Nanoscopic optical rulers beyond the FRET distance limit: fundamentals and applications

Förster Resonance Energy Transfer-Activated Processes in Smart Nanotheranostics Fabricated in a Sustainable Manner

Multilayer nanocarriers loaded with optically activated payloads are gaining increasing attention due to their anticipated crucial role for providing new mechanisms of energy transfers in the health-oriented applications, as well as for energy storage and environmental protection. The combination of careful selection of optical components for efficient Förster resonance energy transfer, and surface engineering of the nanocarriers, allowed us to synthesize and characterize novel theranostic nanosystems for diagnosis and therapy of deep-seated tumors. The cargo, constrained within the oil core of the nanocapsules, composed of NaYF₄ :Tm⁺³ , Yb⁺³ up-converting nanoparticles together with a second-generation porphyrin-based photosensitizing agent-Verteporfin, assured requisite diagnostic and therapeutic functions under near-IR laser excitation. The outer polyaminoacid shell of the nanocapsules was functionalized with a ligand-poly(l-glutamic acid) functionalized by PEG-ylated folic acid-to ensure both a "stealth" effect and active targeting towards human breast cancer cells. The preparation criteria of all nanocarrier building blocks meet the requirements for sustainable and green chemistry practices. The multifunctionality of the proposed nanocarriers is a consequence of both the surface-functionalized organic exterior part, which was accessible for selective accumulation in cancer cells, and the hydrophobic optically active interior, which shows phototoxicity upon irradiation within the first biological window.

Assembly of DNA Probes into Superstructures for Dramatically Enhancing Enzymatic Stability and Signal-to-Background Ratio

DNA fluorescent probes are versatile tools that are widely used for biological detection in tubes. Using DNA probes in living systems, however, represents a significant challenge because of the endogenous nuclease-induced DNA degradation and strong background fluorescence in complex biological environments. Here, we show that assembling DNA probes into core-satellite gold nanoparticle (AuNP) superstructures could unprecedentedly enhance enzymatic stability and reduce background interference. The embedded DNA probes are protected from interaction with nuclease, eliminating the enzymatic degradation. In the meantime, the AuNP superstructures show extremely high quenching efficiency (>98%) toward the embedded DNA probes, whose fluorescence can be instantly turned on by the target binding, resulting in high signal-to-background ratio. To demonstrate these distinct properties, we made use of the assembled nanoprobes to monitor the ATP levels under different stimuli in living cells. The assembly strategy leads to a new opportunity for accurately sensing targets in living systems.

A "turn-on" fluorometric assay for kanamycin detection by using silver nanoclusters and surface plasmon enhanced energy transfer

A rapid method is described for the determination of the antibiotic kanamycin. It integrates a kanamycin-binding aptamer and surface plasmon enhanced energy transfer (SPEET) between DNA-templated silver nanoclusters (AgNCs) and gold nanoparticles (AuNPs). The AgNCs and AuNPs were selected as energy donor and energy acceptor, respectively. The aptamer was designed to regulate the energy transfer between AgNCs and AuNPs. The aptamer was adsorbed on the AuNPs. Upon addition of kanamycin, the aptamer-kanamycin complex is formed, and this results in the aggregation of the AuNPs in high salt concentration, the formation of a blue coloration, and in the suppression of the SPEET process. The fluorescence of the AgNCs (with excitation/emission peaks at 560/600 nm) is quenched by the aptamer protected AuNPs in absence of kanamycin. The fluorescence on addition of kanamycin increases linearly in the 5 to 50 nM concentration range, with a lower detection limit of 1.0 nM (at S/N = 3). The assay can be performed within 30 min. It was successfully applied to the determination of kanamycin in spiked milk samples, and recoveries ranged between 90.2 and 95.4%. Conceivably, the strategy has a wide potential for screening by simply changing the aptamer. Graphical abstract Schematic presentation of the aptamer regulated surface plasmon enhance energy transfer (SPEET) between silver nanoclusters (Ag NCs) and gold nanoparticles (Au NCs) in high salt concentration buffer, and of the procedure for the detection of kanamycin.

Horizontal Plasmonic Ruler Based on the Scattering Far-Field Pattern

A novel method is proposed to detect the horizontal shift of a specific nanoblock relative to a reference nanoblock using surface plasmon modes at nanometer resolution. To accomplish this task, two orthogonal localized surface plasmon resonances were excited within the air gap region between the silver nanoblocks at the respective wavelengths, 890 nm, and 1100 nm. This technique utilized the scattering far-field intensities of the two block nanostructures at the two specific wavelengths at two specific directional spots. The ratio of the scattering intensities at the two spots changed according to the horizontal shift of the block that moved. Correspondingly, this ratio can be used to provide the precise location of the block. This method can be applied to many fields, including label-free bio-sensing, bio-analysis and alignment during nano-fabrication, owing to the high resolution and simplicity of the process.

