DNA-Directed Assembly of Nanogold Dimers: A Unique Dynamic Light Scattering Sensing Probe for Transcription Factor Detection

Signal Transduction Strategies for Analyte Detection Using DNA-Based Nanostructures

The use of DNA-based nanostructures as probes has led to significant advances in chemical and biological sensing, allowing the detection of analytes in complex media, the understanding of fundamental biological processes, and the ability to diagnose diseases based on molecular signatures. The utility of these structures arises both from DNA's inherent ability to selectively recognize and bind a variety of chemical species and from the unique properties observed when DNA is restructured at the nanoscale. In this Minireview, we chronicle the most commonly used signal transduction strategies that have been interfaced with various DNA-based nanostructures. We discuss the types of analytes and the detection scenarios that are sought after, delineate the advantages and disadvantages of each signaling strategy, and outline the key considerations that guide the selection of each signaling method.

Metal Nanoparticles-Enhanced Biosensors: Synthesis, Design and Applications in Fluorescence Enhancement and Surface-enhanced Raman Scattering

Metal nanoparticles (NP) that exhibit localized surface plasmon resonance play an important role in metal-enhanced fluorescence (MEF) and surface-enhanced Raman scattering (SERS). Among the optical biosensors, MEF and SERS stand out to be the most sensitive techniques to detect a wide range of analytes from ions, biomolecules to macromolecules and microorganisms. Particularly, anisotropic metal NPs with strongly enhanced electric field at their sharp corners/edges under a wide range of excitation wavelengths are highly suitable for developing the ultrasensitive plasmon-enhanced biosensors. In this review, we first highlight the reliable methods for the synthesis of anisotropic gold NPs and silver NPs in high yield, as well as their alloys and composites with good control of size and shape. It is followed by the discussion of different sensing mechanisms and recent advances in the MEF and SERS biosensor designs. This includes the review of surface functionalization, bioconjugation and (directed/self) assembly methods as well as the selection/screening of specific biorecognition elements such as aptamers or antibodies for the highly selective bio-detection. The right combinations of metal nanoparticles, biorecognition element and assay design will lead to the successful development of MEF and SERS biosensors targeting different analytes both in-vitro and in-vivo. Finally, the prospects and challenges of metal-enhanced biosensors for future nanomedicine in achieving ultrasensitive and fast medical diagnostics, high-throughput drug discovery as well as effective and reliable theranostic treatment are discussed.

Metal-enhancement study of dual functional photosensitizers with aggregation-induced emission and singlet oxygen generation

Photosensitizers with aggregation-induced emission (AIE-PS) are attractive for image-guided photodynamic therapy due to their dual functional role in generating singlet oxygen and producing high fluorescent signal in the aggregated state. However, their brightness and treatment efficiency maybe limited in current practice. Herein we report the first systematic investigation on the metal-enhanced fluorescence (MEF) and singlet oxygen generation (ME-SOG) ability of our newly synthesized AIE-photosensitizers. The Ag@AIE-PS of varied sizes were prepared via layer-by-layer assembly with controlled distance between silver nanoparticles (AgNPs) and AIE-PS. A maximum of 6-fold enhancement in fluorescence and 2-fold increment in SOG were observed for the 85nmAg@AIE-PS. Comprehensive characterization and simulation were conducted to unravel the plasmon-enhancement mechanisms of Ag@AIE-PS. Results show that MEF of AIE-PS is determined by the enhanced electric field around AgNPs, while ME-SOG is dictated by the scattering efficiency of the metal core, where bigger AgNPs would result in larger enhancement factor. Furthermore, the optimum distance between AgNPs and AIE-PS to achieve maximum SOG enhancement is shorter than that required for the highest MEF. The correlation of MEF and ME-SOG found in this study is useful for designing new a generation of AIE-photosensitizers with high brightness and treatment efficiency towards practical theranostic application in the future.

