Langmuir analysis of nanoparticle polyvalency in DNA-mediated adsorption

Immobilization of Multivalent Titanium Cations on Magnetic Composite Microspheres for Highly Efficient DNA Extraction and Amplification

Magnetic-assisted DNA testing technology has attracted much attention in genetics, clinical diagnostics, environmental microbiology, and molecular biology. However, achieving satisfying DNA adsorption and desorption efficiency in real samples is still a big challenge. In this paper, a new kind of high-quality magnetic composite microsphere of MM@PGMA-PA-Ti4+ was designed and prepared for DNA extraction and detection based on the strong interaction of Ti4+ and phosphate groups. By taking the advantages of high magnetic susceptibility and high Ti4+ content, the MM@PGMA-PA-Ti4+ microspheres possessed remarkable extraction capacity for mimic biological samples (salmon sperm specimens) with saturated loadings up to 533.0 mg/g. When the DNA feeding amount was 100 μg and the MM@PGMA-PA-Ti4+ dosage was 1 mg, the adsorption and desorption efficiencies were 80 and 90%, respectively. The kinetic and equilibrium extraction data were found to fit well with the pseudo-second-order model and Freundlich isotherm model. Furthermore, the MM@PGMA-PA-Ti4+ microspheres were successfully employed for DNA extraction from mouse epithelial-like fibroblasts. The extraction ability (84 ± 4 μg/mg) and DNA purity were superior to the comparative commercial spin kits, as evaluated by electrophoresis assays and qPCR analysis. The experimental results suggest that the MM@PGMA-PA-Ti4+ microspheres possess great potential as an adsorbent for DNA purification from complex biological samples.

Magnetic Bead Spherical Nucleic Acid Microstructure for Reliable DNA Preservation and Repeated DNA Reading

DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, and sequencing technologies. Despite progress in these subareas, the most challenging hurdle in the deployment of DNA storage remains the reliability of preservation and the repeatability of reading. Herein, we report the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure and its use as a cost-effective platform for reliable DNA preservation and repeated reading. MB-SNA has an inner core of silica@γ-Fe2O3@silica microbeads and an outer spherical shell of double-stranded DNA (dsDNA) with a density as high as 34 pmol/cm2. For MB-SNA, each strand of dsDNA stored a piece of data, and the high-density packing of dsDNA achieved high-capacity storage. MB-SNA was advantageous in terms of reliable preservation over free DNA. By accelerated aging tests, the data of MB-SNA is demonstrated to be readable after 0.23 million years of preservation at -18 °C and 50% relative humidity. Moreover, MB-SNA facilitated repeated reading by facile PCR-magnetic separation. After 10 cycles of PCR access, the retention rate of dsDNA for MB-SNA is demonstrated to be as high as 93%, and the accuracy of sequencing is more than 98%. In addition, MB-SNA makes cost-effective DNA storage feasible. By serial dilution, the physical limit for MB-SNA to achieve accurate reading is probed to be as low as two microstructures.

Programmable Matter: The Nanoparticle Atom and DNA Bond

Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the "atoms") functionalized with DNA (the "bonding elements"), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the "atom" (e.g., the nanoparticle shape, size, and composition) and the "bond" (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. In this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.

Synthesis of magnetic nanocomposite microparticles for binding of chlorinated organics in contaminated water sources

In this work, the development of novel magnetic nanocomposite microparticles (MNMs) via free radical polymerization for their application in the remediation of contaminated water is presented. Acrylated plant-based polyphenols, curcumin multiacrylate (CMA) and quercetin multiacrylate (QMA), were incorporated as functional monomers to create high affinity binding sites for the capture of polychlorinated biphenyls (PCBs), as a model pollutant. The MNMs were characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, dynamic light scattering, and UV-visible spectroscopy. The affinity of these novel materials for PCB 126 was evaluated and fitted to the nonlinear Langmuir model to determine binding affinities (K D). The results suggest the presence of the polyphenolic moieties enhances the binding affinity for PCB 126, with K D values comparable to that of antibodies. This demonstrates that these nanocomposite materials have promising potential as environmental remediation adsorbents for harmful contaminants.

