Fluorescence quenching of quantum dots by gold nanoparticles: a potential long range spectroscopic ruler

Freeze response indicators in sugarcane (Saccharum spp. hybrids)

A recent series of extreme weather events in Southern U.S. (2022 winter freeze followed by 2023 summer drought) calls for quantitative markers to expedite the release of climate resilient sugarcane varieties. A cluster analysis revealed potential markers for freeze damage including fluorescent amino acids. Of 8 cultivars investigated, tolerant variety HoCP 04-838 sustained 3-5 fold lower stalk fracture from the freeze; contained among the highest fiber; and maintained the lowest particulate juice decomposition byproducts (p<0.05). Based on those observations, fluorescence cellular markers were developed in fiber components of sugarcane to assess cold tolerance. Fluorescence microscopy visualized a cluster of markers in lignin cells around the vascular bundles of HoCP 04-838, within the far-red emission ranges attributable to lipids and other hydrophobic components. Cellular distributions of markers were made visible using fluorescent nanoparticles designed to enhance cellular uptake and imaging at wider wavelengths. Developed chemical phenotyping approaches offer advantages over post-freeze damage assessment currently used in the breeding program, as no genetic marker exists for cold tolerance of sugarcane.

Towards the Development of an Optical Biosensor for the Detection of Human Blood for Forensic Analysis

Blood is a common biological fluid in forensic investigations, offering significant evidential value. Currently employed presumptive blood tests often lack specificity and are sample destructive, which can compromise downstream analysis. Within this study, the development of an optical biosensor for detecting human red blood cells (RBCs) has been explored to address such limitations. Aptamer-based biosensors, termed aptasensors, offer a promising alternative due to their high specificity and affinity for target analytes. Aptamers are short, single-stranded DNA or RNA sequences that form stable three-dimensional structures, allowing them to bind to specific targets selectively. A nanoflare design has been employed within this work, consisting of a quenching gold nanoparticle (AuNP), DNA aptamer sequences, and complementary fluorophore-labelled flares operating through a fluorescence resonance energy transfer (FRET) mechanism. In the presence of RBCs, the aptamer-flare complex is disrupted, restoring fluorescence and indicating the presence of blood. Two aptamers, N1 and BB1, with a demonstrated binding affinity to RBCs, were selected for inclusion within the nanoflare. This study aimed to optimise three features of the design: aptamer conjugation to AuNPs, aptamer hybridisation to complementary flares, and flare displacement in the presence of RBCs. Fluorescence restoration was achieved with both the N1 and BB1 nanoflares, demonstrating the potential for a functional biosensor to be utilised within the forensic workflow. It is hoped that introducing such an aptasensor could enhance the forensic workflow. This aptasensor could replace current tests with a specific and sensitive reagent that can be used for real-time detection, improving the standard of forensic blood analysis.

Energy Transfer Between i-Motif DNA Encapsulated Silver Nanoclusters and Fluorescein Amidite Efficiently Visualizes the Redox State of Live Cells

The redox regulation, maintaining a balance between oxidation and reduction in living cells, is vital for cellular homeostasis, intricate signaling networks, and appropriate responses to physiological and environmental cues. Here, a novel redox sensor, based on DNA-encapsulated silver nanoclusters (DNA/AgNCs) and well-defined chemical fluorophores, effectively illustrating cellular redox states in live cells is introduced. Among various i-motif DNAs, the photophysical property of poly-cytosines (C20)-encapsulated AgNCs that sense reactive oxygen species (ROS) is adopted. However, the sensitivity of C20/AgNCs is insufficient for evaluating ROS levels in live cells. To overcome this drawback, the ROS sensing mechanism of C20/AgNCs through gel electrophoresis, mass spectrometry, and small-angle X-ray scattering is primarily defined. Then, by tethering fluorescein amidite (FAM) and Cyanine 5 (Cy5) dyes to each end of the C20/AgNCs sensor, an Energy Transfer (ET) between AgNCs and FAM is achieved, resulting in intensified green fluorescence upon ROS detection. Taken together, the FAM-C20/AgNCs-Cy5 redox sensor enables dynamic visualization of intracellular redox states, yielding insights into oxidative stress-related processes in live cells.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

Lab-on-a-DNA origami: nanoengineered single-molecule platforms

DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.

Tailoring of hydroxyapatite nanoparticle surfaces of varying morphologies to facilitate counterion diffusion and subsequent protein denaturation

Rapid advances in nanotechnology have led to the synthesis and development of various nanomaterials with complex structures and appropriate surface functionalization in recent years. Specifically designed and functionalized nanoparticles (NPs) are increasingly researched and hold great potential in biomedical applications (for example, imaging, diagnostics and therapeutics). Yet, the surface functionalization and biodegradability of NPs play a significant role in their application. Understanding the interactions occurring at the interface between the NPs and the biological components is thus crucial for predicting the fate of the NPs. In this work we study the effect of trilithium citrate functionalization of the hydroxyapatite NPs (HAp NPs) with and without cysteamine modification and their subsequent interaction with hen egg white lysozyme and corroborate the conformational changes of the protein with effective diffusion of the lithium (Li⁺) counter ion.

