Direct Surface‐Enhanced Raman Scattering Analysis of DNA Duplexes

The exploration of the genetic information carried by DNA has become a major scientific challenge. Routine DNA analysis, such as PCR, still suffers from important intrinsic limitations. Surface‐enhanced Raman spectroscopy (SERS) has emerged as an outstanding opportunity for the development of DNA analysis, but its application to duplexes (dsDNA) has been largely hampered by reproducibility and/or sensitivity issues. A simple strategy is presented to perform ultrasensitive direct label‐free analysis of unmodified dsDNA with the means of SERS by using positively charged silver colloids. Electrostatic adhesion of DNA promotes nanoparticle aggregation into stable clusters yielding intense and reproducible SERS spectra at nanogram level. As potential applications, we report the quantitative recognition of hybridization events as well as the first examples of SERS recognition of single base mismatches and base methylations (5‐methylated cytosine and N6‐methylated Adenine) in duplexes.     

INHIBIT‐Inspired Two‐Output DNA Logic Gates Based on Surface‐Enhanced Raman Scattering

Herein, we presented a novel logic gate based on an INHIBITION gate that performs parallel readouts. Logic gates performing INHIBITION and YES/OR were constructed using surface‐enhanced Raman scattering as optical outputs for the first time. The strategy allowed for simultaneous reading of outputs in one tube. The applicability of this strategy has been successfully exemplified in the construction of half‐adder using the two‐output logic gates as reporting gates. This reporting strategy provides additional design flexibility for dynamic DNA devices.     

Ultrasensitive Direct Quantification of Nucleobase Modifications in DNA by Surface‐Enhanced Raman Scattering: The Case of Cytosine

Recognition of chemical modifications in canonical nucleobases of nucleic acids is of key importance since such modified variants act as different genetic encoders, introducing variability in the biological information contained in DNA. Herein, we demonstrate the feasibility of direct SERS in combination with chemometrics and microfluidics for the identification and relative quantification of 4 different cytosine modifications in both single‐ and double‐stranded DNA. The minute amount of DNA required per measurement, in the sub‐nanogram regime, removes the necessity of pre‐amplification or enrichment steps (which are also potential sources of artificial DNA damages). These findings show great potentials for the development of fast, low‐cost and high‐throughput screening analytical devices capable of detecting known and unknown modifications in nucleic acids (DNA and RNA) opening new windows of activity in several fields such as biology, medicine and forensic sciences.     

Simultaneous Capture,Detection, and Inactivation of Bacteria as Enabled by a Surface‐Enhanced Raman Scattering Multifunctional Chip

Herein, we present a multifunctional chip based on surface‐enhanced Raman scattering (SERS) that effectively captures, discriminates, and inactivates pathogenic bacteria. The developed SERS chip is made of a silicon wafer decorated with silver nanoparticles and modified with 4‐mercaptophenylboronic acid (4‐MPBA). It was prepared in a straightforward manner by chemical reduction assisted by hydrogen fluoride etching, followed by the conjugation of 4‐MPBA through Ag? S bonds. The dominant merits of the fabricated SERS chip include excellent reproducibility with a relative standard deviation (RSD) value smaller than 11.0 %, adaptable bacterial‐capture efficiency (ca. 60 %) at low concentrations (500–2000 CFU mL^?1), a low detection limit (down to a concentration of 1.0×10² cells mL^?1), and high antibacterial activity (an antibacterial rate of ca. 97 %). The SERS chip enabled sensitive and specific discrimination of Escherichia coli and Staphylococcus aureus from human blood.     

Simultaneous Capture,Detection, and Inactivation of Bacteria as Enabled by a Surface‐Enhanced Raman Scattering Multifunctional Chip

Herein, we present a multifunctional chip based on surface‐enhanced Raman scattering (SERS) that effectively captures, discriminates, and inactivates pathogenic bacteria. The developed SERS chip is made of a silicon wafer decorated with silver nanoparticles and modified with 4‐mercaptophenylboronic acid (4‐MPBA). It was prepared in a straightforward manner by chemical reduction assisted by hydrogen fluoride etching, followed by the conjugation of 4‐MPBA through Ag S bonds. The dominant merits of the fabricated SERS chip include excellent reproducibility with a relative standard deviation (RSD) value smaller than 11.0 %, adaptable bacterial‐capture efficiency (ca. 60 %) at low concentrations (500–2000 CFU mL⁻¹), a low detection limit (down to a concentration of 1.0×10² cells mL⁻¹), and high antibacterial activity (an antibacterial rate of ca. 97 %). The SERS chip enabled sensitive and specific discrimination of Escherichia coli and Staphylococcus aureus from human blood.     

DNA Origami Directed Assembly of Gold Bowtie Nanoantennas for Single‐Molecule Surface‐Enhanced Raman Scattering

Metallic bowtie nanoarchitectures can produce dramatic electric field enhancement, which is advantageous in single‐molecule analysis and optical information processing. Plasmonic bowtie nanostructures were successfully constructed using a DNA origami‐based bottom‐up assembly strategy, which enables precise control over the geometrical configuration of the bowtie with an approximate 5 nm gap. A single Raman probe was accurately positioned at the gap of the bowtie. Single‐molecule surface‐enhanced Raman scattering (SM‐SERS) of individual nanostructures, including ones containing an alkyne group, was observed. The design achieved repeatable local field enhancement of several orders of magnitude. This method opens the door on a novel strategy for the fabrication of metal bowtie structures and SM‐SERS, which can be utilized in the design of highly‐sensitive photonic devices.     

