Direct Quantification of DNA Base Composition by Surface-Enhanced Raman Scattering Spectroscopy

Design of ultrasensitive DNA sensors based on the unique physical properties of plasmonic nanostructures has become one of the most exciting areas in nanomedicine. However, despite the vast number of proposed applications, the determination of the base composition in nucleic acids, a fundamental parameter in genomic analyses and taxonomic classification, is still restricted to time-consuming and poorly sensitive conventional methods. Herein, we demonstrate the possibility of determining the base composition in single- and double-stranded DNA by using a simple, low-cost, high-throughput, and label-free surface-enhanced Raman scattering (SERS) method in combination with cationic nanoparticles

Analysis of the SERS Spectrum by Theoretical Methodology: Evaluating a Classical Dipole Model and the Detuning of the Excitation Frequency

Surface-enhanced Raman scattering (SERS) spectroscopy is gaining prominence as one of the most powerful ultradetection techniques. The SERS outcome is essentially a complicated pattern of vibrational bands that allows multiplex analysis but, at the same time, makes difficult the interpretation of unknown analytes or known substances in the presence of complex unknown chemical environments. Herein, we show two computational methods to reproduce the spectral shape of the SERS spectra. The first, based in the modification of the classical dipole model, reproduces with a notable similarity the experimental spectrum excited far to the red of the localized surface plasmon resonance (LSPR). This light and time-efficient model is of great interest to elucidate the orientation of the target on the plasmonic surface or even to accurately identify suspected unknown targets in real samples. However, the experimental SERS spectrum in resonance with the LSPR is also modeled by using a more classical CPHF approach. This method provides also good agreement with the experiment but at the expense of much more computational time

Fast Optical Chemical and Structural Classification of RNA

As more biological activities of ribonucleic acids continue to emerge, the development of efficient analytical tools for RNA identification and characterization is necessary to acquire an in-depth understanding of their functions and chemical properties. Herein, we demonstrate the capacity of label-free direct surface-enhanced Raman scattering (SERS) analysis to access highly specific structural information on RNAs at the ultrasensitive level. This includes the recognition of distinctive vibrational features of RNAs organized into a variety of conformations (micro-, fully complementary duplex-, small interfering- and short hairpin-RNAs) or characterized by subtle chemical differences (single-base variances, nucleobase modifications and backbone composition). This method represents a key advance in the ribonucleic acid analysis and will have a direct impact in a wide range of different fields, including medical diagnosis, drug design, and biotechnology, by enabling the rapid, high-throughput, simple, and low-cost identification and classification of structurally similar RNAs

Synthesis and Optical Properties of Homogeneous Nanoshurikens

During the last years the controlled synthesis of Au nanoparticles (NPs) has almost become a reality, and structures such as spheres, cubes, rods, decahedra, or octahedra can be prepared with <i>a la carte</i> dimensions in a very homogeneous manner. However, the fabrication of spiked particles, the most efficient plasmonic NPs, with controllable geometric parameters remains elusive. Here we show how to prepare highly homogeneous spiked nanoparticles composed of a penta-twinned core and five tips. These nanoparticles, reminiscent of ninja nanoshurikens (throwing stars), exhibit the ability to concentrate large electromagnetic fields at the apexes of the tips upon illumination. The apexes also present high affinity for analytes, giving rise to an unprecedented capacity for quantitative optical ultradetection with SERS

Universal One-Pot and Scalable Synthesis of SERS Encoded Nanoparticles

Encoded particles are one of the most powerful approaches for multiplex high-throughput screening. Surface-enhanced Raman scattering (SERS) based codification can, in principle, avoid many of the intrinsic limitations due to conventional alternatives, as it decreases the reading time and particle size while allowing for almost unlimited codification. Unfortunately, methods for the synthetic preparation of these particles are tedious; often subjected to limited reproducibility (associated with large fluctuations in the size distributions of the polymers employed in the standard protocols); and to date, limited to a small amount of molecules. Herein, we report a universal, one-pot, inexpensive, and scalable synthetic protocol for the fabrication of SERS-encoded nanoparticles. This synthetic strategy is highly reproducible, independent of the chemical nature and size of the Raman code used (31 different codes were tested) and scalable in the liter range without affecting the final properties of the encoded structures. Furthermore, the SERS efficiency of the fabricated encoded nanoparticles is superior to that of the materials produced by conventional methods, while showing a remarkable reproducibility from batch to batch. This encoding strategy can easily be applied to nanoparticles of different materials and shapes

Boosting the Quantitative Inorganic Surface-Enhanced Raman Scattering Sensing to the Limit: The Case of Nitrite/Nitrate Detection