A hybrid photonic-plasmonic resonator based on a partially encapsulated 1D photonic crystal waveguide and a plasmonic nanoparticle

In this paper, a hybrid photonic-plasmonic resonator is proposed. The device consists of a partially encapsulated 1D photonic crystal waveguide and a plasmonic nanoparticle to yield high radiation efficiency for integrated photonic platforms, owing to a high Q-factor and a small mode volume. The design of the resonator is accomplished in two consecutive steps: first of all, a partially encapsulated photonic crystal nanobeam with a robust mechanical stability and a high-Q factor is prepared; secondly, a plasmonic nanoparticle is placed on the surface of the nanobeam to interact the optical mode with the localized surface plasmons of the gold nanoparticle which is being present in the vicinity of the radiating dipole. Strongly enhanced electromagnetic field, regenerated through the optical mode field inside the hybrid resonator, enables to reduce the optical mode volume of the device and significantly enhance the Purcell factor.

One-Step Ligand-Exchange Method to Produce Quantum Dot-DNA Conjugates for DNA-Directed Self-Assembly

To address the current challenges in making bright, stable, and small DNA-functionalized quantum dots (QDs), we have developed a one-step ligand-exchange method to produce QD-DNA conjugates from commonly available hydrophobic QDs. We show that by systematically adjusting the reaction conditions such as ligand-to-nanoparticle molar ratio, pH, and solvent composition, stable and highly photoluminescent water-soluble QD-DNA conjugates with relatively high ligand loadings can be produced. Moreover, by site specifically binding these QD-DNA conjugates to a DNA origami template, we demonstrate that these bioconjugates have sufficient colloidal stability for DNA-directed self-assembly. Fluorescence quenching by an adjacent gold nanoparticle (AuNP) was demonstrated. Such QD-AuNP dimers may serve as biosensors with improved sensitivity and reproducibility. Moreover, our simple method can facilitate the assembly of QDs into more complex superlattices and discrete clusters that may enable novel photophysical properties.

Dye-sensitized lanthanide containing nanoparticles for luminescence based applications

Due to their exceptional luminescent properties, lanthanide (Ln) complexes represent a unique palette of probes in the spectroscopic toolkit. Their extremely weak brightness due to forbidden Ln electronic transitions can be overcome by indirect dye-sensitization from the antenna effect brought by organic ligands. Despite the improvement brought by the antenna effect, (bio)analytical applications with discrete Ln complexes as luminescent markers still suffers from low sensitivity as they are limited by the complex brightness. Thus, there is a need to develop nano-objects that cumulate the spectroscopic properties of multiple Ln ions. This review firstly gives a brief introduction of the spectral properties of lanthanides both in complexes and in nanoparticles (NPs). Then, the research progress of the design of Ln-doped inorganic NPs with capping antennas, Ln-complex encapsulated NPs and Ln-complex surface functionalized NPs is presented along with a summary of the various photosensitizing ligands and of the spectroscopic properties (excited-state lifetime, brightness, quantum yield). The review also emphasizes the problems and limitations encountered over the years and the solutions provided to address them. Finally, a comparison of the advantages and drawbacks of the three types of NP is provided as well as a conclusion about the remaining challenges both in the design of brighter NPs and in the luminescence based applications.

Back to the Drawing Board: A Unifying First-Principle Model for Correlating Sample UV-Vis Absorption and Fluorescence Emission

The popular textbook and literature model I(λ_x,λ_m) = K(λx,λm)(1-10-Ax) or its variants for correlating the sample absorption and fluorescence often fails even for the simplest samples where the fluorophore is the only light absorber. Reported is a first-principle model I(λ_x,λ_m) = K(λx,λm)Ax,f10-(Ax,sdx+Am,sdm) for correlating the sample fluorescence measured with a conventional spectrofluorometer and its UV-vis absorbance quantified with a conventional UV-vis spectrophotometer. This model can be simplified or expanded for a variety of fluorescence analyses. First, it enables curve-fitting fluorescence intensity as a function of the fluorophore or sample absorbance over a sample concentration range impossible with existing models. Second, it provides the theoretical foundation for an inner-filter-effect (IFE)-correction method developed earlier and explains mathematically the linearity between the IFE-corrected fluorescence and the fluorophore concentration or absorbance. Third, this model can be expanded for quantitative mechanistic studies of fluorescence intensity variations triggered by stimuli treatments. One demonstrated example is to quantify temperature effects on the emission-wavelength-specific and total fluorescence quantum yield of anthracene. We expect that this first-principle model will be broadly adopted for both student education that promotes evidence-based learning and a variety of fluorescence applications where disentangling sample absorption and emission are critical for reliable data analysis.