Single-crystal Winterbottom constructions of nanoparticle superlattices

Colloidal nanoparticle assembly methods can serve as ideal models to explore the fundamentals of homogeneous crystallization phenomena, as interparticle interactions can be readily tuned to modify crystal nucleation and growth. However, heterogeneous crystallization at interfaces is often more challenging to control, as it requires that both interparticle and particle-surface interactions be manipulated simultaneously. Here, we demonstrate how programmable DNA hybridization enables the formation of single-crystal Winterbottom constructions of substrate-bound nanoparticle superlattices with defined sizes, shapes, orientations and degrees of anisotropy. Additionally, we show that some crystals exhibit deviations from their predicted Winterbottom structures due to an additional growth pathway that is not typically observed in atomic crystals, providing insight into the differences between this model system and other atomic or molecular crystals. By precisely tailoring both interparticle and particle-surface potentials, we therefore can use this model to both understand and rationally control the complex process of interfacial crystallization.

Fabrication of Single-Nanocrystal Arrays

To realize the full potential of nanocrystals in nanotechnology, it is necessary to integrate single nanocrystals into addressable structures; for example, arrays and periodic lattices. The current methods for achieving this are reviewed. It is shown that a combination of top-down lithography techniques with directed assembly offers a platform for attaining this goal. The most promising of these directed assembly methods are reviewed: capillary force assembly, electrostatic assembly, optical printing, DNA-based assembly, and electrophoretic deposition. The last of these appears to offer a generic approach to fabrication of single-nanocrystal arrays.

Liposomal Spherical Nucleic Acid Scaffolded Site-Selective Hybridization of Nanoparticles for Visual Detection of MicroRNAs

In this study, the advanced liposomal spherical nucleic acid (L-SNA) is exploited for the first time to establish a spherical, three-dimensional biosensing platform by hybridizing with a set of nanoparticles. By hydrophilic and hydrophobic interactions as well as programmable base-pairing, red-emission quantum dots (QDs), green-emission QDs, and gold nanoparticles (AuNPs) are encapsulated into the internal aqueous core, the intermediate lipid bilayer, and the outer SNA shell, respectively, producing an L-SNA-nanoparticle hybrid. As a result of the site-selective encapsulation, the hybrid constitutes a liposomal fluorescent "core-resonance energy transfer" system surrounded by a SNA shell, as is imaged at the single-particle resolution by confocal microscopy. With the outer SNA shell as three-dimensional substrate for duplex-specific nuclease target recycling reaction, the hybrid is capable of amplified detection of microRNAs, featuring one target to many AuNP-manipulated, dual-emission QD-based ratiometric fluorescence. More importantly, the ratiometric fluorescence facilitates the hybrid to visualize microRNAs with remarkably high resolution, which is exemplified by traffic light-type transition in fluorescence color for diagnosing circulating microRNAs in clinical serum samples. Substantially, the controllable hybridization with functional nanoparticles opens an avenue for the exciting biomedical applications of liposomal spherical nucleic acids.

Controlled Symmetry Breaking in Colloidal Crystal Engineering with DNA

The programmed crystallization of particles into low-symmetry lattices represents a major synthetic challenge in the field of colloidal crystal engineering. Herein, we report an approach to realizing such structures that relies on a library of low-symmetry Au nanoparticles, with synthetically adjustable dimensions and tunable aspect ratios. When modified with DNA ligands and used as building blocks for colloidal crystal engineering, these structures enable one to expand the types of accessible lattices and to answer mechanistic questions about phase transitions that break crystal symmetry. Indeed, crystals formed from a library of elongated rhombic dodecahedra yield a rich phase space, including low-symmetry lattices (body-centered tetragonal and hexagonal planar). Molecular dynamics simulations corroborate and provide insight into the origin of these phase transitions. In particular, we identify an unexpected asymmetry in the DNA shell, distinct from both the particle and lattice symmetries, which enables directional, nonclose-packed interactions.