A high-performance ionic-sensing platform has been developed by an interdisciplinary approach, combining the classical colorimetric Griess reaction and new concepts of nanotechnology, such as plasmonic coupling of nanoparticles and surface-enhanced Raman scattering (SERS) spectroscopy. This approach exploits the advantages of combined SERS/surface-enhanced resonant Raman Scattering (SERRS) by inducing the formation of homogeneous hot spots and a colored complex in resonance with the laser line, to yield detection limits for nitrite down to the subpicomolar level. The performance of this new method was compared with the classical Griess reaction and ionic chromatography showing detection limits about 6 and 3 orders of magnitude lower, respectively

Directed Assembly of DNA-Functionalized Gold Nanoparticles Using Pyrrole–Imidazole Polyamides

Traditional methods for the construction of nanoparticle arrays and lattices exploit Watson–Crick base pairing of single-stranded DNA sequences as a proxy for self-assembly. Although this approach has been utilized in a variety of applications in nanoassembly, diagnostics, and biomedicine, the diversity of this recognition lexicon could be considerably increased by developing strategies that recognize the base-pairing landscape of double-stranded DNA (dsDNA) sequences. Herein we describe the first report of programmed gold nanoparticle (GNP) aggregation directed by the recognition of dsDNA sequences using pyrrole–imidazole polyamide–GNP (PA–GNP) conjugates. We demonstrate the reversibility and selectivity of this strategy for forming GNP aggregates in the presence of fully matched dsDNA sequences relative to dsDNA sequences containing one- and two-base-pair mismatches

Highly Sensitive SERS Quantification of the Oncogenic Protein c‑Jun in Cellular Extracts

A surface-enhanced Raman scattering (SERS)-based sensor was developed for the detection of the oncoprotein c-Jun at nanomolar levels. c-Jun is a member of the bZIP (basic zipper) family of dimeric transcriptional activators, and its overexpression has been associated with carcinogenic mechanisms in several human cancers. For our sensing purpose, we exploited the ability of c-Jun to heterodimerize with its native protein partner, c-Fos, and therefore designed a c-Fos peptide receptor chemically modified to incorporate a thiophenol (TP) group at the N-terminal site. The TP functionality anchors the c-Fos protein onto the metal substrate and works as an effective SERS probe to sense the structural rearrangements associated with the c-Fos/c-Jun heterodimerization

SERS Detection of Amyloid Oligomers on Metallorganic-Decorated Plasmonic Beads

Protein misfolded proteins are among the most toxic endogenous species of macromolecules. These chemical entities are responsible for neurodegenerative disorders such as Alzheimer’s, Parkinson’s, Creutzfeldt–Jakob’s and different non-neurophatic amyloidosis. Notably, these oligomers show a combination of marked heterogeneity and low abundance in body fluids, which have prevented a reliable detection by immunological methods so far. Herein we exploit the selectivity of proteins to react with metallic ions and the sensitivity of surface-enhanced Raman spectroscopy (SERS) toward small electronic changes in coordination compounds to design and engineer a reliable optical sensor for protein misfolded oligomers. Our strategy relies on the functionalization of Au nanoparticle-decorated polystyrene beads with an effective metallorganic Raman chemoreceptor, composed by Al³⁺ ions coordinated to 4-mercaptobenzoic acid (MBA) with high Raman cross-section, that selectively binds aberrant protein oligomers. The mechanical deformations of the MBA phenyl ring upon complexation with the oligomeric species are registered in its SERS spectrum and can be quantitatively correlated with the concentration of the target biomolecule. The SERS platform used here appears promising for future implementation of diagnostic tools of aberrant species associated with protein deposition diseases, including those with a strong social and economic impact, such as Alzheimer’s and Parkinson’s diseases

Effect of Metal–Liquid Interface Composition on the Adsorption of a Cyanine Dye onto Gold Nanoparticles

Synthesis of asymmetric nanoparticles, such as gold nanorods, with tunable optical properties providing metal structures with improved SERS performance is playing a critical role in expanding the use of SERS to imaging and sensing applications. However, the synthetic methods usually require surfactants or polymers as shape-directing agents. These chemicals normally remain firmly bound to the metal after the synthesis, preventing the direct adsorption of a large number of potential analytes and often hampering the chemical functionalization of the surface unless extended, and critical for the nanoparticle stability, postremoval steps were performed. For this reason, it is of great importance for the full exploitation of these nanostructures to gain a deeper insight into the dependence of the analyte–metal interaction to the metal–liquid interface composition. In this article, we investigated in detail the role played by each component of the gold nanorod (GNR) interface in the adsorption of indocyanine green (ICG) as a probe molecule. Citrate-reduced gold nanospheres were used as a model substrate since the negative citrate anions adsorbed onto the metal surface can be easily displaced by those chemicals usually involved in the GNR synthesis, allowing the GNR-like interface composition to be progressively rebuilt and modified at will on the citrate-capped nanoparticles. The obtained results provide a meticulous description of the role played by each individual component of the metal–liquid interface on the ICG interaction with the metal, illustrating how apparently minor experimental changes can dramatically modify the affinity and optical properties of the ICG probe adsorbed onto the nanoparticle