and in vivo are crucial in our understanding of the roles of metal ions in biological systems, and yet there is a very limited number of ...methods to probe metal ions with high space and time resolution, especially in vivo. To overcome this limitation, we report a Zn2+-specific near-infrared (NIR) DNAzyme nanoprobe for real-time metal ion tracking with spatiotemporal control in early embryos and larvae of zebrafish. By conjugating photocaged DNAzymes onto lanthanide-doped upconversion nanoparticles (UCNPs), we have achieved upconversion of a deep tissue penetrating NIR 980 nm light into 365 nm emission. The UV photon then efficiently photodecages a substrate strand containing a nitrobenzyl group at the 2′-OH of adenosine ribonucleotide, allowing enzymatic cleavage by a complementary DNA strand containing a Zn2+-selective DNAzyme. The product containing a visible FAM fluorophore that is initially quenched by BHQ1 and Dabcyl quenchers is released after cleavage, resulting in higher fluorescent signals. The DNAzyme–UCNP probe enables Zn2+ sensing by exciting in the NIR biological imaging window in both living cells and zebrafish embryos and detecting in the visible region. In this study, we introduce a platform that can be used to understand the Zn2+ distribution with spatiotemporal control, thereby giving insights into the dynamical Zn2+ ion distribution in intracellular and in vivo models.
DNA-mediated synthesis of nanoparticles is a powerful method to access exclusive shapes and surface properties. Previous studies employed seeds containing low-energy facets, such as a simple cubic ...palladium seed, in the synthesis of Pd-Au bimetallic nanoparticles; however, few studies have investigated whether DNA molecules are influential when a seed containing high-energy facets is used. Seeds enclosed by high-energy facets act as facile nucleation sites in nanoparticle growth and could suppress the effect of DNA. We report the DNA-encoded control of the morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a concave palladium nanocube seed containing high-indexed facets. Based on detailed spectroscopic and microscopic studies of time-dependent growth of bimetallic nanoparticles, we found that the DNA molecules containing 10 repeating units of thymine, guanine, cytosine, or adenine (referred to as T10, G10, C10, and A10, respectively) show a unique interaction with the surface of the seed and the precursor. The most important factor is the binding affinity of the nucleobase to the Pd surface; A10 shows the highest binding affinity and can stabilize the high energy surfaces of the seed. Initially, the growth of bases with lower binding affinities (T10, G10, and C10) is completely dictated by the seed’s surface energy, but later growth can be influenced by different DNA sequences, providing four Pd@Au bimetallic nanoparticles with unique morphologies. The effect of these DNA molecules with medium or low binding affinities can only be observed when more Au is deposited. We propose a scheme for DNA-controlled growth. These results provide insights into the factors governing the DNA-mediated growth of core-shell structures using seeds with high-energy sites, and the insights can be readily applied to other bimetallic systems.
Systematically controlling the morphology of nanoparticles, especially those growing from gold nanorod (AuNR) seeds, are underexplored; however, the AuNR and its related morphologies have shown ...promises in many applications. Herein we report the use of programmable DNA sequences to control AuNR overgrowth, resulting in gold nanoparticles varying from nanodumbbell to nanooctahedron, as well as shapes in between, with high yield and reproducibility. Kinetic studies revealed two representative pathways for the shape control evolving into distinct nanostructures. Furthermore, the geometric and plasmonic properties of the gold nanoparticles could be precisely controlled by adjusting the base compositions of DNA sequences or by introducing phosphorothioate modifications in the DNA. As a result, the surface plasmon resonance (SPR) peaks of the nanoparticles can be fine‐tuned in a wide range, from visible to second near‐infrared (NIR‐II) region beyond 1000 nm.
Controlling nanoparticle morphology was achieved by tuning the overgrowth of gold nanorods using DNA as a capping ligand. Kinetic studies show two representative pathways for the shape control. Furthermore, the geometric and plasmonic properties of the gold nanoparticles could be precisely controlled by adjusting the base composition of the DNA sequences or by introducing phosphorothioate modifications in the DNA.