Simulation guided design of silver nanostructures for plasmon-enhanced fluorescence, singlet oxygen generation and SERS applications

Plasmonic nanostructures such as gold and silver could alter the intrinsic properties of fluorophores, photosensitizers or Raman reporters in their close vicinity. In this study, we have conducted systematic simulations to provide insight for the design of silver nanostructures with appropriate geometrical features for metal-enhanced fluorescence (MEF), metal-enhanced singlet oxygen generation (ME-SOG) and surface-enhanced Raman scattering (SERS) applications. The size-dependent optical properties and electric field enhancement of single and dimeric nanocubes were simulated. The extinction spectra of silver nanocubes were analysed by the multipole expansion method. Results show that a suitable size of Ag nanocubes for MEF and ME-SOG can be selected based on their maximum light scattering yield, the excitation and emission wavelengths of a particular fluorophore/photosensitizer and their maximum spectral overlap. Simulations of the 'hot-spot' or gap distance between two silver nanocubes with different configurations (i.e., face-to-face, edge-to-edge and corner-to-corner) were also performed. A direct correlation was found between the size and enhanced electric field around the Ag nanocubes simulated under 15 common Raman laser wavelengths from the UV to near-infrared region. The maximum SERS enhancement factor can be achieved by selecting the silver nanocubes with the right orientation, suitable edge length and gap distance that give the highest electric field at a specific Raman laser wavelength. It was also found that the higher order of silver nanostructures, e.g., trimer and tetramer, can lead to better enhancement effects. These simulation results can serve as generic guidelines to rationally design metal-enhancement systems including MEF, ME-SOG and SERS for different application needs without cumbersome optimization and tedious trial-and-error experimentation.

Recent development of nucleic acid nanosensors to detect sequence-specific binding interactions: From metal ions, small molecules to proteins and pathogens

DNA carries important genetic instructions and plays vital roles in regulating biological activities in living cells. Proteins such as transcription factors binds to DNA to regulate the biological functions of DNA, and similarly many drug molecules also bind to DNA to modulate its functions. Due to the importance of protein-DNA and drug-DNA binding, there has been intense effort in developing novel nanosensors in the same length scale as DNA, to effectively study these binding interactions in details. In addition, aptamers can be artificially selected to detect metal ions and pathogens such as bacteria and viruses, making nucleic acid nanosensors more versatile in detecting a large variety of analytes. In this minireview, we first explained the different types and binding modes of protein-DNA and drug-DNA interactions in the biological systems, as well as aptamer-target binding. This was followed by the review of five types of nucleic acid nanosensors based on optical or electrochemical detection. The five types of nucleic acid nanosensors utilizing colorimetric, dynamic light scattering (DLS), surface-enhanced Raman spectroscopy (SERS), fluorescence and electrochemical detections have been recently developed to tackle some of the challenges in high-throughput screening technology for large scale analysis, which is especially useful for drug development and mass screening for pandemic outbreak such as SARS or COVID-19.

Gold@Silica Nanoparticles Functionalized with Oligonucleotides: A Prominent Tool for the Detection of the Methylated Reprimo Gene in Gastric Cancer by Dynamic Light Scattering

Reprimo (RPRM) is a tumor suppressor gene involved in the development of gastric cancer. Hypermethylation of the RPRM promoter region has been found in tumor tissue and plasma samples from patients with gastric cancer. These findings suggest that circulating methylated DNA of RPRM could be a candidate for a noninvasive detection of gastric cancer. We designed a nanosystem based on the functionalization of silica coated gold nanoparticles with oligonucleotides that recognize a specific DNA fragment of the RPRM promoter region. The functionality of the oligonucleotide on the surface of the nanoparticle was confirmed by polymerase chain reaction (PCR). The nanoparticles were incubated with a synthetic DNA fragment of methylated DNA of RPRM and changes in the size distribution after hybridization were evaluated by dynamic light scattering (DLS). A difference in the size distribution of nanoparticles hybridized with genomic DNA from the KATO III gastric cancer cell line was observed when was compared with DNA from the GES-1 normal cell line. These results showed that this nanosystem may be a useful tool for the specific and sensitive detection of methylated DNA of RPRM in patients at risk of developing gastric cancer.

The bioconjugation of DNA with gold nanoparticles towards the spectrophotometric genosensing of pathogenic bacteria

The investigation of important bio-molecular events such as expression of special genes has shown promise with the advent of nanotechnology.