Carboxymethylated polyethylenimine modified magnetic nanoparticles specifically for purification of His-tagged protein

Employing immobilized metal-ion affinity chromatography and magnetic separation could ideally provide a useful analytical strategy for purifying His-tagged protein. In the current study, a facile route was designed to prepare CMPEI-Ni²⁺ @SiO₂ @Fe₃ O₄ (CMPEI=carboxymethylated polyethyleneimine) magnetic nanoparticles composed of a strong magnetic core of Fe₃ O₄ and a Ni²⁺ -immobilized carboxymethylated polyethyleneimine coated outside shell, which was formed by electrostatic interactions between polyanionic electrolyte of carboxymethylated polyethyleneimine and positively charged surface of 3-(trimethoxysilyl)propylamin modified SiO₂ @Fe₃ O₄ . The resulting CMPEI-Ni²⁺ @SiO₂ @Fe₃ O₄ composite nanoparticles displayed well-uniform structure and high magnetic responsiveness. Hexa His-tagged peptides and purified His-tagged recombinant retinoid X receptor alpha were chosen as the model samples to evaluate the adsorption, capacity, and reusability of the composite nanoparticles. The results demonstrated the CMPEI-Ni²⁺ @SiO₂ @Fe₃ O₄ nanoparticles possessed rapid adsorption, large capacity, and good recyclability. The obtained nanoparticles were further used to purify His-tagged protein in practical environment. It was found that the nanoparticles could selectively capture His-tagged recombinant retinoid X receptor protein from complex cell lysate. Owing to its easy synthesis, large binding capacity, and good reusability, the prepared CMPEI-Ni²⁺ @SiO₂ @Fe₃ O₄ magnetic nanoparticles have great potential for application in biotechnological fields.

DNA-Directed Non-Langmuir Deposition of Programmable Atom Equivalents

Particle assembly at interfaces via programmed DNA interactions allows for independent modification of both nanoparticle-surface interaction strength and the magnitude of interparticle repulsion. Together, these factors allow for modification of the deposited thin film morphology via alterations in DNA binding sequence. Importantly, both Langmuir and random sequential adsorption models yield insights into the thermodynamics of deposition but cannot fully explain particle coverage as a function of all relevant variables, indicating that the particle deposition mechanism for DNA-grafted colloids is more complex than prior adsorption phenomena. Here, it is shown that these deviations from standard behavior arise from the fact that each nanoparticle is attached to the surface via multiple weak DNA duplex interactions, enabling diffusion of adsorbed colloids across the substrate. Thus, surface migration of individual particles causes reorganization of the deposited monolayer, leading to the unusual behavior of coverage increasing at elevated temperatures that are just below the particle desorption temperature. The programmability of DNA-directed particle deposition therefore allows for precise control over the morphology of monolayer films, as well as the ability to generate crystalline materials with controllable surface roughness and grain size through layer-by-layer growth. The increased control over thin film morphology potentially enables tailoring of mechanical and optical properties and holds promise for use in a variety of applications.

Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand-Apoprotein Complex

In this work, the hybridization and dehybridization of ssDNA with 20 bases at gold coated sensor surfaces modified with complementary 20 bases capture probe ssDNA was investigated at 18 °C by quartz crystal microbalance measurements with dissipation monitoring (QCM-D). A sequence of 20 base pairs with a melting temperature of about 64 °C was chosen, since in many biosensor studies the target molecules are DNA or RNA oligomers of similar length. It turned out that at the applied experimental conditions the DNA hybridization was irreversible, and therefore the hybridization and dehybridization process could not be described by the Langmuir model of adsorption. Nevertheless, quantitative dehybridization could be achieved by rinsing the sensor surface thoroughly with pure water. When in contrast the hybridization of a target with only 10 bases complementary to the outermost 10 bases of the 20 bases capture probe was studied, binding and unbinding were reversible, and the hybridization/dehybridization process could be satisfactorily described by the Langmuir model. For the 10 base pair sequence, the melting temperature was about 36 °C. Apparently, for Langmuir behavior, it is important that the experiments are applied at a temperature sufficiently close to the melting temperature of the sequence under investigation to ensure that at least traces of the target molecules are unhybridized (i.e., there needs to be an equilibrium between hybridized and dehybridized target molecules). To validate the reliability of our experimental approach we also studied the reconstitution and disassembly of the flavoprotein dodecin at flavin-terminated DNA monolayers, as according to previous studies it is assumed that the apododecin-flavin system can be well described by the Langmuir model. As a result, this assumption could be verified. Using three different approaches, K_D values were obtained that differ not more than by a factor of 4.