Fluorescence DNA Switch for Highly Sensitive Detection of miRNA Amplified by Duplex-Specific Nuclease

DNA is a type of promising material for the construction of sensors owing to its sequence programmability to control the formation of certain structures. MicroRNA (miRNA) can be applied as promising biomarkers for the diagnosis of a range of diseases. Herein, a novel fluorescent sensing strategy for miRNA is proposed combining duplex-specific nuclease (DSN)-mediated amplification and dumbbell DNA structural switch. Gold nanoparticles (AuNPs) are employed, which provide a 3D reaction interface. They also act as effective fluorescence quenchers. The proposed sensor exhibits high sensitivity (sub-femtomolar level) with a wide dynamic range. In addition, excellent selectivity to distinguish homology sequences is achieved. It also performs satisfactorily in biological samples. Overall, this fluorescent sensor provides a powerful tool for the analysis of miRNA levels and can be applied for related biological studies and clinical diagnosis.

Recent Progress of Magnetically Actuated DNA Micro/Nanorobots

In the past few decades, the field of DNA origami-based micro/nanotechnology has developed dramatically and spawned attention increasingly, as its high integrality, rigid structure, and excellent resistance ability to enzyme digestion. Many two-dimensional and three-dimensional DNA nanostructures coordinated with optical, chemical, or magnetic triggers have been designed and assembled, extensively used as versatile templates for molecular robots, nanosensors, and intracellular drug delivery. The magnetic field has been widely regarded as an ideal driving and operating system for micro/nanomaterials, as it does not require high-intensity lasers like light control, nor does it need to change the chemical composition similar to chemical activation. Herein, we review the recent achievements in the induction and actuation of DNA origami-based nanodevices that respond to magnetic fields. These magnetic actuation-based DNA nanodevices were regularly combined with magnetic beads or gold nanoparticles and applied to generate single-stranded scaffolds, assemble various DNA nanostructures, and purify specific DNA nanostructures. Moreover, they also produced artificial magnetism or moved regularly driven by external magnetic fields to explain deeper scientific issues.

Targeting the Extracellular Matrix in Traumatic Brain Injury Increases Signal Generation from an Activity-Based Nanosensor

Traumatic brain injury (TBI) is a critical public health concern and major contributor to death and long-term disability. After the initial trauma, a sustained secondary injury involving a complex continuum of pathophysiology unfolds, ultimately leading to the destruction of nervous tissue. One disease hallmark of TBI is ectopic protease activity, which can mediate cell death, extracellular matrix breakdown, and inflammation. We previously engineered a fluorogenic activity-based nanosensor for TBI (TBI-ABN) that passively accumulates in the injured brain across the disrupted vasculature and generates fluorescent signal in response to calpain-1 cleavage, thus enabling in situ visualization of TBI-associated calpain-1 protease activity. In this work, we hypothesized that actively targeting the extracellular matrix (ECM) of the injured brain would improve nanosensor accumulation in the injured brain beyond passive delivery alone and lead to increased nanosensor activation. We evaluated several peptides that bind exposed/enriched ECM constituents in the brain and discovered that nanomaterials modified with peptides that target hyaluronic acid (HA) displayed widespread distribution across the injury lesion, in particular colocalizing with perilesional and hippocampal neurons. Modifying TBI-ABN with HA-targeting peptide led to increases in activation in a ligand-valency-dependent manner, up to 6.6-fold in the injured cortex compared to a nontargeted nanosensor. This robust nanosensor activation enabled 3D visualization of injury-specific protease activity in a cleared and intact brain. In our work, we establish that targeting brain ECM with peptide ligands can be leveraged to improve the distribution and function of a bioresponsive imaging nanomaterial.

An ultra-sensitive optical aptasensor based on gold nanoparticles/poly vinyl alcohol hydrogel as acceptor/emitter pair for fluorometric detection of digoxin with on/off/on strategy

A novel nanobiosensor was prepared by aptamer and gold nanoparticles conjugate in poly vinyl alcohol hydrogel for sensitive detection of digoxin in human plasma samples. The developed nanobiosensor was characterized by Fourier transform infrared spectroscopy, transmission electron microscopy, and dynamic light scattering instrument. In this sensor the hydrogel acted as a fluorescent probe. The fluorescence intensity of the hydrogel was quenched by aptamer stabilized gold nanoparticles as energy acceptor. Upon addition of digoxin, the aptamer/drug complex was formed and the fluorescence of the hydrogel was restored because of destabilization and aggregation of gold nanoparticles in the presence of salt. The affecting parameters on the nanobiosensor performance were assessed and under the optimized conditions the external and in plasma calibration curves were linear in the 10-1000 ng L^-1 digoxin concentration range with detection limits of 2.9 and 3.1 ng L^-1, respectively. The relative standard deviations for 5 replicate determinations of 50, 250, and 500 ng L^-1 of digoxin, were 7.3, 5.1, and 3.8%, respectively. This nanofluoroprobe was successfully applied for determination of digoxin in spiked plasma samples without any pretreatment procedure.

