Discovery of and Insights into DNA "Codes" for Tunable Morphologies of Metal Nanoparticles.

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.

Bottom-Up Strategy To Prepare Nanoparticles with a Single DNA Strand.

We describe the preparation of cross-linked, polymeric organic nanoparticles (ONPs) with a single, covalently linked DNA strand. The structure and functionalities of the ONPs are controlled by the synthesis of their parent linear block copolymers that provide monovalency, fluorescence and narrow size distribution. The ONP can also guide the deposition of chloroaurate ions allowing gold nanoparticles (AuNPs) to be prepared using the ONPs as templates. The DNA strand on AuNPs is shown to preserve its functions.

DNA-Mediated Morphological Control of Pd-Au Bimetallic Nanoparticles.

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.

Mechanistic Insight into DNA-Guided Control of Nanoparticle Morphologies.

Although shapes and surface characteristics of nanoparticles are known to play important roles in defining their properties, it remains challenging to fine-tune the morphologies systematically and predictably. Recently, we have shown that DNA molecules can serve as programmable ligands to fine-tune the morphologies of nanomaterials. Despite this discovery, the mechanism of how the morphology can be controlled and the roles of the DNA molecules in contributing to such control are not understood. We herein report mechanistic investigation of DNA-mediated morphological evolution of gold nanoprism seeds into nonagon, hexagon, and six-pointed stars, some of which display rough surfaces, in the presence of homo-oligomeric T30, G20, C30, and A30. The growth, elucidated through various analytical methods including UV-vis, SEM, TEM, zeta potential, fluorescence, and cyclic voltammetry, is found to occur in two stages: control of shape, followed by control of thickness. A careful analysis of diffraction patterns of the nanoprism seeds as well as the resulting intermediate shapes by TEM allowed us to deduce the exact sequence of shape evolution. Through systematic comparison of the nanoparticle growth process, the DNA molecules were found to play important roles by influencing diffusion of the Au precursor to the seed and modulating the growth through differences in DNA desorption, density, and mobility on the seed surface. These insights into the mechanism of DNA-guided control of nanomaterial morphologies provide deeper understanding of the interactions between the DNA and nanomaterials and will allow better control of the shapes and surface properties of many nanomaterials.

DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles.

CONSPECTUS: Several properties of nanomaterials, such as morphologies (e.g., shapes and surface structures) and distance dependent properties (e.g., plasmonic and quantum confinement effects), make nanomaterials uniquely qualified as potential choices for future applications from catalysis to biomedicine. To realize the full potential of these nanomaterials, it is important to demonstrate fine control of the morphology of individual nanoparticles, as well as precise spatial control of the position, orientation, and distances between multiple nanoparticles. In addition, dynamic control of nanomaterial assembly in response to multiple stimuli, with minimal or no error, and the reversibility of the assemblies are also required. In this Account, we summarize recent progress of using DNA as a powerful programmable tool to realize the above goals. First, inspired by the discovery of genetic codes in biology, we have discovered DNA sequence combinations to control different morphologies of nanoparticles during their growth process and have shown that these effects are synergistic or competitive, depending on the sequence combination. The DNA, which guides the growth of the nanomaterial, is stable and retains its biorecognition ability. Second, by taking advantage of different reactivities of phosphorothioate and phosphodiester backbone, we have placed phosphorothioate at selective positions on different DNA nanostructures including DNA tetrahedrons. Bifunctional linkers have been used to conjugate phosphorothioate on one end and bind nanoparticles or proteins on the other end. In doing so, precise control of distances between two or more nanoparticles or proteins with nanometer resolution can be achieved. Furthermore, by developing facile methods to functionalize two hemispheres of Janus nanoparticles with two different DNA sequences regioselectively, we have demonstrated directional control of nanomaterial assembly, where DNA strands with specific hybridization serve as orthogonal linkers. Third, by using functional DNA that includes DNAzyme, aptamer, and aptazyme, dynamic control of assemblies of gold nanoparticles, quantum dots, carbon nanotubes, and iron oxide nanoparticles in response to one or more stimuli cooperatively have been achieved, resulting in colorimetric, fluorescent, electrochemical, and magnetic resonance signals for a wide range of targets, such as metal ions, small molecules, proteins, and intact cells. Fourth, by mimicking biology, we have employed DNAzymes as proofreading units to remove errors in nanoparticle assembly and further used DNAzyme cascade reactions to modify or repair DNA sequences involved in the assembly. Finally, by taking advantage of different affinities of biotin and desthiobiotin toward streptavidin, we have demonstrated reversible assembly of proteins on DNA origami.