Observation of long-range dipole-dipole interactions in hyperbolic metamaterials

Dipole-dipole interactions (V _dd) between closely spaced atoms and molecules are related to real photon and virtual photon exchange between them and decrease in the near field connected with the characteristic Coulombic dipole field law. The control and modification of this marked scaling with distance have become a long-standing theme in quantum engineering since dipole-dipole interactions govern Van der Waals forces, collective Lamb shifts, atom blockade effects, and Förster resonance energy transfer. We show that metamaterials can fundamentally modify these interactions despite large physical separation between interacting quantum emitters. We demonstrate a two orders of magnitude increase in the near-field resonant dipole-dipole interactions at intermediate field distances (10 times the near field) and observe the distance scaling law consistent with a super-Coulombic interaction theory curtailed only by absorption and finite size effects of the metamaterial constituents. We develop a first-principles numerical approach of many-body dipole-dipole interactions in metamaterials to confirm our theoretical predictions and experimental observations. In marked distinction to existing approaches of engineering radiative interactions, our work paves the way for controlling long-range dipole-dipole interactions using hyperbolic metamaterials and natural hyperbolic two-dimensional materials.

Investigating supramolecular systems using Förster resonance energy transfer

Supramolecular systems have applications in areas as diverse as materials science, biochemistry, analytical chemistry, and nanomedicine. However, analyzing such systems can be challenging due to the wide range of time scales, binding strengths, distances, and concentrations at which non-covalent phenomena take place. Due to their versatility and sensitivity, Förster resonance energy transfer (FRET)-based techniques are excellently suited to meet such challenges. Here, we detail the ways in which FRET has been used to study non-covalent interactions in both synthetic and biological supramolecular systems. Among other topics, we examine methods to measure molecular forces, determine protein conformations, monitor assembly kinetics, and visualize in vivo drug release from nanoparticles. Furthermore, we highlight multiplex FRET techniques, discuss the field's limitations, and provide a perspective on new developments.

Photoprogramming Allostery in Human Serum Albumin

Developing strategies to interfere with allosteric interactions in proteins not only promises to deepen our understanding of vital cellular processes but also allows their regulation using external triggers. Light is particularly attractive as a trigger being spatiotemporally selective and compatible with the physiological environment. Here, we engineered a hybrid protein in which irradiation with light opens a new allosteric communication route that is not inherent to the natural system. We select human serum albumin, a promiscuous protein responsible for transporting a variety of ligands in plasma, and show that by covalently incorporating a synthetic photoswitch to subdomain IA we achieve optical control of the ligand binding in subdomain IB. Molecular dynamics simulations confirm the allosteric nature of the interactions between IA and IB in the engineered protein. Specifically, upon illumination, photoconversion of the switch is found to correlate with a less-coordinated motion of the two subdomains and an increased flexibility of the binding pocket in subdomain IB, whose fluctuations are cooperatively enhanced by the presence of ligands, ultimately facilitating their release. Our combined experimental and computational work demonstrates how harnessing artificial molecular switches enables photoprogramming the allosteric regulation of binding activities in such a prominent protein.

In situ monitoring of the structural change of microemulsions in simulated gastrointestinal conditions by SAXS and FRET

Microemulsions are promising drug delivery systems for the oral administration of poorly water-soluble drugs. However, the evolution of microemulsions in the gastrointestinal tract is still poorly characterized, especially the structural change of microemulsions under the effect of lipase and mucus. To better understand the fate of microemulsions in the gastrointestinal tract, we applied small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) to monitor the structural change of microemulsions under the effect of lipolysis and mucus. First, the effect of lipolysis on microemulsions was studied by SAXS, which found the generation of liquid crystalline phases. Meanwhile, FRET spectra indicated micelles with smaller particle sizes were generated during lipolysis, which could be affected by CaCl2, bile salts and lecithin. Then, the effect of mucus on the structural change of lipolysed microemulsions was studied. The results of SAXS and FRET indicated that the liquid crystalline phases disappeared, and more micelles were generated. In summary, we studied the structural change of microemulsions in simulated gastrointestinal conditions by SAXS and FRET, and successfully monitored the appearance and disappearance of the liquid crystalline phases and micelles.

Zero-Mode Waveguide Nanophotonic Structures for Single Molecule Characterization

Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (μM - mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer (smFRET), and fluorescence correlation spectroscopy (FCS) for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs (E-ZMW). In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

The Trace Detection of Nitrite Ions Using Neutral Red Functionalized SH-β-Cyclodextrin @Au Nanoparticles

A novel fluorescence sensor of NR-β-CD@AuNPs was prepared for the trace detection of nitrite in quantities as low as 4.25 × 10-3 μg∙mL-1 in an aqueous medium. The fluorescence was due to the host-guest inclusion complexes between neutral red (NR) molecules and gold nanoparticles (AuNPs), which were modified by per-6-mercapto-beta-cyclodextrins (SH-β-CDs) as both a reducing agent and a stabilizer under microwave radiation. The color of the NR-β-CD@AuNPs changed in the presence of nitrite ions. A sensor was applied to the determination of trace nitrites in environmental water samples with satisfactory results.

