Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Modulating the Bond Strength of DNA-Nanoparticle Superlattices.

ABSTRACT: A method is introduced for modulating the bond strength in DNA-programmable nanoparticle (NP) superlattice crystals. This method utilizes noncovalent interactions between a family of [Ru(dipyrido[2,3-a:3',2'-c]phenazine)(N-N)2](2+)-based small molecule intercalators and DNA duplexes to postsynthetically modify DNA-NP superlattices. This dramatically increases the strength of the DNA bonds that hold the nanoparticles together, thereby making the superlattices more resistant to thermal degradation. In this work, we systematically investigate the relationship between the structure of the intercalator and its binding affinity for DNA duplexes and determine how this translates to the increased thermal stability of the intercalated superlattices. We find that intercalator charge and steric profile serve as handles that give us a wide range of tunability and control over DNA-NP bond strength, with the resulting crystal lattices retaining their structure at temperatures more than 50 °C above what nonintercalated structures can withstand. This allows us to subject DNA-NP superlattice crystals to conditions under which they would normally melt, enabling the construction of a core-shell (gold NP-quantum dot NP) superlattice crystal.

SUBMITTER: Seo SE

PROVIDER: S-EPMC8189661 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Diamond family of nanoparticle superlattices.

Project description:Diamond lattices formed by atomic or colloidal elements exhibit remarkable functional properties. However, building such structures via self-assembly has proven to be challenging because of the low packing fraction, sensitivity to bond orientation, and local heterogeneity. We report a strategy for creating a diamond superlattice of nano-objects via self-assembly and demonstrate its experimental realization by assembling two variant diamond lattices, one with and one without atomic analogs. Our approach relies on the association between anisotropic particles with well-defined tetravalent binding topology and isotropic particles. The constrained packing of triangular binding footprints of truncated tetrahedra on a sphere defines a unique three-dimensional lattice. Hence, the diamond self-assembly problem is solved via its mapping onto two-dimensional triangular packing on the surface of isotropic spherical particles.

| S-EPMC5275765 | biostudies-literature

Defect tolerance and the effect of structural inhomogeneity in plasmonic DNA-nanoparticle superlattices.

Project description:Bottom-up assemblies of plasmonic nanoparticles exhibit unique optical effects such as tunable reflection, optical cavity modes, and tunable photonic resonances. Here, we compare detailed simulations with experiment to explore the effect of structural inhomogeneity on the optical response in DNA-gold nanoparticle superlattices. In particular, we explore the effect of background environment, nanoparticle polydispersity (>10%), and variation in nanoparticle placement (∼5%). At volume fractions less than 20% Au, the optical response is insensitive to particle size, defects, and inhomogeneity in the superlattice. At elevated volume fractions (20% and 25%), structures incorporating different sized nanoparticles (10-, 20-, and 40-nm diameter) each exhibit distinct far-field extinction and near-field properties. These optical properties are most pronounced in lattices with larger particles, which at fixed volume fraction have greater plasmonic coupling than those with smaller particles. Moreover, the incorporation of experimentally informed inhomogeneity leads to variation in far-field extinction and inconsistent electric-field intensities throughout the lattice, demonstrating that volume fraction is not sufficient to describe the optical properties of such structures. These data have important implications for understanding the role of particle and lattice inhomogeneity in determining the properties of plasmonic nanoparticle lattices with deliberately designed optical properties.

| S-EPMC4547218 | biostudies-literature

Binary nanoparticle superlattices of soft-particle systems.

Project description:The solid-phase diagram of binary systems consisting of particles of diameter σA = σ and σB = γσ (γ ≤ 1) interacting with an inverse p = 12 power law is investigated as a paradigm of a soft potential. In addition to the diameter ratio γ that characterizes hard-sphere models, the phase diagram is a function of an additional parameter that controls the relative interaction strength between the different particle types. Phase diagrams are determined from extremes of thermodynamic functions by considering 15 candidate lattices. In general, it is shown that the phase diagram of a soft repulsive potential leads to the morphological diversity observed in experiments with binary nanoparticles, thus providing a general framework to understand their phase diagrams. Particular emphasis is given to the two most successful crystallization strategies so far: evaporation of solvent from nanoparticles with grafted hydrocarbon ligands and DNA programmable self-assembly.

| S-EPMC4534282 | biostudies-literature

Importance of the DNA "bond" in programmable nanoparticle crystallization.

Project description:If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling's rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.

| S-EPMC4210335 | biostudies-literature

Modular and Chemically Responsive Oligonucleotide "Bonds" in Nanoparticle Superlattices.

Project description:Chemical bonds are a key determinant of the structure and properties of a material. Thus, rationally designing arbitrary materials requires complete control over the bond. While atomic bonding is dictated by the identity of the atoms, nanoparticle superlattice engineering, where nanoparticle "atoms" are held together by DNA "bonds", offers a route to design crystal lattices in a way that nature cannot: through altering the oligonucleotide bond. Herein, the use of RNA, as opposed to DNA, is explored by synthesizing superlattices in which nanoparticles are bonded by DNA/DNA, RNA/RNA, and DNA/RNA duplexes. By moving beyond nanoparticle superlattices assembled only with DNA, a new degree of freedom is introduced, providing programmed responsiveness to enzymes and greater bond versatility. Therefore, the oligonucleotide bond can have programmable function beyond dictating the structure of the material and moves nanoparticle superlattices closer to naturally occurring biomaterials, where the line between structural and functional elements is blurred.

| S-EPMC5490073 | biostudies-literature

Design principles for photonic crystals based on plasmonic nanoparticle superlattices.