Fluorescence-based immunoassay for the detection of Xanthomonas oryzae pv. oryzae in rice leaf

The identification of rice bacterial leaf blight disease requires a simple, rapid, highly sensitive, and quantitative approach that can be applied as an early detection monitoring tool in rice health. This paper highlights the development of a turn-off fluorescence-based immunoassay for the early detection of Xanthomonas oryzae pv. oryzae (Xoo), a gram-negative bacterium that causes rice bacterial leaf blight disease. Antibodies against Xoo bacterial cells were produced as specific bio-recognition molecules and the conjugation of these antibodies with graphene quantum dots and gold nanoparticles was performed and characterized, respectively. The combination of both these bio-probes as a fluorescent donor and metal quencher led to changes in the fluorescence signal. The immunoreaction between AntiXoo-GQDs, Xoo cells, and AntiXoo-AuNPs in the immuno-aggregation complex led to the energy transfer in the turn-off fluorescence-based quenching system. The change in fluorescence intensity was proportional to the logarithm of Xoo cells in the range of 10⁰-10⁵ CFU mL^-1. The limit of detection was achieved at 22 CFU mL^-1 and the specificity test against other plant disease pathogens showed high specificity towards Xoo. The detection of Xoo in real plant samples was also performed in this study and demonstrated satisfactory results.

Metal nanoparticle alters adenine induced charge transfer kinetics of vitamin K3 in magnetic field

In this article, we highlight the alterations in the photoinduced electron transfer (ET) and hydrogen atom transfer (HAT) pathways between an anti-tumor drug vitamin-K3 (MQ) and a nucleobase adenine (ADN) in the presence of gold (Au) and iron (Fe) nanoparticles (NPs). Inside the confined micellar media, with laser flash photolysis corroborated with an external magnetic field (MF), we have detected the transient geminate radicals of MQ and ADN, photo-generated through ET and HAT. We observe that the presence of AuNP on the MQ-ADN complex (^AuMQ-ADN) assists HAT by limiting the ET channel, on the other hand, FeNP on the MQ-ADN complex (^FeMQ-ADN) mostly favors a facile PET. We hypothesize that through selective interactions of the ADN molecules with AuNP and MQ molecules with FeNP, a preferential HAT and PET process is eased. The enhanced HAT and PET have been confirmed by the escape yields of radical intermediates by time-resolved transient absorption spectroscopy in the presence of MF.

Enhancing FRET biosensing beyond 10 nm with photon avalanche nanoparticles

Förster Resonance Energy Transfer (FRET) between donor (D) and acceptor (A) molecules is a phenomenon commonly exploited to study or visualize biological interactions at the molecular level. However, commonly used organic D and A molecules often suffer from photobleaching and spectral bleed-through, and their spectral properties hinder quantitative analysis. Lanthanide-doped upconverting nanoparticles (UCNPs) as alternative D species offer significant improvements in terms of photostability, spectral purity and background-free luminescence detection, but they bring new challenges related to multiple donor ions existing in a single large size UCNP and the need for nanoparticle biofunctionalization. Considering the relatively short Förster distance (typically below 5-7 nm), it becomes a non-trivial task to assure sufficiently strong D-A interaction, which translates directly to the sensitivity of such bio-sensors. In this work we propose a solution to these issues, which employs the photon avalanche (PA) phenomenon in lanthanide-doped materials. Using theoretical modelling, we predict that these PA systems would be highly susceptible to the presence of A and that the estimated sensitivity range extends to distances 2 to 4 times longer (i.e. 10-25 nm) than those typically found in conventional FRET systems. This promises high sensitivity, low background and spectral or temporal biosensing, and provides the basis for a radically novel approach to combine luminescence imaging and self-normalized bio-molecular interaction sensing.

A novel strategy for detection of small molecules based on aptamer/gold nanoparticles/graphitic carbon nitride nanosheets as fluorescent biosensor

Herein, a novel ultrasensitive strategy has been developed by designing a label free fluorescent nano-aptasensor for monitoring of small moecules in human plasma. In this nano-aptasensor, graphitic carbon nitride nanosheets were used as fluorescent probe. The fluorescence intensity of the probe was decreased by interaction between graphitic carbon nitride nanosheets and label-free aptamer/gold nanoparticles conjugate, via Fluorescence resonance energy transfer mechanism. Upon addition of the analyte, the fluorescence of graphitic carbon nitride nanosheets was restored due to the aptamer/analyte interaction, and the aggregation of gold nanoparticles in the presence of salt. The influence of various factors on sensing method was investigated, and under the approved conditions, the fluorescence signal showed a linear relation with Digoxin concentration in the range of 10-500 ng L^-1 with limit of detection down to 3.2 ng L^-1 relative standard deviations for 25, 100 and 500 ng L^-1 of analyte concentrations were 2.6, 4.0 and 6.5%, respectively. This strategy provided a simple, rapid, cost effective and reproducible experimental model, with successful application for determination of Digoxin in plasma samples without any pretreatment steps.