Color-tunable AIE-active conjugated polymer nanoparticles as drug carriers for self-indicating cancer therapy via intramolecular FRET mechanism

In this paper, two novel AIE-active conjugated polymers were synthesized by Pd-catalyzed Suzuki coupling polymerization reaction.

A real-time in vitro assay to evaluate the release of macromolecules from liposomes

The availability of a real-time assay to experimentally investigate the release of encapsulated proteins would be beneficial given the interest in the use of liposomes as a drug delivery vehicle. Although simple assays for small molecular weight substances exist, assays to evaluate macromolecules do not. Here we describe a method that detects the release of model macromolecules from liposomes in real time. The assay employs the intermolecular distance-dependent phenomenon of fluorescence resonance energy transfer (FRET) between the fluorophore donor, fluorescein (FITC), and fluorescent quencher, QSY^® 9. The macromolecular species were conjugated to the markers fluorescein (44kDa dextran) and QSY^® 9 (67 kDa bovine serum albumin, BSA). Following confirmation of quenching between FITC-Dex and QSY^® 9-BSA, liposomes were loaded with the macromolecular markers and subjected to various treatments (high-pressure extrusion and Triton X solubilisation) to cause release from liposomes. An increase in FITC fluorescence was observed when liposomes were subjected to extrusion cycles. Surprisingly, the addition of Triton X did not cause an increase in fluorescence probably because the FRET pair became associated with mixed micelles. This assay method should be useful in studies to investigate the mechanisms by which macromolecules are released from liposomes, particularly when liposomes are exposed to release-triggers (eg, temperature change, pH change, ultrasound). Such understanding will underpin the formulation of triggered liposomal delivery systems for macromolecules.

Responsive Nanogel Probe for Ratiometric Fluorescent Sensing of pH and Strain in Hydrogels

In this study a new pH-responsive nanogel probe containing a complementary nonradiative resonance energy transfer (NRET) fluorophore pair is investigated and its ability to act as a versatile probe of network-related changes in three hydrogels demonstrated. Fluorescent sensing using NRET is a powerful method for studying relationships between Angstrom length-scale structure and macroscopic properties of soft matter. Unfortunately, inclusion of NRET fluorophores into such materials requires material-specific chemistry. Here, low concentrations of preformed nanogel probes were included into hydrogel hosts. Ratiometric photoluminescence (PL) data for the gels labeled with the nanogel probes enabled pH-triggered swelling and deswelling to be studied as well as Ca²⁺-triggered collapse and solute release. PL measurements during compression of a nanogel probe-labeled nanocomposite gel demonstrated mechanochromic behavior and strain sensing. The new nanogel probes have excellent potential for investigating the internal structures of gels and provide a versatile ratiometric fluorescent platform for studying pH and strain.

Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution

Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.

Fluorescence Resonance Energy Transfer Systems in Supramolecular Macrocyclic Chemistry

The fabrication of smart materials is gradually becoming a research focus in nanotechnology and materials science. An important criterion of smart materials is the capacity of stimuli-responsiveness, while another lies in selective recognition. Accordingly, supramolecular host-guest chemistry has proven a promising support for building intelligent, responsive systems; hence, synthetic macrocyclic hosts, such as calixarenes, cucurbiturils, cyclodextrins, and pillararenes, have been used as ideal building blocks. Meanwhile, manipulating and harnessing light artificially is always an intensive attempt for scientists in order to meet the urgent demands of technological developments. Fluorescence resonance energy transfer (FRET), known as a well-studied luminescent activity and also a powerful tool in spectroscopic area, has been investigated from various facets, of which the application range has been broadly expanded. In this review, the innovative collaboration between FRET and supramolecular macrocyclic chemistry will be presented and depicted with typical examples. Facilitated by the dynamic features of supramolecular macrocyclic motifs, a large variety of FRET systems have been designed and organized, resulting in promising optical materials with potential for applications in protein assembly, enzyme assays, diagnosis, drug delivery monitoring, sensing, photosynthesis mimicking and chemical encryption.

