DNA nanostructure decoration: a how-to tutorial

DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.

Functionalized silver nanoparticles for SERS amplification with enhanced reproducibility and for ultrasensitive optical fiber sensing in environmental and biochemical assays

Plasmonic sensors have broad application potential in many fields and are promising to replace most bulky sensors in the future. There are various method-based chemical reduction processes for silver nanoparticle production with flexible structural shapes due to their simplicity and rapidity in nanoparticle fabrication. In this study, self-assembled silver nanoparticles (Ag NPs) with a plasmon peak at 424 nm were successfully coated onto -NH2-functionalized glass and optical fiber sensors. These coatings were rapidly produced via two denaturation reactions in plasma oxygen, respectively, and an APTES ((3-aminopropyl)triethoxysilane) solution was shown to have high strength and uniformity. With the use of Ag NPs for surface-enhanced Raman scattering (SERS), excellent results and good stability with the detection limit up to 10-10 M for rhodamine B and 10-8 M for methylene blue, and a signal degradation of only ∼20% after storing for 30 days were achieved. In addition, the optical fiber sensor with Ag NP coatings exhibited a higher sensitivity value of 250 times than without coatings to the glycerol solution. Therefore, significant enhancement of these ultrasensitive sensors demonstrates promising alternatives to cumbersome tests of dye chemicals and biomolecules without any complicated process.

Design and Simple Assembly of Gold Nanostar Bioconjugates for Surface-Enhanced Raman Spectroscopy Immunoassays

Immunoassays using Surface-Enhanced Raman Spectroscopy are especially interesting on account not only of their increased sensitivity, but also due to its easy translation to point-of-care formats. The bases for these assays are bioconjugates of polyclonal antibodies and anisotropic gold nanoparticles functionalized with a Raman reporter. These bioconjugates, once loaded with the antigen analyte, can react on a sandwich format with the same antibodies immobilized on a surface. This surface can then be used for detection, on a microfluidics or immunochromatographic platform. Here, we have assembled bioconjugates of gold nanostars functionalized with 4-mercaptobenzoic acid, and anti-horseradish peroxidase antibodies. The assembly was by simple incubation, and agarose gel electrophoresis determined a high gold nanostar to antibody binding constant. The functionality of the bioconjugates is easy to determine since the respective antigen presents peroxidase enzymatic activity. Furthermore, the chosen antibody is a generic immunoglobulin G (IgG) antibody, opening the application of these principles to other antibody-antigen systems. Surface-Enhanced Raman Spectroscopy analysis of these bioconjugates indicated antigen detection down to 50 µU of peroxidase activity. All steps of conjugation were fully characterized by ultraviolet-visible spectroscopy, dynamic light scattering, ζ -Potential, scanning electron microscopy, and agarose gel electrophoresis. Based on the latter technique, a proof-of-concept was established for the proposed immunoassay.

A DNA origami plasmonic sensor with environment-independent read-out

DNA origami is a promising technology for its reproducibility, flexibility, scalability and biocompatibility. Among the several potential applications, DNA origami has been proposed as a tool for drug delivery and as a contrast agent, since a conformational change upon specific target interaction may be used to release a drug or produce a physical signal, respectively. However, its conformation should be robust with respect to the properties of the medium in which either the recognition or the read-out take place, such as pressure, viscosity and any other unspecific interaction other than the desired target recognition. Here we report on the read-out robustness of a tetragonal DNA-origami/gold-nanoparticle hybrid structure able to change its configuration, which is transduced in a change of its plasmonic properties, upon interaction with a specific DNA target. We investigated its response when analyzed in three different media: aqueous solution, solid support and viscous gel. We show that, once a conformational variation is produced, it remains unaffected by the subsequent physical interactions with the environment.

Measurement of adsorption constants of laccase on gold nanoparticles to evaluate the enhancement in enzyme activity of adsorbed laccase

Adsorption of enzymes to nanoparticles and the mechanisms responsible for enzyme activity modulation of adsorbed enzymes are not well understood. In this work, gold nanoparticles were used for electrostatic adsorption of a plant-derived laccase. Adsorption constants were determined by four independent techniques: dynamic light scattering, electrophoretic light scattering, agarose gel electrophoresis and fluorescence quenching. Stable bionanoconjugates were formed with log K in the range 6.8-8.9. An increase in enzyme activity was detected, in particular at acidic and close to neutral pH values, a feature that expands the useful pH range of the enzyme. A model for the adsorption was developed, based on geometrical considerations and volume increase data from dynamic light scattering. This indicates that enzymes adsorbed to gold nanoparticles are ca. 9 times more active than the free enzyme.