Project description:Photonic crystals have been widely studied due to their broad technological applications in lasers, sensors, optical telecommunications, and display devices. Typically, photonic crystals are periodic structures of touching dielectric materials with alternating high and low refractive indices, and to date, the variables of interest have focused primarily on crystal symmetry and the refractive indices of the constituent materials, primarily polymers and semiconductors. In contrast, finite difference time domain (FDTD) simulations suggest that plasmonic nanoparticle superlattices with spacer groups offer an alternative route to photonic crystals due to the controllable spacing of the nanoparticles and the high refractive index of the lattices, even far away from the plasmon frequency where losses are low. Herein, the stopband features of 13 Bravais lattices are characterized and compared, resulting in paradigm-shifting design principles for photonic crystals. Based on these design rules, a simple cubic structure with an ∼130-nm lattice parameter is predicted to have a broad photonic stopband, a property confirmed by synthesizing the structure via DNA programmable assembly and characterizing it by reflectance measurements. We show through simulation that a maximum reflectance of more than 0.99 can be achieved in these plasmonic photonic crystals by optimizing the nanoparticle composition and structural parameters.

| S-EPMC6048504 | biostudies-literature

Supramolecular Semiconductivity through Emerging Ionic Gates in Ion-Nanoparticle Superlattices.

Project description:The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the "band gap" requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice's cavities.

| S-EPMC9835987 | biostudies-literature

The Significance of Multivalent Bonding Motifs and "Bond Order" in DNA-Directed Nanoparticle Crystallization.

Project description:Multivalent oligonucleotide-based bonding elements have been synthesized and studied for the assembly and crystallization of gold nanoparticles. Through the use of organic branching points, divalent and trivalent DNA linkers were readily incorporated into the oligonucleotide shells that define DNA-nanoparticles and compared to monovalent linker systems. These multivalent bonding motifs enable the change of "bond strength" between particles and therefore modulate the effective "bond order." In addition, the improved accessibility of strands between neighboring particles, either due to multivalency or modifications to increase strand flexibility, gives rise to superlattices with less strain in the crystallites compared to traditional designs. Furthermore, the increased availability and number of binding modes also provide a new variable that allows previously unobserved crystal structures to be synthesized, as evidenced by the formation of a thorium phosphide superlattice.

| S-EPMC4928491 | biostudies-literature

Fabrication of three-dimensionally interconnected nanoparticle superlattices and their lithium-ion storage properties.

Project description:Three-dimensional superlattices consisting of nanoparticles represent a new class of condensed materials with collective properties arising from coupling interactions between close-packed nanoparticles. Despite recent advances in self-assembly of nanoparticle superlattices, the constituent materials have been limited to those that are attainable as monodisperse nanoparticles. In addition, self-assembled nanoparticle superlattices are generally weakly coupled due to the surface-coating ligands. Here we report the fabrication of three-dimensionally interconnected nanoparticle superlattices with face-centered cubic symmetry without the presynthesis of the constituent nanoparticles. We show that mesoporous carbon frameworks derived from self-assembled supercrystals can be used as a robust matrix for the growth of nanoparticle superlattices with diverse compositions. The resulting interconnected nanoparticle superlattices embedded in a carbon matrix are particularly suitable for energy storage applications. We demonstrate this by incorporating tin oxide nanoparticle superlattices as anode materials for lithium-ion batteries, and the resulting electrochemical performance is attributable to their unique architectures.

| S-EPMC4366534 | biostudies-literature

Dimer Rhenium Tetrafluoride with a Triple Bond Re-Re: Structure, Bond Strength.

Project description:Based on the data of the gas electron diffraction/mass spectrometry (GED/MS) experiment, the composition of the vapor over rhenium tetrafluoride at T = 471 K was established, and it was found that species of the Re2F8 is present in the gas phase. The geometric structure of the Re2F8 molecule corresponding to D4h symmetry was found, and the following geometric parameters of the rh1 configuration were determined: rh1(Re-Re) = 2.264(5) Å, rh1(Re-F) = 1.846(4) Å, α(Re-Re-F) = 99.7(0.2)°, φ(F-Re-Re-F) = 2.4 (3.6)°. Calculations by the self-consistent field in full active space approximation showed that for Re2F8, the wave function of the 1A1g ground electronic state can be described by the single closed-shell determinant. For that reason, the DFT method was used for a structural study of Re2X8 molecules. The description of the nature of the Re-Re bond was performed in the framework of Atom in Molecules and Natural Bond Orbital analysis. The difference in the experimental values of r(Re-Re) in the free Re2F8 molecule and the [Re2F8]2- dianion in the crystal corresponds to the concept of a triple σ2π4 (ReIV-ReIV) bond and a quadruple σ2π4δ2 (ReIII-ReIII) bond, respectively, which are formed between rhenium atoms due to the interaction of d-atomic orbitals. The enthalpy of dissociation of the Re2F8 molecular form in two monomers ReF4 (ΔdissH°(298) = 109.9 kcal/mol) and the bond energies E(Re-Re) and E(Re-X) in the series Re2F8→Re2Cl8→Re2Br8 molecules were estimated. It is shown that the Re-Re bond energy weakly depends on the nature of the halogen, while the symmetry of the Re2Br8 (D4d) geometric configuration differs from the symmetry of the Re2F8 and Re2Cl8 (D4h) molecules.

| S-EPMC10179812 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data