Detecting transcription factors with allosteric DNA-Silver nanocluster switches

Sensitive and efficient detection of protein markers, such as transcription factors (TFs), is an important issue in postgenomic era. In this paper, we report a DNA nanodevice, allosteric DNA-silver nanocluster switches (AgSwitches), for TFs detection. The mechanism of this nanodevice is based on the binding-induced allostery whereby the binding between AgSwitches and TFs alters the conformation of AgSwitches. This alteration brings DNA-silver nanocluster (DNA-AgNCs) and guanine-rich enhancer sequences (GRS) into close proximity, generating fluorescent enhancement for quantifications. Our results revealed that the sequence design of AgSwitches can be rationally optimized according to stimulated free energy, and we demonstrated that this method can not only be used for detecting TFs in nuclear extracts of cells, but also be developed as a tool for screening inhibitors of TFs. Overall, this work expanded the category allosteric DNA nanodevices by first introducing DNA-AgNCs into this area, and the obtained method was efficient for TFs-related investigations.

Spectroscopic and Hydrodynamic Characterisation of DNA-Linked Gold Nanoparticle Dimers in Solution using Two-Photon Photoluminescence

Two-photon photoluminescence (TPPL) emission spectra of DNA-gold nanoparticle (AuNP) monoconjugates and the corresponding DNA-linked AuNP dimers are obtained by photon time-of-flight spectroscopy. This technique is combined with two-photon photoluminescence fluctuation correlation spectroscopy (TPPL-FCS) to simultaneously monitor the optical and hydrodynamic behaviour of these nano-assemblies in solution, with single-particle sensitivity and microsecond temporal resolution. In this study, the AuNPs have an average core diameter of 12 nm, which renders their dark-field plasmonic light scattering too weak for single-particle imaging. Moreover, as a result of the lack of plasmonic coupling in the dimers, the optical extinction, scattering and photoluminescence spectra of the DNA-AuNP complexes are not sufficiently different to distinguish between monomers and dimers. The use of TPPL-FCS successfully addresses these bottlenecks and enables the distinction between AuNP monomers and AuNP dimers in solution by measurement of their hydrodynamic rotational and translational diffusion.

A simple and sensitive sensor for silver ions based on unmodified gold nanoparticles by using dynamic light scattering techniques

A simple and sensitive assay for Ag+ was developed with unmodified gold nanoparticles (AuNPs) by using dynamic light scattering techniques. Ag+ could induce the oligonucleotide (5′-ATC ACT ATA TCA TAT ACT CAT-3′) to change from a single-stranded structure to a double-stranded structure and desorb from the surface of AuNPs, which triggered the aggregation of AuNPs in the salt solution. The average hydrodynamic diameter of aggregated AuNPs could be detected by using dynamic light scattering techniques. Under the optimum conditions, the average hydrodynamic diameter of AuNPs is proportional to the concentration of Ag+ within the range of 13.3–100.0 nmol/L, with a detection limit of 3.2 nmol/L. The method is easy to operate and has low sample consumption, high sensitivity and selectivity.

Single-Step DNA Detection Assay Monitoring Dual-Color Light Scattering from Individual Metal Nanoparticle Aggregates

Efficiently detecting DNA sequences within a limited time is vital for disease screening and public health monitoring. This calls for a new method that combines high sensitivity, fast read-out time, and easy manipulation of the sample, avoiding the extensive steps of DNA amplification, purification, or grafting to a surface. Here, we introduce photon cross-correlation spectroscopy as a new method for specific DNA sensing with high sensitivity in a single-step homogeneous solution phase. Our approach is based on confocal dual-color illumination and detection of the scattering intensities from individual silver nanoparticles and gold nanorods. In the absence of the target DNA, the nanoparticles move independently and their respective scattering signals are uncorrelated. In the presence of the target DNA, the probe-functionalized gold and silver nanoparticles assemble via DNA hybridization with the target, giving rise to temporal coincidence between the signals scattered by each nanoparticle. The degree of coincidence accurately quantifies the amount of target DNA. To demonstrate the efficiency of our technique, we detect a specific DNA sequence of sesame, an allergenic food ingredient, for a range of concentration from 5 pM to 1.5 nM with a limit of detection of 1 pM. Our method is sensitive and specific enough to detect single nucleotide deletion and mismatch. With the dual-color scattering signals being much brighter than fluorescence-based analogs, the analysis is fast, quantitative, and simple to operate, making it valuable for biosensing applications.