Programmable Assembly of Iron Oxide Nanoparticles Using DNA Origami

Magnetic iron oxide nanoparticles (IONPs) have received significant interest for the use in biomedical applications. The assembly of IONPs into larger superstructures has been used to modify the properties and functionality of these particles. For example, the clustering of IONPs can lead to improvements in MRI contrast generation, changes in heat generation during magnetic fluid hyperthermia, and alterations to pharmacokinetics and biodistribution. Nevertheless, the IONP clustering leads to significant heterogeneity in the assembly. Here, we demonstrate a method for using DNA origami to precisely control the number and positions of IONPs. We also showed how this technique can be used to module the functionality of IONP clusters by showing how MRI contrast generation efficiency can be tuned by altering the number and spacing of IONPs. Finally, we show that these property changes can be dynamically regulated, demonstrating the possibility for this technology to be used in biosensing applications.

Colloidal Assembly of Au-Quantum Dot-Au Sandwiched Nanostructures with Strong Plasmon-Exciton Coupling

Strong plasmon-exciton coupling could occur in hybrid metal-dye/semiconductor nanostructures, where the fast energy exchange between plasmons and excitons leads to two new eigenmodes of the system, known as Rabi splitting. In experiments, strongly coupled nanosystems are difficult to obtain because they require some strict conditions, such as low plasmonic damping, small plasmon mode volume, and good spectral overlap. This work demonstrates strongly coupled metal-semiconductor nanostructures can be constructed using colloidal assembly. Specifically, sandwiched Au-quantum dot-Au nanostructures were created through the assembly of Au nanoparticles and colloidal quantum dots (QDs). The sizes of the QDs and the assembly conditions were varied to control the mode volume of the plasmonic cavity formed between the two Au nanoparticles. With a decreased gap size, Rabi splitting was observed in both dark-field scattering and fluorescence spectra of single Au-QD-Au nanostructures. Theoretical simulations revealed that the strong coupling occurred between the excitons and the octupolar plasmon modes.

Long-Range Single-Molecule Förster Resonance Energy Transfer between Alexa Dyes in Zero-Mode Waveguides

Zero-mode waveguide (ZMW) nano-apertures milled in metal films were proposed to improve the Förster resonance energy transfer (FRET) efficiency and enable single-molecule FRET detection beyond the 10 nm barrier, overcoming the restrictions of diffraction-limited detection in a homogeneous medium. However, the earlier ZMW demonstrations were limited to the Atto 550-Atto 647N fluorophore pair, asking the question whether the FRET enhancement observation was an artifact related to this specific set of fluorescent dyes. Here, we use Alexa Fluor 546 and Alexa Fluor 647 to investigate single-molecule FRET at large donor-acceptor separations exceeding 10 nm inside ZMWs. These Alexa fluorescent dyes feature a markedly different chemical structure, surface charge, and hydrophobicity as compared to their Atto counterparts. Our single molecule data on Alexa 546-Alexa 647 demonstrate enhanced FRET efficiencies at large separations exceeding 10 nm, extending the spatial range available for FRET and confirming the earlier conclusions. By showing that the FRET enhancement inside a ZMW does not depend on the set of fluorescent dyes, this report is an important step to establish the relevance of ZMWs to extend the sensitivity and detection range of FRET, while preserving its ability to work on regular fluorescent dye pairs.

One-step and ultrasensitive ATP detection by using positively charged nano-gold@graphene oxide as a versatile nanocomposite

A versatile nanocomposite was simply prepared based upon the electrostatic adsorption of positively charged gold nanoparticles with negatively charged graphene oxide (nano-gold@GO), and utilized as a novel fluorescence quenching platform for ultrasensitive detection of adenosine triphosphate (ATP). In the designed system, DNA-stabilized Ag nanoclusters (DNA/AgNCs) were used as fluorescent probes, DNA duplex was formed in the presence of ATP, and they can electrostatically adsorb onto the surface of nano-gold@GO to quench the fluorescence signal. Upon the addition of exonuclease III (Exo III), the DNA duplex would be hydrolyzed into DNA fragments and resulted in the recovery of the fluorescence signals due to the diffusion of AgNCs away from nano-gold@GO. Based on these, sensitive detection of ATP was realized with a detection range of 5.0 pM-20 nM. Notably, a good recovery in the range of 94-104% was obtained when detecting ATP in human serum samples, indicating a promising application value in early disease diagnosis. Graphical abstract A functional positively charged nano-gold@graphene oxide was fabricated and utilized as an enhanced fluorescence quenching platform for the detection of ATP, coupled with exonuclease III-assisted signal amplification.