Controllable Photodynamic Therapy Implemented by Regulating Singlet Oxygen Efficiency

With singlet oxygen (1O2) as the active agent, photodynamic therapy (PDT) is a promising technique for the treatment of various tumors and cancers. But it is hampered by the poor selectivity of most traditional photosensitizers (PS). In this review, we present a summary of controllable PDT implemented by regulating singlet oxygen efficiency. Herein, various controllable PDT strategies based on different initiating conditions (such as pH, light, H2O2 and so on) have been summarized and introduced. More importantly, the action mechanisms of controllable PDT strategies, such as photoinduced electron transfer (PET), fluorescence resonance energy transfer (FRET), intramolecular charge transfer (ICT) and some physical/chemical means (e.g. captivity and release), are described as a key point in the article. This review provide a general overview of designing novel PS or strategies for effective and controllable PDT.

Distance-dependent magnetic resonance tuning as a versatile MRI sensing platform for biological targets

Nanoscale distance-dependent phenomena, such as Förster resonance energy transfer, are important interactions for use in sensing and imaging, but their versatility for bioimaging can be limited by undesirable photon interactions with the surrounding biological matrix, especially in in vivo systems. Here, we report a new type of magnetism-based nanoscale distance-dependent phenomenon that can quantitatively and reversibly sense and image intra-/intermolecular interactions of biologically important targets. We introduce distance-dependent magnetic resonance tuning (MRET), which occurs between a paramagnetic 'enhancer' and a superparamagnetic 'quencher', where the T₁ magnetic resonance imaging (MRI) signal is tuned ON or OFF depending on the separation distance between the quencher and the enhancer. With MRET, we demonstrate the principle of an MRI-based ruler for nanometre-scale distance measurement and the successful detection of both molecular interactions (for example, cleavage, binding, folding and unfolding) and biological targets in in vitro and in vivo systems. MRET can serve as a novel sensing principle to augment the exploration of a wide range of biological systems.

Novel Ratiometric Fluorescent Nanothermometers Based on Fluorophores-Labeled Short Single-Stranded DNA

Novel ratiometric fluorescent short single-stranded DNA (ssDNA) nanothermometers (ssDNA FT) were developed using the fluorescence resonance energy transfer (FRET) effect of the ssDNA's end labeled fluorophores. An optimal ssDNA sequence and associated ssDNA FT were determined through combined MD simulation and temperature-related FRET analysis. Their fluorescence properties and thermo-responsivities were analyzed using fluorescence spectra. The influences of ssDNA' sequence length, sequence composition and fluorescent labels for temperature sensing were investigated. Results revealed the prepared, optimized ssDNA FT showed a high average temperature sensitivity of 7.04% °C^1-, wide linear response range of 0-100 °C, and excellent stability with various environmental factors. Furthermore, this ssDNA FT was successfully used for intracellular temperature sensing in cancer cells and was used for in vivo thermos-imaging during microwave hyperthermia of tumor tissue. Advantages in size, sensitivity, and stability proved the feasibility of ssDNA FT in nanoscale thermometry applications, and this novel fluorescent thermometry mechanism is of large potential in the development of FTs. This investigation of ssDNA's molecular thermosensitivity could give rise to a new prospective in the nanothermometry field.

Dual-Recognition Förster Resonance Energy Transfer Based Platform for One-Step Sensitive Detection of Pathogenic Bacteria Using Fluorescent Vancomycin-Gold Nanoclusters and Aptamer-Gold Nanoparticles

The effective monitoring, identification, and quantification of pathogenic bacteria is essential for addressing serious public health issues. In this study, we present a universal and facile one-step strategy for sensitive and selective detection of pathogenic bacteria using a dual-molecular affinity-based Förster (fluorescence) resonance energy transfer (FRET) platform based on the recognition of bacterial cell walls by antibiotic and aptamer molecules, respectively. As a proof of concept, Vancomycin (Van) and a nucleic acid aptamer were employed in a model dual-recognition scheme for detecting Staphylococcus aureus (Staph. aureus). Within 30 min, by using Van-functionalized gold nanoclusters and aptamer-modified gold nanoparticles as the energy donor and acceptor, respectively, the FRET signal shows a linear variation with the concentration of Staph. aureus in the range from 20 to 10⁸ cfu/mL with a detection limit of 10 cfu/mL. Other nontarget bacteria showed negative results, demonstrating the good specificity of the approach. When employed to assay Staph. aureus in real samples, the dual-recognition FRET strategy showed recoveries from 99.00% to the 109.75% with relative standard derivations (RSDs) less than 4%. This establishes a universal detection platform for sensitive, specific, and simple pathogenic bacteria detection, which could have great impact in the fields of food/public safety monitoring and infectious disease diagnosis.

Metal-enhanced Förster resonance energy transfer (ME-FRET) in anthracene/tetracene-doped crystal systems

Energy transfer in host–guest acene crystals fostered by metal nanoparticles resulting in efficient down-converted emission.