Design Rules for Template-Confined DNA-Mediated Nanoparticle Assembly

Template-based strategies are becoming increasingly important for controlling the position of nanoparticle-based (NP-based) structures on surfaces for a wide variety of encoding and device fabrication strategies. Thus, there is an increasing need to understand the behavior of NPs in confined spaces. Herein, a systematic investigation of the diffusion and adsorption properties of DNA-modified NPs is presented in lithographically defined, high-aspect-ratio pores using a template-confined, DNA-mediated assembly. Leveraging the sequence-specific binding affinity of DNA, it is discovered that although NP adsorption in deep polymer pores follows a traditional Langmuir adsorption model when under thermodynamic control, such NPs kinetically follow Fick's classical law of diffusion. Importantly, these observations allow one to establish design rules for template-confined, DNA-mediated NP assembly on substrates based on pore dimensions, NP size and shape, NP concentration, temperature, and time. As a proof-of-concept example, these design rules are used to engineer a vertical, four-layer assembly consisting of individual octahedral NPs stacked on top of one another, with in-plane positioning defined by pores generated by e-beam lithography.

Polyvalent Spherical Nucleic Acids for Universal Display of Functional DNA with Ultrahigh Stability

For nanomaterials that are difficult to functionalize by covalent attachment of DNA, we herein communicate a general method taking advantage of the high avidity of polyvalent binding and the 3D structure of densely functionalized spherical nucleic acids (SNAs). Using DNA-functionalized gold nanoparticles, simple mixing leads to the formation of highly stable conjugates on 11 different materials including metals, metal oxides, metal-organic frameworks, transition-metal dichalcogenides, nanocarbons, and polymers. The adsorption affinity of SNAs can be over thousand-fold higher than that of free DNA of the same sequence, and practically irreversible conjugates are formed withstanding various denaturing agents. The surface attachment and molecular recognition functions of DNA are spatially separated, showing a key advantage of SNAs. The functionalized materials possess the properties of both the substrate and the SNA, allowing specific DNA hybridization in buffer and in serum.

DNA-Mediated Size-Selective Nanoparticle Assembly for Multiplexed Surface Encoding

Multiplexed surface encoding is achieved by positioning two different sizes of gold nanocubes on gold surfaces with precisely defined locations for each particle via template-confined, DNA-mediated nanoparticle assembly. As a proof-of-concept demonstration, cubes with 86 and 63 nm edge lengths are assembled into arrangements that physically and spectrally encrypt two sets of patterns in the same location. These patterns can be decrypted by mapping the absorption intensity of the substrate at λ = 773 and 687 nm, respectively. This multiplexed encoding platform dramatically increases the sophistication and density of codes that can be written using colloidal nanoparticles, which may enable high-security, high-resolution encoding applications.

Building superlattices from individual nanoparticles via template-confined DNA-mediated assembly

DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. Specifically, the assembly of individual colloidal plasmonic nanoparticles with different shapes and sizes is controlled by oligonucleotides containing “locked” nucleic acids and confined environments provided by polymer pores to yield oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer- and micrometer-length scales. These structures, which would be difficult to construct by other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach are explored by identifying a broadband absorber with a solvent polarity response that allows dynamic tuning of visible light absorption.

The nature and implications of uniformity in the hierarchical organization of nanomaterials

In this Perspective, we present a framework that defines how to understand and control material structure across length scales with inorganic nanoparticles. Three length scales, frequently discussed separately, are unified under the topic of hierarchical organization: atoms arranged into crystalline nanoparticles, ligands arranged on nanoparticle surfaces, and nanoparticles arranged into crystalline superlattices. Through this lens, we outline one potential pathway toward perfect colloidal matter that emphasizes the concept of uniformity. Uniformity is of both practical and functional importance, necessary to increase structural sophistication and realize the promise of nanostructured materials. Thus, we define the nature of nonuniformity at each length scale as a means to guide ongoing research efforts and highlight potential problems in the field.