Controlling morphologies of nanomaterials such as their shapes and surface features has been a major endeavor in the field of nanoscale science and engineering, because the morphology is a major ...determining factor for functional properties of nanomaterials. Compared with conventional capping ligands based on organic molecules or polymers, the programmability of biomolecules makes them attractive alternatives for morphology-controlled nanomaterials synthesis. Towards the goal of predictable control of the synthesis, many studies have been performed on using different sequences of biomolecules to generate specific nanomaterial morphology. In this review, we summarize recent studies in the past few years on using DNA and peptide sequences to control inorganic nanomaterial morphologies, focusing on both case studies and mechanistic investigations. The functional properties resulting from such a sequence-specific control are also discussed, along with strengths and limitations of different approaches to achieving the goal.
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•Recent progress in sequence-specific control of inorganic nanomaterial morphologies by DNA and peptides are reviewed.•Mechanisms for the sequence-specific control of inorganic nanomaterial morphologies are discussed.•Properties resulting from the sequence-specific controlled inorganic nanomaterial morphologies are presented.•Strengths and limitations of the methods to discover biomolecular controlled inorganic material morphologies are summarized.
Palladium (Pd) nanoparticles enclosed by high-energy facets have displayed superior catalytic properties over that of their low-indexed counterparts. However, current methods of the synthesis are ...neither scalable nor cost-effective. In this study, we report a simple silver-assisted seed-mediated protocol to yield monodisperse palladium tetrahexahedral (THH) nanoparticles enclosed by the high-energy {730} facets. Additionally, their structural variants, truncated and stellated Pd THHs, with tunable size and sharpness have been synthesized. We show that introducing silver ions in the growth solution plays a key role in the growth of the nanoparticles. On the basis of kinetic studies, we find that the basis for the formation of these open structures is the underpotential deposition of Ag that stabilizes these high-energy surfaces and the overall mechanism of the growth is proposed. This study establishes a synthetic procedure that is scalable and is both chemically and economically more accessible than the existing protocols for Pd THH nanoparticles, making it possible for much wider applications of the Pd THH nanoparticles and its variants. Finally, these particles displayed higher electrocatalytic activity for ethanol oxidation reaction compared to low-indexed faceted Pd nanoparticles and commercially available Pd catalysts.
It is desirable to rationally engineer plasmonic metal nanostructures with sets of structural parameters that lead to specific functions. However, it is still challenging to predict the ...nanostructured outcome of a synthesis reaction by design because not only the exact kinetic path for the structural evolution is very complicated but also the relationships among various functional and structural parameters are often tangled. It is necessary to deconvolute the structure–function relationships and understand the co-evolution of structural and functional parameters as the nanostructures grow. DNA is a programable biomolecular capping ligand that was shown to be capable of precisely controlling the evolution of metal nanostructures. In this study, we systematically analyzed the evolution of two structural parameters and several functional parameters in the growth of Au–Ag nanostructures controlled by two DNA sequences. We deconvoluted the contributions from the two structural parameters in affecting the plasmonic properties in different kinetic and geometric domains. We further designed new nanostructures by exchanging DNA sequences in the growth environment, which also changed their evolution pathways. The resulting structural and functional parameters could be predictively tuned by the timing of the exchange. This study demonstrates the powerful toolbox provided by programable biomolecules in producing novel nanostructures in a predictable manner. It also shows that by understanding the kinetic evolution of the structural parameters and their relationships with the function parameters, it is possible to design the precise combinations of structural and functional parameters in the nanostructured products.
DNAzymes are a promising platform for metal ion detection, and a few DNAzyme‐based sensors have been reported to detect metal ions inside cells. However, these methods required an influx of metal ...ions to increase their concentrations for detection. To address this major issue, the design of a catalytic hairpin assembly (CHA) reaction to amplify the signal from photocaged Na+‐specific DNAzyme to detect endogenous Na+ inside cells is reported. Upon light activation and in the presence of Na+, the NaA43 DNAzyme cleaves its substrate strand and releases a product strand, which becomes an initiator that trigger the subsequent CHA amplification reaction. This strategy allows detection of endogenous Na+ inside cells, which has been demonstrated by both fluorescent imaging of individual cells and flow cytometry of the whole cell population. This method can be generally applied to detect other endogenous metal ions and thus contribute to deeper understanding of the role of metal ions in biological systems.
Cha cha cha: A catalytic hairpin assembly (CHA) reaction was designed to amplify the signal from photocaged Na+‐specific DNAzyme cleavage to detect endogenous Na+ inside cells. After light activation and in the presence of Na+, the NaA43 DNAzyme cleaves its substrate strand and releases a product strand, which becomes an initiator that can trigger the subsequent CHA signal amplification reaction.
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