Tuning Gold Nanoparticles Plasmonic Properties by DNA Nanotechnology

The engineering of the optical and plasmonic properties of metallic nanostructure is one of the key ingredients for the complete control of materials at the nanoscale. Here we show how it is possible to control the plasmonic resonance of complex architectures of gold nanoparticles using the peculiar properties of DNA Watson and Crick pairing rules. In this chapter, we will first introduce all the steps required to generate, purify, and characterize DNA nanostructures, then we will guide the reader to the main steps required to decorate them with a precise amount of gold nanoparticles and, finally, we will describe the main approach used to characterize their plasmonic response.

Physics Models of Plasmonics: Single Nanoparticle, Complex Single Nanoparticle, Nanodimer, and Single Nanoparticle over Metallic Thin Film

The physics models of plasmonics for single nanoparticle, complex single nanoparticle, nanodimer, and single nanoparticle over a metallic thin film with an isolation layer, have been reviewed in this article. In nanoscale, the localized plasmonics from the single nanoparticle, hybrid single nanoparticle, and nanodimer, can be illustrated by classical electrodynamics. When the space of a nanodimer downs to subnanometer, the classical electrodynamics would fail to predict the resonance spectrum or dispersion of the nanostructures. The quantum model and quantum-corrected electrodynamics model, are introduced to deal with this problem. For the single nanoparticle over a metallic thin film with an isolation layer, the plasmonic resonance and the enhanced local field depend on the thickness of the isolation layer strongly. When the isolation layer thickness goes down to subnanometer, the classical electromagnetics model would be replaced by the quantum model for illustrating of the plasmonics. The physics models of plasmonics have wide applications in design and fabrication of the metallic nanostructure for further research.

'Squeezed' interparticle properties for plasmonic coupling and SERS characteristics of duplex DNA conjugated/linked gold nanoparticles of homo/hetero-sizes

The formation of interparticle duplex DNA conjugates with gold nanoparticles constitutes the basis for interparticle plasmonic coupling responsible for surface-enhanced Raman scattering signal amplification, but understanding of its correlation with interparticle spatial properties and particle sizes, especially in aqueous solutions, remains elusive. This report describes findings of an investigation of interparticle plasmonic coupling based on experimental measurements of localized surface plasmon resonance and surface enhanced Raman scattering characteristics for gold nanoparticles in aqueous solutions upon introduction of interparticle duplex DNA conjugates to define the interparticle spatial properties. Theoretical simulations of the interparticle optical properties and electric field enhancement based on a dimer model have also been performed to aid the understanding of the experimental results. The results have revealed a 'squeezed' interparticle spatial characteristic in which the duplex DNA-defined distance is close or shorter than A-form DNA conformation, which are discussed in terms of the interparticle interactions, providing fresh insight into the interparticle double-stranded DNA-defined interparticle spatial properties for the design of highly-sensitive nanoprobes in solutions for biomolecular detection.

Monitoring Early-Stage Nanoparticle Assembly in Microdroplets by Optical Spectroscopy and SERS

Microfluidic microdroplets have increasingly found application in biomolecular sensing as well as nanomaterials growth. More recently the synthesis of plasmonic nanostructures in microdroplets has led to surface-enhanced Raman spectroscopy (SERS)-based sensing applications. However, the study of nanoassembly in microdroplets has previously been hindered by the lack of on-chip characterization tools, particularly at early timescales. Enabled by a refractive index matching microdroplet formulation, dark-field spectroscopy is exploited to directly track the formation of nanometer-spaced gold nanoparticle assemblies in microdroplets. Measurements in flow provide millisecond time resolution through the assembly process, allowing identification of a regime where dimer formation dominates the dark-field scattering and SERS. Furthermore, it is shown that small numbers of nanoparticles can be isolated in microdroplets, paving the way for simple high-yield assembly, isolation, and sorting of few nanoparticle structures.

Gel electrophoretic analysis of differently shaped interacting and non-interacting bioconjugated nanoparticles

Gel electrophoresis is demonstrated for monitoring bioaffinity interactions between protein-functionalized nanoparticles featuring different shapes as well as for particle separation.

Plasmon resonance tuning using DNA origami actuation

A strategy for an innovative, continuous and reversible LSPR tuning using DNA origami actuation to modulate the nanometric separation of two gold nanoparticles has been developed. The actuation mechanism is based on DNA hybridization, in particular three different DNA sequences were shown to induce resonance shift of up to 6 nm.

A simple and effective strategy for the directed and high-yield assembly of large-sized gold nanoparticles driven by bithiol-modified complementary dsDNA architectures

A simple strategy for the high-yield assembly of large-sized Au NPs has been demonstrated by bithiol-modified complementary dsDNA architectures, which obviate the traditional conjugate of Au NPs to long ssDNA.