DNA-Encoded Tuning of Geometric and Plasmonic Properties of Nanoparticles Growing from Gold Nanorod Seeds.

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.

DNA sequence-dependent morphological evolution of silver nanoparticles and their optical and hybridization properties.

A systematic investigation of the effects of different DNA sequences on the morphologies of silver nanoparticles (AgNPs) grown from Ag nanocube seeds is reported. The presence of 10-mer oligo-A, -T, and -C directed AgNPs growth from cubic seeds into edge-truncated octahedra of different truncation extents and truncated tetrahedral AgNPs, while AgNPs in the presence of oligo-G remained cubic. The shape and morphological evolution of the nanoparticle growth for each system is investigated using SEM and TEM and correlated with UV-vis absorption kinetic studies. In addition, the roles of oligo-C and oligo-G secondary structures in modulating the morphologies of AgNPs are elucidated, and the morphological evolution for each condition of AgNPs growth is proposed. The shapes were found to be highly dependent on the binding affinity of each of the bases and the DNA secondary structures, favoring the stabilization of the Ag{111} facet. The AgNPs synthesized through this method have morphologies and optical properties that can be varied by using different DNA sequences, while the DNA molecules on these AgNPs are also stable against glutathione. The AgNP functionalization can be realized in a one-step synthesis while retaining the biorecognition ability of the DNA, which allows for programmable assembly.

Facile and efficient preparation of anisotropic DNA-functionalized gold nanoparticles and their regioselective assembly.

Anisotropic nanoparticles can provide considerable opportunities for assembly of nanomaterials with unique structures and properties. However, most reported anisotropic nanoparticles are either difficult to prepare or to functionalize. Here we report a facile one-step solution-based method to prepare anisotropic DNA-functionalized gold nanoparticles (a-DNA-AuNP) with 96% yield and with high DNA density (120 ± 20 strands on the gold hemisphere). The method is based on the competition between a thiolated hydrophilic DNA and a thiolated hydrophobic phospholipid and has been applied to prepare a-DNA-AuNPs of different sizes and with a variety of DNA sequences. In addition, DNA strands on the a-DNA-AuNPs can be exchanged with other DNA strands with a different sequence. The anisotropic nature of the a-DNA-AuNPs allows regioselective hetero- and homonuclear assembly with high monodispersity, as well as regioselective functionalization of two different DNA strands for more diverse applications.

Nano-encrypted Morse code: a versatile approach to programmable and reversible nanoscale assembly and disassembly.

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code "NANO" and reversible exchange of uppercase letter "I" with lowercase "i". The yields of the conjugations are high (>90%), and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates.

Discovery of the DNA "genetic code" for abiological gold nanoparticle morphologies.

DNA is in control: Different combinations of DNA nucleotides can control the shape and surface roughness of gold nanoparticles during their synthesis. These nanoparticles were synthesized in the presence of either homogenous oligonucleotides or mixed-base oligonucleotides using gold nanoprisms as seeds. The effect of the individual DNA bases and their combinations on shape control are shown in the figure.

Controlled alignment of multiple proteins and nanoparticles with nanometer resolution via backbone-modified phosphorothioate DNA and bifunctional linkers.