Aptamer-based cocaine assay using a nanohybrid composed of ZnS/Ag2Se quantum dots, graphene oxide and gold nanoparticles as a fluorescent probe

Authors report on a new fluoro-graphene-plasmonic nanohybrid aptamer-based fluorescent nanoprobe for cocaine. To construct the nanoprobe, newly synthesized glutathione-capped ZnS/Ag₂Se quantum dots (QDs) were first conjugated to graphene oxide (GO) to form a QD-GO nanocomposite. The binding interaction resulted in a fluorescence turn-ON. Thereafter, cetyltrimethylammonium bromide (CTAB)-gold nanoparticles (AuNPs) were directly adsorbed on the QD-GO nanocomposite to form a novel QD-GO-CTAB-AuNP nanohybrid assembly that resulted in a fluorescence turn-OFF. Streptavidin (strep) was then adsorbed on the QDs-GO-CTAB-AuNP nanohybrid assembly which allowed binding to a biotinylated MNS 4.1 anticocaine DNA aptamer (B) receptor. The addition of cocaine into the strep-B-QDs-GO-CTAB-AuNP aptamer nanoprobe system aided affinity to the aptamer receptor and in turn turned on the fluorescence of the nanoprobe in a concentration-dependent manner. Under optimum experimental conditions, we found the strep-B-QD-GO-CTAB-AuNP to be far superior in its sensitivity to cocaine than the tested strep-B-QDs (no GO and CTAB-AuNPs), strep-B-QD-CTAB-AuNP (no GO) and strep-B-QD-GO (no CTAB-AuNP). In addition, the investigation of localized surface plasmon resonance (LSPR) amplified signal from tested plasmonic NPs shows that CTAB-AuNPs was far superior in amplifying the fluorescence signal of the nanoprobe. A detection limit of 4.6 nM (1.56 ng.mL⁻¹), rapid response time (~2 min) and excellent selectivity against other drugs, substances and cocaine metabolites was achieved. The strep-B-QD-GO-CTAB-AuNP aptamer-based fluorescent nanoprobe was successfully applied for the determination of cocaine in seized adulterated cocaine samples.

Graphical abstract

NIR-Emitting Gold Nanoclusters-Modified Gelatin Nanoparticles as a Bioimaging Agent in Tissue

Gold nanocluster (AuNC) synthesis using a well-distinguished polymer for nanoparticle-mediated drug delivery paves the way for developing efficient theranostics based on pharmaceutically accepted materials. Gelatin-stabilized AuNCs are synthesized and modified by glutathione for tuning the emission spectra. Addition of silver ions enhances the fluorescence, reaching also high quantum yield (26.7%). A simplified model can be proposed describing the nanoclusters' properties-structure relationship based on X-ray photoelectron spectroscopy data and synthesis sequence. Furthermore, these modifications improve fluorescence stability toward pH changes and enzymatic degradation, offering different AuNCs for various applications. The impact of nanocluster formation on gelatin structure integrity is investigated by Fourier transform infrared spectrometry and matrix-assisted laser desorption/ionization time of flight mass spectroscopy, being important to further formulate gelatin nanoparticles (GNPs). The 218 nm-sized NPs show no cytotoxicity up to 600 µg mL^-1 and are imaged in skin, as a challenging autofluorescent tissue, by confocal microscopy, when transcutaneously delivered using dissolving microneedles. Linear unmixing allows simultaneous imaging of AuNCs-GNPs and skin with accurate signal separation. This underlines the great potential for bioimaging of this system to better understand nanomaterials' behavior in tissue. Additionally, it is drug delivery system also potentially serving as a theranostic system.

Luminescence enhancement of alloyed quantum dots bound to gold nanoparticles by mercaptocarboxylic acids in colloidal complexes

The understanding of the physical mechanisms of the nanoobjects interaction within the nanostructured complex materials is one of the main tasks for the development of novel materials with tunable properties. In this work, we develop a formation procedure of the colloidal complexes based on alloyed CdZnSe/ZnS quantum dots and gold nanoparticles where the various mercaptocarboxylic acids are used as the binding molecules. The QD photoluminescence enhancement (up to ×3.1) can be achieved by the control of the interparticle distance in colloidal solutions. We provide a detailed discussion on the influence of the linking molecules on the nanoparticle complexes optical parameters through the steady-state and time-resolved spectral measurements.

Functional Macromolecule-Enabled Colloidal Synthesis: From Nanoparticle Engineering to Multifunctionality

The synthesis of well-defined inorganic colloidal nanostructures using functional macromolecules is an enabling technology that offers the possibility of fine-tuning the physicochemical properties of nanomaterials and has contributed to a broad range of practical applications. The utilization of functional reactive polymers and their colloidal assemblies leads to a high level of control over structural parameters of inorganic nanoparticles that are not easily accessible by conventional methods based on small-molecule ligands. Recent advances in polymerization techniques for synthetic polymers and newly exploited functions of natural biomacromolecules have opened up new avenues to monodisperse and multifunctional nanostructures consisting of integrated components with distinct chemistries but complementary properties. Here, the evolution of colloidal synthesis of inorganic nanoparticles is revisited. Then, the new developments of colloidal synthesis enabled by functional macromolecules and practical applications associated with the resulting optical, catalytic, and structural properties of colloidal nanostructures are summarized. Finally, a perspective on new and promising pathways to novel colloidal nanostructures built upon the continuous development of polymer chemistry, colloidal science, and nanochemistry is provided.