Understanding the effect of size and shape of gold nanomaterials on nanometal surface energy transfer

Gold Nanomaterials (GNMs) interact with fluorophores via electromagnetic coupling under excitation. In this particular work we carried out (to the best of our knowledge for the first time) a comprehensive study of systematic quenching of a blue emitter 2-Anthracene Sulfonate (2-AS) in the presence of gold nanoparticles of different size and shape. We synthesized gold nanomaterials of four different dimensions [nanoparticle (0D), nanorod (1D), nanotriangle (2D) and nanobipyramids (3D)] and realized the underlying effect on the emitting dipole in terms of steady and time resolved fluorescence. Nanometal Surface Energy Transfer (NSET) has already been proved to be the best long range spectroscopic ruler so far. Many attempts have been made to understand the interaction between a fluorescent molecule and gold nanomaterials. But not a single model can interpret alone the interaction phenomena. We have opted three different models to compare the experimental and theoretical data. Due to the presence of size dependent absorptivity and dielectric function, modified CPS-Kuhn model was proved to be the worthiest to comprehend variance of behavior of an emitting dipole in close proximity to nanometal surface by coupling with the image dipole of gold nanomaterials.

Three-in-One: Sensing, Self-Assembly, and Cascade Catalysis of Cyclodextrin Modified Gold Nanoparticles

We herein present a three-in-one nanoplatform for sensing, self-assembly, and cascade catalysis, enabled by cyclodextrin modified gold nanoparticles (CD@AuNPs). Monodisperse AuNPs 15-20 nm in diameter are fabricated in an eco-friendly way by the proposed one-step colloidal synthesis method using CD as both reducing agents and stabilizers. First, the as-prepared AuNPs are employed as not only scaffolds but energy acceptors for turn-on fluorescent sensing based on guest replacement reaction. Then, the macrocyclic supramolecule functionalized AuNPs can be controllably assembled and form well-defined one- and two-dimensional architectures using tetrakis(4-carboxyphenyl)porphyrin as mediator. Finally, in addition to conventional host-guest interaction based properties, the CD@AuNPs possess unpredictable catalytic activity and exhibit mimicking properties of both glucose oxidase and horseradish peroxidase simultaneously. Especially, the cascade reaction (glucose is first catalytically oxidized and generates gluconic acid and H₂O₂; then the enzymatic H₂O₂ and preadded TMB (3,3',5,5'-tetramethylbenzidine) are further catalyzed into H₂O and oxTMB, respectively) is well-achieved using the AuNPs as the sole catalyst. By employing a joint experimental-theoretical study, we reveal that the unique catalytic properties of the CD@AuNPs probably derive from the special topological structures of CD molecules and the resulting electron transfer effect from the AuNP surface to the appended CD molecules.

Multifunctional theranostic Pluronic mixed micelles improve targeted photoactivity of Verteporfin in cancer cells

Nanotechnology development provides new strategies to treat cancer by integration of different treatment modalities in a single multifunctional nanoparticle. In this scenario, we applied the multifunctional Pluronic P123/F127 mixed micelles for Verteporfin-mediated photodynamic therapy in PC3 and MCF-7 cancer cells. Micelles functionalization aimed the targeted delivery by the insertion of biotin moiety on micelle surface and fluorescence image-based through rhodamine-B dye conjugation in the polymer chains. Multifunctional Pluronics formed spherical nanoparticulated micelles that efficiently encapsulated the photosensitizer Verteporfin maintaining its favorable photophysical properties. Lyophilized formulations were stable at least for 6months and readily reconstituted in aqueous media. The multifunctional micelles were stable in protein-rich media due to the dual Pluronic mixed micelles characteristic: high drug loading capacity provided by its micellar core and high kinetic stability due its biocompatible shell. Biotin surface functionalized micelles showed higher internalization rates due biotin-mediated endocytosis, as demonstrated by competitive cellular uptake studies. Rhodamine B-tagged micelles allowed monitoring cellular uptake and intracellular distribution of the formulations. Confocal microscopy studies demonstrated a larger intracellular distribution of the formulation and photosensitizer, which could drive Verteporfin to act on multiple cell sites. Formulations were not toxic in the dark condition, but showed high Verteporfin-induced phototoxicity against both cancer cell lines at low drug and light doses. These results point Verteporfin-loaded multifunctional micelles as a promising tool to further developments in photodynamic therapy of cancer.

Gold-Quantum Dot Core-Satellite Assemblies for Lighting Up MicroRNA In Vitro and In Vivo

A high yield DNA-driven gold-quantum dot core-satellite is developed for miRNA detection in vitro and vivo. In the presence of the target miRNA, the DNA hairpin between core and satellite is ruined, resulting in the recovery of fluorescence. The limit of detection for miRNA-21 detection in living cells reaches 296 copies per cell.