Size-Selective Nanoparticle Assembly on Substrates by DNA Density Patterning

The vision of nanoscale self-assembly research is the programmable synthesis of macroscale structures with controlled long and short-range order that exhibit a desired set of properties and functionality. However, strategies to reliably isolate and manipulate the nanoscale building blocks based on their size, shape, or chemistry are still in their infancy. Among the promising candidates, DNA-mediated self-assembly has enabled the programmable assembly of nanoparticles into complex architectures. In particular, two-dimensional assembly on substrates has potential for the development of integrated functional devices and analytical systems. Here, we combine the high-resolution patterning capabilities afforded by electron-beam lithography with the DNA-mediated assembly process to enable direct-write grayscale DNA density patterning. This method allows modulation of the functionally active DNA surface density to control the thermodynamics of interactions between nanoparticles and the substrate. We demonstrate that size-selective directed assembly of nanoparticle films from solutions containing a bimodal distribution of particles can be realized by exploiting the cooperativity of DNA binding in this system. To support this result, we study the temperature-dependence of nanoparticle assembly, analyze the DNA damage by X-ray photoelectron spectroscopy and fluorescence microscopy, and employ molecular dynamics simulations to explore the size-selection behavior.

Critical Undercooling in DNA-Mediated Nanoparticle Crystallization

The nucleation of DNA-functionalized nanoparticle superlattices is observed to exhibit a temperature hysteresis between melting (superlattice dissociation) and freezing (particle association) transitions that allows for the study of nucleation thermodynamics. Through detailed study of the assembly of these particles, which can be considered programmable atom equivalents (PAEs), we identify this hysteresis as critical undercooling-a phase transition phenomenon related to a thermodynamic barrier to nucleation. The separable nature of the DNA bonding elements and nanoparticle core enables the PAE platform to pose unique questions about the microscopic dependencies of critical undercooling and, ultimately, to control the nucleation pathway. Specifically, we find that the undercooling required to initiate nucleation increases as the nanoparticle coordination number increases (number of particles to which a single particle can bind).

Anisotropic nanoparticle complementarity in DNA-mediated co-crystallization

Whether two species will co-crystallize depends on the chemical, physical and structural complementarity of the interacting components. Here, by using DNA as a surface ligand, we selectively co-crystallize mixtures of two different anisotropic nanoparticles and systematically investigate the effects of nanoparticle size and shape complementarity on the resultant crystal symmetry, microstrain, and effective 'DNA bond' length and strength. We then use these results to understand a more complicated system where both size and shape complementarity change, and where one nanoparticle can participate in multiple types of directional interactions. Our findings offer improved control of non-spherical nanoparticles as building blocks for the assembly of sophisticated macroscopic materials, and provide a framework to understand complementarity and directional interactions in DNA-mediated nanoparticle crystallization.

Strong Coupling between Plasmonic Gap Modes and Photonic Lattice Modes in DNA-Assembled Gold Nanocube Arrays

Control of both photonic and plasmonic coupling in a single optical device represents a challenge due to the distinct length scales that must be manipulated. Here, we show that optical metasurfaces with such control can be constructed using an approach that combines top-down and bottom-up processes, wherein gold nanocubes are assembled into ordered arrays via DNA hybridization events onto a gold film decorated with DNA-binding regions defined using electron beam lithography. This approach enables one to systematically tune three critical architectural parameters: (1) anisotropic metal nanoparticle shape and size, (2) the distance between nanoparticles and a metal surface, and (3) the symmetry and spacing of particles. Importantly, these parameters allow for the independent control of two distinct optical modes, a gap mode between the particle and the surface and a lattice mode that originates from cooperative scattering of many particles in an array. Through reflectivity spectroscopy and finite-difference time-domain simulation, we find that these modes can be brought into resonance and coupled strongly. The high degree of synthetic control enables the systematic study of this coupling with respect to geometry, lattice symmetry, and particle shape, which together serve as a compelling example of how nanoparticle-based optics can be useful to realize advanced nanophotonic structures that hold implications for sensing, quantum plasmonics, and tunable absorbers.

Uniform circular disks with synthetically tailorable diameters: two-dimensional nanoparticles for plasmonics

Herein, we report the synthesis of structurally uniform gold circular disks as two-dimensional plasmonic nanostructures that complement the well-established one-dimensional rod and three-dimensional shell structures. We show that a Au conproportionation reaction can be used to etch a collection of nonuniform triangular prisms into a uniform circular disk product with thickness and diameter varying <10%. These new particles have broadly tunable plasmon resonances (650-1000 nm) with narrow bandwidths (0.23-0.28 eV) and can be described as "effectively two-dimensional" plasmonic structures, as they do not support a significant transverse mode.