Compact quantum dot surface modification to enable emergent behaviors in quantum dot-DNA composites

Quantum dot (QD) biological imaging and sensing applications often require surface modification with single-stranded deoxyribonucleic acid (ssDNA) oligonucleotides. Furthermore, ssDNA conjugation can be leveraged for precision QD templating via higher-order DNA nanostructures to exploit emergent behaviors in photonic applications. Use of ssDNA-QDs across these platforms requires compact, controlled conjugation that engenders QD stability over a wide pH range and in solutions of high ionic strength. However, current ssDNA-QD conjugation approaches suffer from limitations, such as the requirement for thick coatings, low control over ssDNA labeling density, requirement of large amounts of ssDNA, or low colloidal or photostability, restraining implementation in many applications. Here, we combine thin, multidentate, phytochelatin-3 (PC3) QD passivation techniques with strain-promoted copper-free alkyne-azide click chemistry to yield functional ssDNA-QDs with high stability. This process was broadly applicable across QD sizes (i.e., λ_em = 540, 560, 600 nm), ssDNA lengths (i.e., 10-16 base pairs, bps), and sequences (poly thymine, mixed bps). The resulting compact ssDNA-QDs displayed a fluorescence quenching efficiency of up to 89% by hybridization with complementary ssDNA-AuNPs. Furthermore, ssDNA-QDs were successfully incorporated with higher-order DNA origami nanostructure templates. Thus, this approach, combining PC3 passivation with click chemistry, generates ssDNA-PC3-QDs that enable emergent QD properties in DNA-based devices and applications.

Gold nanostructures for the sensing of pH using a smartphone

Recently, metal nanostructures have been found to be capable of recognizing small changes in their surrounding environment, which can be utilized as significant sensing tools. In this study, we demonstrated colorimetric sensing of pH by gold nanostructures (GNs) using a simple smartphone. An indigenously developed Android app based on the CIELab 1931 analysis, which could run in a smartphone, was used for the precise determination of the pH value of liquid media. The pH value of an unknown solution obtained from the developed Android app was also compared with that obtained from the conventional ratiometric technique and a commercial pH meter. In another endeavor, it was found that the synthesized GNs demonstrated a high energy transfer efficiency from a donor (namely, the rhodamine 6G, (Rh 6G)) dye. This property of the GNs can be utilized further in the future for studying different bimolecular activities within the human body. It was found that the photoluminescence (PL) of Rh 6G was quenched when it was kept in the vicinity of the synthesized GNs, which was explained in terms of the Förster energy transfer mechanism. Thus, the present study will open up a plethora of opportunities for researchers to employ the nanostructures of gold and other metals in developing low-cost and Internet of Things (IoT)-based sensing devices using only a smart phone.

Extending Single-Molecule Förster Resonance Energy Transfer (FRET) Range beyond 10 Nanometers in Zero-Mode Waveguides

Single-molecule Förster resonance energy transfer (smFRET) is widely used to monitor conformations and interaction dynamics at the molecular level. However, conventional smFRET measurements are ineffective at donor-acceptor distances exceeding 10 nm, impeding the studies on biomolecules of larger size. Here, we show that zero-mode waveguide (ZMW) apertures can be used to overcome the 10 nm barrier in smFRET. Using an optimized ZMW structure, we demonstrate smFRET between standard commercial fluorophores up to 13.6 nm distance with a significantly improved FRET efficiency. To further break into the classical FRET range limit, ZMWs are combined with molecular constructs featuring multiple acceptor dyes to achieve high FRET efficiencies together with high fluorescence count rates. As we discuss general guidelines for quantitative smFRET measurements inside ZMWs, the technique can be readily applied for monitoring conformations and interactions on large molecular complexes with enhanced brightness.

Multilayered Dual Functional SiO2@Au@SiO2@QD Nanoparticles for Simultaneous Intracellular Heating and Temperature Measurement

This paper discusses synthesis and application of dual functional SiO₂@Au@SiO₂@QD composite nanoparticles for integrated intracellular heating with temperature motoring. The particles are of multilayered concentric structure, consisting of Au nanoshells covered with quantum dots, with the former for infrared heating through localized surface plasma resonance while the later for temperature monitoring. The key to integrate plasmonic-heating/thermal-monitoring on a single composite nanoparticle is to ensure that the quantum dots be separated at a certain distance away from the Au shell surface in order to ensure a detectable quantum yield. Direct attachment of the quantum dots onto the Au shell would render the quantum dots practically functionless for temperature monitoring. To integrate quantum dots into Au nanoshells, a quantum quenching barrier of SiO₂ was created by modifying a Stöber-like process. Materials, optical and thermal characterization was made of these composite nanoparticles. Cellular uptake of the nanoparticles was discussed. Experiments were performed on simultaneous in vitro heating and temperature monitoring in a cell internalized with the dual-functional SiO₂@Au@SiO₂@QD composite nanoparticles.

Fluorescence microscopy for visualizing single-molecule protein dynamics

BACKGROUND

Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically.