Dual-Shell Fluorescent Nanoparticles for Self-Monitoring of pH-Responsive Molecule-Releasing in a Visualized Way

The rational design and controlled synthesis of a smart device with flexibly tailored response ability is all along desirable for bioapplication but long remains a considerable challenge. Here, a pH-stimulated valve system with a visualized "on-off" mode is constructed through a dual-shell fluorescence resonance energy transfer (FRET) strategy. The dual shells refer to carbon dots and fluorescent molecules embedded polymethacrylic acid (F-PMAA) layers successively coating around a SiO2 core (ca. 120 nm), which play the roles as energy donor and acceptor, respectively. The total thickness of the dual-shell in the solid composite is ca. 10 nm. The priorities of this dual-shell FRET nanovalve stem from three facts: (1) the thin shell allows the formation of efficient FRET system without chemical bonding between energy donor and acceptor; (2) the maximum emission wavelength of CD layer is tunable in the range of 400-600 nm, thus providing a flexible energy donor for a wide variety of energy acceptors; (3) the outer F-PMAA shell with a pH-sensitive swelling-shrinking (on-off) behavior functions as a valve for regulating the FRET process. As such, a sensitive and stable pH ratiometric sensor with a working pH range of 3-6 has been built by simply encapsulating pH-responsive fluorescein isothiocyanate (FITC) into PMAA; a pH-dependent swelling-shrinking shuttle carrier with a finely controllable molecule-release behavior has been further fabricated using rhodamine B isothiocyanate (RBITC) as the energy donor and model guest molecule. Significantly, the controlled releasing process is visually self-monitorable.

Investigating the Energy Transfer from Dye Molecules to DNA Stabilized Au Nanoparticles

Double-stranded DNA stabilized gold nanoparticles (Au NPs) are synthesized by chemical reduction method and characterized with different spectroscopic techniques such as UV-Visible absorption, Fourier transform infrared (FTIR), & circular-dichroism (CD) as well as transmission electron microscopy (TEM). These NPs show absorption maximum at 520 nm and size of most of the particles are of the order of 3.5 ± 1.0 nm. These Au NPs show crystalline nature as confirmed from electron diffraction pattern. The effect of formation of Au NPs on the macromolecule has been studied using infrared and circular dichroism spectroscopy. Formation of NPs causes conformational changes in the DNA molecules. These Au NPs are further used as resonant energy acceptor of fluorescence emission from dye molecules (Rhodamine 6G). The fluorescence intensity of Rhodamine 6G (R6G) is quenched in presence of Au NPs. The effect of DNA molecules on the fluorescence quenching and the rate of energy transfer from R6G molecules to Au NPs have been explored.

Designing a multicolor long range nanoscopic ruler for the imaging of heterogeneous tumor cells

Tumor heterogeneity is one of the biggest challenges in cancer treatment and diagnosis. A multicolor optical ruler is essential to address the heterogeneous tumor cell complexity. Driven by this need, the current article reports the design of a multicolor long range nanoscopic ruler for screening tumor heterogeneity by accurately identifying epithelial cells and cancer stem cells (CSCs) simultaneously. A nanoscopic surface energy transfer (NSET) ruler has been developed using blue fluorescence polymer dots (PDs) and red fluorescence gold cluster dots (GCDs) as multicolor fluorescence donor and plasmonic gold nanoparticle (GNP) acts as an excellent acceptor. Reported experimental results demonstrated that the multicolor nanoscopic ruler's working window is above 35 nm distances, which is more than three times farther than that of Förster resonance energy transfer (FRET) distance limit. Theoretical modeling using Förster dipole-dipole coupling and dipole to nanoparticle surface energy transfer have been used to discuss the possible mechanism for multicolor nanoscopic ruler's long-range capability. Using RNA aptamers that are specific for the target cancer cells, experimental data demonstrate that the nanoscopic ruler can be used for screening epithelial and CSCs simultaneously from a whole blood sample with a detection capability of 10 cells per mL. Experimental data show that the nanoscopic ruler can distinguish targeted cells from non-targeted cells.

An albumin nanocomplex-based endosomal pH-activatable on/off probe system

Albumin has gained considerable interest as a material for fabricating nanoparticulate systems due to its biomedical advantages, such as biocompatibility and chemical functionality. Here, we report a new pH-sensitive albumin nanocomplex prototype with a zinc-imidazole coordination bond. Albumin was conjugated with 1-(3-aminopropyl)imidazole and mPEG10kDa-NHS, and the resulting albumin conjugate (PBI) was then modified with either Cy5.5 or BHQ-3. The newly formed albumin nanocomplex (C/BQ-PBI Zn NCs: ∼116nm) system was facilely self-assembled around pH 7.4 in the presence of Zn(2+), but it quickly disassembled in an acidic environment (∼pH 5.0). Based on this pH-sensitivity, C/BQ-PBI Zn NCs emitted strong near-infrared fluorescence and released Zn(2+), turning "off" at pH ∼7.4 (e.g., plasma) and "on" at pH ∼5.0 (e.g., endo/lysosomes in tumor cells) on account of fluorescence resonance energy transfer. C/BQ-PBI Zn NCs displayed significant cytotoxicity due to an increase in cellular Zn(2+) in response to endosomal pH (∼5.0) in breast cancer MCF-7 cells and lung adenocarcinoma A549 cells. Particularly, confocal laser scanning microscopic images showed a strong fluorescence signal caused by the disassembly of C/BQ-PBI Zn NCs in the endosomal region of MCF-7 cells. Based on these results, we believe that this albumin nanocomplex is an attractive biocompatible tumor targeting probe carrier for the theranostic purpose.