Controlled alignment of streptavidin (STV), myoglobin, and nanoparticles with nanometer resolution has been achieved via backbone-modified phosphorothioate DNA and biotin- and maleimide-containing bifunctional linkers. Introducing triplet biotin modifications in three adjacent PSs significantly increased the STV conjugation yield. By placing phosphorothioate modifications at multiple positions of a double stranded DNA template, monomer, dimer, and trimer STV-DNA assemblies were formed with the STVs placed at controlled positions. The activity of the conjugated protein has been demonstrated by binding biotinylated AuNPs onto STV-DNA complexes, indicating the use of the system as a template for the formation of AuNP dimers and trimers with STVs separated by distances of 10-30 nm. Furthermore, a melting temperature experiment carried out with an STV-dsDNA assembly showed that the bifunctional-linker-modified PS-DNA system is much more stable than base-modified conjugation systems. This method allows for high yield, nanoscale-precision conjugation of multiple proteins to DNA. The linker can be designed to conjugate any proteins and nanomaterials specifically for a wide range of applications.

Independent control over size, valence, and elemental composition in the synthesis of DNA-nanoparticle conjugates.

DNA-nanoparticle conjugates have found widespread use in sensing, imaging, and as components of devices. However, their synthesis remains relatively complicated and empirically based, often requiring specialized protocols for conjugates of different size, valence, and elemental composition. Here we report a novel, bottom-up approach for the synthesis of DNA-nanoparticle conjugates, based on ring-opening metathesis polymerization (ROMP), intramolecular crosslinking, and template synthesis. Using size, valence, and elemental composition as three independent synthetic parameters, various conjugates can be obtained using a facile and universal procedure. Examples are given to show the usefulness of these conjugates as sensing probes, building blocks for self-assembly, and as model particles for structure-property relationship studies.

High-purity separation of gold nanoparticle dimers and trimers.

An effective method was developed for separating gold-nanoparticle clusters in high resolution; dimer and trimer samples were obtained with 95% and 81% purity, respectively.

Facile fabrication of triple-layer (Au@Ag)@polypyrrole core-shell and (Au@H2O)@polypyrrole yolk-shell nanostructures.

Triple-layer (Au@Ag)@polypyrrole core-shell nanoparticles are fabricated by a one-step synthesis involving simultaneous reduction of AgNO3 and polymerization of pyrrole in the presence of Au nanoparticles; the Ag layer in the resulting nanoparticles is etched to give a (Au@H2O)@polypyrrole yolk-shell structure.

Controlled assembly of eccentrically encapsulated gold nanoparticles.

Controlled partial attachment of polymer on gold nanoparticles breaks the symmetry of their surface functionalities, allowing tailored assembly of the nanoparticles.

DNA-Encoded Morphological Evolution of Bimetallic Pd@Au Core-shell Nanoparticles from a High-indexed Core.

DNA-mediated synthesis of nanoparticles with different morphologies has proven to be a powerful method to synthesize and access many exclusive shapes and surface properties. While previous studies employ seeds that contain relatively low-energy facets, such as a simple cubic palladium seed in the synthesis of Pd-Au bimetallic nanoparticles, few studies have investigated whether DNA molecules can still exert their influence when the synthesis uses a seed that contains high-energy facets. Seeds that are enclosed by such high-energy facets or sites are known to act as easy nucleation sites in nanoparticles growth and could potentially suppress the effect of DNA. To answer this question, we herein report DNA-encoded control of morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a concave palladium nanocube seed that contains high indexed facets. Based on detailed spectroscopic and SEM studies of time-dependent growth of the bimetallic nanoparticles, we found that each of 10-mer DNA molecules (T10, G10, C10 and A10) has a unique way of interacting with both the seed's surface and the precursor. Among them, the most important factor is the binding affinity of the nucleobase to the Pd surface, with the A10 possessing the highest binding affinity and thus capable of stabilizing the seed's high energy surfaces. Furthermore, for bases with lower binding affinity (T10, G10 and C10) than A10, the growth is completely dictated by the seed's surface energy initially, but the later growth can still be influenced by the different DNA sequences, resulting in four unique morphologically different Pd@Au bimetallic nanoparticles. The effect of these DNA molecules with medium binding affinity can only be observed when there is more deposition of Au. Based on the above results, a scheme for the DNA controlled growth is proposed. Together these results have provided insights into factors governing DNA-mediated growth of core-shell structures using seeds with high-energy sites, and the insights can readily be applied to other bimetallic systems that adopt seed-mediated synthesis.

DNAzyme-functionalized gold nanoparticles for biosensing.

Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.

Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials.

In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.