SCOPE OF REVIEW

This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy.

MAJOR CONCLUSIONS

smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on.

GENERAL SIGNIFICANCE

Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.

DNA-Based Assembly of Quantum Dots into Dimers and Helices

Owing to their unique optical properties, colloidal quantum dots (QDs) have attracted much attention as versatile fluorescent markers with broad biological and physical applications. On the other hand, DNA-based assembly has proven to be a powerful bottom-up approach to create designer nanoscale objects and to use these objects for the site-directed arrangement of guest components. To achieve good colloidal stability and accurate positioning of QDs on DNA templates, robust QD surface functionalization is crucial. Here, we present a simple and reliable conjugation method for the direct attachment of DNA molecules to QDs. Phosphorothiolated regions of chimera oligonucleotides are attached and incorporated into a ZnS layer freshly growing in situ on QDs that were rendered water soluble with hydrophilic ligands in a prior step. The reaction can be completed in a 2 mL plastic tube without any special equipment. The utility of these DNA-labeled QDs is demonstrated via prototypical assemblies such as QDs dimers with various spacings and chiral helical architectures.

Chemistries for DNA Nanotechnology

The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

Sensing with photoluminescent semiconductor quantum dots

Fluorescent sensors benefit from high signal-to-noise and multiple measurement modalities, enabling a multitude of applications and flexibility of design. Semiconductor nanocrystal quantum dots (QDs) are excellent fluorophores for sensors because of their extraordinary optical properties. They have high thermal and photochemical stability compared to organic dyes or fluorescent proteins and are extremely bright due to their large molar cross-sections. In contrast to organic dyes, QD emission profiles are symmetric, with relatively narrow bandwidths. In addition, the size tunability of their emission color, which is a result of quantum confinement, make QDs exceptional emitters with high color purity from the ultra-violet to near infrared wavelength range. The role of QDs in sensors ranges from simple fluorescent tags, as used in immunoassays, to intrinsic sensors that utilize the inherent photophysical response of QDs to fluctuations in temperature, electric field, or ion concentration. In more complex configurations, QDs and biomolecular recognition moieties like antibodies are combined with a third component to modulate the optical signal via energy transfer. QDs can act as donors, acceptors, or both in energy transfer-based sensors using Förster resonance energy transfer (FRET), nanometal surface energy transfer (NSET), or charge or electron transfer. The changes in both spectral response and photoluminescent lifetimes have been successfully harnessed to produce sensitive sensors and multiplexed devices. While technical challenges related to biofunctionalization and the high cost of laboratory-grade fluorimeters have thus far prevented broad implementation of QD-based sensing in clinical or commercial settings, improvements in bioconjugation methods and detection schemes, including using simple consumer devices like cell phone cameras, are lowering the barrier to broad use of more sensitive QD-based devices.

Excitation Wavelength-Dependent Photoluminescence Decay of Hybrid Gold/Quantum Dot Nanostructures

Hybrid nanostructures comprised of metal nanoparticles (MNPs) and quantum dots (QDs) have been found to exhibit unique, new optical properties due to the interaction that occurs between the MNPs and QDs. The aim of this work is to understand how the exciton-plasmon interaction in these systems is dependent on the excitation wavelength. The nanoassemblies consisted of gold (Au) NPs coated in a silica (SiO₂) shell of a controlled thickness and core/shell CdSe/CdS QDs adsorbed onto the SiO₂ shells. Our findings show that the photoluminescence lifetimes of the hybrid constructs are dependent on the excitation wavelength relative to the localized surface plasmon resonance (LSPR) of the Au NPs. When the excitation wavelength is closer to the LSPR, the photoluminescence decay of the hybrid structures is faster. We demonstrate that by tuning the excitation wavelength close to the resonance, there is an enhancement in the exciton-plasmon coupling between the Au NPs and QDs resulting in a shortening in the QD photoluminescence lifetime. We then propose a possible mechanism to explain this excitation wavelength-dependent phenomenon.

High-Performance Biosensing Systems Based on Various Nanomaterials as Signal Transducers

Recently, highly sensitive and selective biosensors have become necessary for improving public health and well-being. To fulfill this need, high-performance biosensing systems based on various nanomaterials, such as nanoparticles, carbon nanomaterials, and hybrid nanomaterials, are developed. Numerous nanomaterials show excellent physical properties, including plasmonic, magnetic, catalytic, mechanical and fluorescence properties and high electrical conductivities, and these unique and beneficial properties have contributed to the fabrication of high-performance biosensors with various applications, including in optical, electrical, and electrochemical detection platforms. In addition, these properties can be transformed to signals for the detection of biomolecules. In this review, various types of nanomaterial-based biosensors are introduced, and they show high sensitivity and selectivity. In addition, the potential applications of these sensors on the biosensing of several types of biomolecules are also discussed. These nanomaterials-based biosensing systems provide a significant improvement on healthcare including rapid monitoring and early detection of infectious disease for public health.