MMP-responsive theranostic nanoplatform based on mesoporous silica nanoparticles for tumor imaging and targeted drug delivery

In this paper, we report on an intelligent mesoporous silica-based multifunctional theranostic nanoplatform (designated as MMTNP) for tumor imaging as well as controlled drug release. This theranostic nanoplatform consists of MCM-41 typical mesoporous silica nanoparticles (MSNs) as a hydrophobic drug carrier, matrix metalloprotease-2 (MMP-2) activated fluorescence imaging peptides on the surface of MSNs served as diagnostic probes as well as enzyme-responsive nanovalves blocking the pores, and cRGD peptides further functionalized on the surface of MSNs for tumor targeting. In the absence of MMP-2 conditions, the proximity between the fluorescent dye 5(6)-carboxytetramethylrhodamine hydrochloride (TAMRA) and the quencher 4,4-dimethylamino-azobenzene-4'-carboxylic acid (Dabcyl) on the surface of MSNs resulted in no fluorescence. When the drug loaded nanoplatform arrived at tumor tissue with overexpressed MMP-2, the fluorescence of TAMRA became recovered efficiently due to the hydrolysis of the MMP-2 sensitive peptide substrate, realizing tumor imaging and triggering drug release. In addition, the further introduced cRGD peptide significantly enhanced the targeting efficiency through receptor-mediated endocytosis in tumor cells.

Triangulating Nucleic Acid Conformations Using Multicolor Surface Energy Transfer

Optical ruler methods employing multiple fluorescent labels offer great potential for correlating distances among several sites, but are generally limited to interlabel distances under 10 nm and suffer from complications due to spectral overlap. Here we demonstrate a multicolor surface energy transfer (McSET) technique able to triangulate multiple points on a biopolymer, allowing for analysis of global structure in complex biomolecules. McSET couples the competitive energy transfer pathways of Förster Resonance Energy Transfer (FRET) with gold-nanoparticle mediated Surface Energy Transfer (SET) in order to correlate systematically labeled points on the structure at distances greater than 10 nm and with reduced spectral overlap. To demonstrate the McSET method, the structures of a linear B-DNA and a more complex folded RNA ribozyme were analyzed within the McSET mathematical framework. The improved multicolor optical ruler method takes advantage of the broad spectral range and distances achievable when using a gold nanoparticle as the lowest energy acceptor. The ability to report distance information simultaneously across multiple length scales, short-range (10-50 Å), mid-range (50-150 Å), and long-range (150-350 Å), distinguishes this approach from other multicolor energy transfer methods.

Gold nanoparticles as sensitive optical probes

Recent advances in Au NP based optical sensing systems for various analytes based on absorption, fluorescence and SERS are summarized.

Revealing the photophysics of gold-nanobeacons via time-resolved fluorescence spectroscopy

We demonstrate that time-resolved fluorescence spectroscopy is a powerful tool to investigate the conformation states of hairpin DNA on the surface of gold nanoparticles (AuNPs) and energy transfer processes in Au-nanobeacons. Long-range fluorescence quenching of Cy5 by AuNPs has been found to be in good agreement with electrodynamics modeling. Moreover, time-correlated single-photon counting (TCSPC) is shown to be promising for real-time monitoring of the hybridization kinetics of Au-nanobeacons, with up to 60% increase in decay time component and 300% increase in component fluorescence fraction observed. Our results also indicate the importance of the stem and spacer designs for the performance of Au-nanobeacons.

Wavelength dependent specific plasmon resonance coupling of single silver nanoparticles with EGFP

Noble metal nanoparticles (NPs) possess unique plasmonic properties, enabling them to serve as sub-diffraction light sources and nano- antennae for a wide range of applications. Here we report the specific interaction of single Ag NPs with single EGFP molecules and a high dependence of their interaction upon localized-surface-plasmon-resonance (LSPR) spectra of single Ag NPs and EGFP. The LSPR spectra of single red Ag NPs show a stunning 60 nm blue-shift during their incubation with EGFP, whereas they remain unchanged during their incubation with bovine serum albumin (BSA). Interestingly, the peak wavelengths of the LSPR spectra of green and blue Ag NPs remain essentially unchanged during their incubation with either EGFP or BSA. These interesting findings suggest that plasmon-resonance-energy-transfer (PRET) from single Ag NPs to EGFP might follow a two-photon excitation mechanism to excite EGFP and the fluorescence of the excited EGFP might couple with the plasmon of single NPs leading to a blue-shift of the red NPs. These distinctive phenomena are only observed by real-time single NP spectroscopic measurements. This study offers exciting new opportunities to design new sensing and imaging tools with high specificity and sensitivity to study long-range molecular interactions and dynamic events in single live cells, and to probe the underlying molecular mechanisms of PRET.