Silver Nanoparticle Thin Films with Nanocavities for Surface‐Enhanced Raman Scattering

The formation of nanometer‐sized gaps between silver nanoparticles is critically important for optimal enhancement in surface‐enhanced Raman scattering (SERS). A simple approach is developed to generate nanometer‐sized cavities in a silver nanoparticle thin film for use as a SERS substrate with extremely high enhancement. In this method, a submicroliter volume of concentrated silver colloidal suspension stabilized with cetyltrimethylammonium bromide (CTAB) is spotted on hydrophobic glass surfaces prepared by the exposure of the glass to dichloromethysilane vapors. The use of a hydrophobic surface helps the formation of a more uniform silver nanoparticle thin film, and CTAB acts as a molecular spacer to keep the silver nanoparticles at a distance. A series of CTAB concentrations is investigated to optimize the interparticle distance and aggregation status. The silver nanoparticle thin films prepared on regular and hydrophobic surfaces are compared. Rhodamine 6G is used as a probe to characterize the thin films as SERS substrates. SERS enhancement without the contribution of the resonance of the thin film prepared on the hydrophobic surface is calculated as 2×10⁷ for rhodamine 6G, which is about one order of magnitude greater than that of the silver nanoparticle aggregates prepared with CTAB on regular glass surfaces and two orders of magnitude greater than that of the silver nanoparticle aggregates prepared without CTAB on regular glass surfaces. A hydrophobic surface and the presence of CTAB have an increased effect on the charge‐transfer component of the SERS enhancement mechanism. The limit of detection for rhodamine 6G is estimated as 1.0×10^?8 M . Scanning electron microscopy and atomic force microscopy are used for the characterization of the prepared substrate.     

Molecular Characterization of DNA Double Strand Breaks with Tip‐Enhanced Raman Scattering

DNA double strand breaks (DSBs) are deadly lesions that can lead to genetic defects and cell apoptosis. Techniques that directly detect DNA DSBs include scanning electron microscopy, atomic force microscopy (AFM), and fluorescence based approaches. While these techniques can be used to identify DSBs they provide no information on the molecular events occurring at the break. Tip‐enhanced Raman scattering (TERS) can provide molecular information from DNA at the nanoscale and in combination with AFM provides a new way to visualize and characterize the molecular structure of DSBs. DSBs result from cleavage at the 3’‐ and 5’‐bonds of deoxyribose upon exposure to UVC radiation based on the observation of P? O? H and methyl/methylene deformation modes enhanced in the TERS spectra. It is hypothesized that strand fragments are hydrogen‐terminated at the lesion, indicating the action of free radicals during photon exposure.     

Distinguishing Individual DNA Bases in a Network by Non‐Resonant Tip‐Enhanced Raman Scattering

The importance of identifying DNA bases at the single‐molecule level is well recognized for many biological applications. Although such identification can be achieved by electrical measurements using special setups, it is still not possible to identify single bases in real space by optical means owing to the diffraction limit. Herein, we demonstrate the outstanding ability of scanning tunneling microscope (STM)‐controlled non‐resonant tip‐enhanced Raman scattering (TERS) to unambiguously distinguish two individual complementary DNA bases (adenine and thymine) with a spatial resolution down to 0.9 nm. The distinct Raman fingerprints identified for the two molecules allow to differentiate in real space individual DNA bases in coupled base pairs. The demonstrated ability of non‐resonant Raman scattering with super‐high spatial resolution will significantly extend the applicability of TERS, opening up new routes for single‐molecule DNA sequencing.     

Monitoring of Endogenous Hydrogen Sulfide in Living Cells Using Surface‐Enhanced Raman Scattering

Hydrogen sulfide (H₂S) has emerged as an important gasotransmitter in diverse physiological processes, although many aspects of its roles remain unclear, partly owing to a lack of robust analytical methods. Herein we report a novel surface‐enhanced Raman scattering (SERS) nanosensor, 4‐acetamidobenzenesulfonyl azide‐functionalized gold nanoparticles (AuNPs/4‐AA), for detecting the endogenous H₂S in living cells. The detection is accomplished with SERS spectrum changes of AuNPs/4‐AA resulting from the reaction of H₂S with 4‐AA on AuNPs. The SERS nanosensor exhibits high selectivity toward H₂S. Furthermore, AuNPs/4‐AA responds to H₂S within 1 min with a 0.1 μM level of sensitivity. In particular, our SERS method can be utilized to monitor the endogenous H₂S generated in living glioma cells, demonstrating its great promise in studies of pathophysiological pathways involving H₂S.     

Noble‐Metal‐Free Materials for Surface‐Enhanced Raman Spectroscopy Detection

Surface‐enhanced Raman spectroscopy (SERS) is an attractive tool for the sensing of molecules in the fields of chemical and biochemical analysis as it enables the sensitive detection of molecular fingerprint information even at the single‐molecule level. In addition to traditional coinage metals in SERS analysis, recent research on noble‐metal‐free materials has also yielded highly sensitive SERS activity. This Minireview presents the recent development of noble‐metal‐free materials as SERS substrates and their potential applications, especially semiconductors and emerging graphene‐based nanostructures. Rather than providing an exhaustive review of this field, possible contributions from semiconductor substrates, characteristics of graphene enhanced Raman scattering, as well as effect factors such as surface plasmon resonance, structure and defects of the nanostructures that are considered essential for SERS activity are emphasized. The intention is to illustrate, through these examples, that the promise of noble‐metal‐free materials for enhancing detection sensitivity can further fuel the development of SERS‐related applications.