Ratiometric Monitoring of Intracellular Drug Release by an Upconversion Drug Delivery Nanosystem

Nanoscale drug delivery systems have been widely investigated due to their well-recognized advantages including controlled delivery of chemotherapeutic agents, enhanced therapeutic effectiveness, and reduced adverse effects compared to conventional chemotherapy with small molecules. However, further progress in the use of nanoscale delivery systems in clinical applications has been hampered by pharmacokinetic studies in biological samples which were associated with significant experimental challenges. Here, we report a rational ratiometric approach to monitor drug release kinetics by quantitatively investigating luminescence resonance energy transfer (LRET) from upconversion nanoparticles to the antitumor drug doxorubicin (DOX). Specifically, DOX molecules within the shell of mesoporous silica-coated upconversion nanoparticles selectively quenched the green emission of upconversion nanoparticles, while the intensity of red emission was essentially unaltered. Consequently, when DOX was gradually released, a steady recovery of green emission was observed. The ability to monitor the intensity ratio of green-to-red luminescence enabled a rational design for real-time investigation of drug delivery release kinetics. Importantly, the internal standard effect of red emission made this ratiometric approach suitable for complex biological microenvironments.

Long-range two-photon scattering spectroscopy ruler for screening prostate cancer cells

Optical rulers have served as a key tool for scientists from different disciplines to address a wide range of biological activity. Since the optical window of state of the art FRET rulers is limited to a 10 nm distance, developing long range optical rulers is very important to monitor real life biological processes. Driven by this need, the current manuscript reports for the first time the design of long-range two-photon scattering (TPS) spectroscopy rulers using gold nano-antenna separated by a bifunctional rigid double strand DNA molecule, which controls the spectroscopy ruler length. Reported data demonstrate that the TPS spectroscopy ruler's working window is a within a 25 nm distance, which is more than twice that of well recognized FRET optical ruler. A possible mechanism for the two-photon spectroscopy ruler's long range capability have been discussed using angle-resolved TPS measurement and FDTD simulations. Solution-phase experimental data demonstrated that a long-range TPS ruler using A9 aptamer can be used for the screening of prostate-specific membrane antigen (PSMA) (+) prostate cancer cells even at 5 cells per mL level. Reported result with PSMA (-) normal skin HaCaT cells indicate that TPS ruler based assay has the capability to enable distinction from non-targeted cell lines. Ultimately, the long range TPS ruler can be used towards better understanding of chemical and biological processes.

Polydopamine-embedded Cu2−xSe nanoparticles as a sensitive biosensing platform through the coupling of nanometal surface energy transfer and photo-induced electron transfer

This study innovatively highlights the mechanistic details of NSET and PET (NSET©PET) coupling processes, and the disclosed mechanism provides new opportunities for sensitive biosensing applications.

Bioconjugated persistent luminescence nanoparticles for Föster resonance energy transfer immunoassay of prostate specific antigen in serum and cell extracts without in situ excitation

A novel Föster resonance energy transfer (FRET) immunoassay based on persistent luminescence nanoparticles (PLNP) for PSA detection in serum and cell extracts in the absence of in situ excitation.

Rationally manipulating aptamer binding affinities in a stem-loop molecular beacon

Single-stranded DNA sequences that are highly specific for a target ligand are called aptamers. While the incorporation of aptamer sequences into stem-loop molecular beacons has become an essential tool in optical biosensors, the design principles that determine the magnitude of binding affinity and its relationship to placement of the aptamer sequence in the stem-loop architecture are not well defined. By controlled placement of the aptamer along the loop region of the molecular beacon, it is observed that the binding affinity can be tuned over 4 orders of magnitude (1.3 nM – 203 μM) for the Huizenga and Szostak ATP DNA aptamer sequence. It is observed that the K_d is enhanced for the fully exposed sequence, with reduced binding affinity when the aptamer is part of the stem region of the beacon. Analysis of the ΔG values indicate a clear correlation between the aptamer hybridized length in the stem and its observed K_d. The use of a nanometal surface energy transfer probe method for monitoring ATP binding to the aptamer sequence allows the observation of negative cooperativity between the two ATP binding events. Maintenance of the high binding affinity of this ATP aptamer and the observation of two separate K_d’s for ATP binding indicate NSET as an effective, nonmanipulative, optical method for tracking biomolecular changes.