Light-Harvesting Nanoparticle Probes for FRET-Based Detection of Oligonucleotides with Single-Molecule Sensitivity

Controlling the emission of bright luminescent nanoparticles by a single molecular recognition event remains a challenge in the design of ultrasensitive probes for biomolecules. Herein, we developed 20-nm light-harvesting nanoantenna particles, built of a tailor-made hydrophobic charged polymer poly(ethyl methacrylate-co-methacrylic acid), encapsulating circa 1000 strongly coupled and highly emissive rhodamine dyes with their bulky counterion. Being 87-fold brighter than quantum dots QDots 605 in single-particle microscopy (with 550-nm excitation), these DNA-functionalized nanoparticles exhibit over 50 % total FRET efficiency to a single hybridized FRET acceptor, a highly photostable dye (ATTO665), leading to circa 250-fold signal amplification. The obtained FRET nanoprobes enable single-molecule detection of short DNA and RNA sequences, encoding a cancer marker (survivin), and imaging single hybridization events by an epi-fluorescence microscope with ultralow excitation irradiance close to that of ambient sunlight.     

Protein‐Sized Bright Fluorogenic Nanoparticles Based on Cross‐Linked Calixarene Micelles with Cyanine Corona

The key challenge in the field of fluorescent nanoparticles (NPs) for biological applications is to achieve superior brightness for sizes equivalent to single proteins (3–7 nm). We propose a concept of shell‐cross‐linked fluorescent micelles, in which PEGylated cyanine 3 and 5 bis‐azides form a covalently attached corona on micelles of amphiphilic calixarene bearing four alkyne groups. The fluorescence quantum yield of the obtained monodisperse NPs, with a size of 7 nm, is a function of viscosity and reached up to 15 % in glycerol. In the on‐state they are circa 2‐fold brighter than quantum dots (QD‐585), which makes them the smallest PEGylated organic NPs of this high brightness. FRET between cyanine 3 and 5 cross‐linkers at the surface of NPs suggests their integrity in physiological media, organic solvents, and living cells, in which the NPs rapidly internalize, showing excellent imaging contrast. Calixarene micelles with a cyanine corona constitute a new platform for the development of protein‐sized ultrabright fluorescent NPs.     

Single‐Nanoparticle Cell Barcoding by Tunable FRET from Lanthanides to Quantum Dots

Fluorescence barcoding based on nanoparticles provides many advantages for multiparameter imaging. However, creating different concentration‐independent codes without mixing various nanoparticles and by using single‐wavelength excitation and emission for multiplexed cellular imaging is extremely challenging. Herein, we report the development of quantum dots (QDs) with two different SiO₂ shell thicknesses (6 and 12 nm) that are coated with two different lanthanide complexes (Tb and Eu). FRET from the Tb or Eu donors to the QD acceptors resulted in four distinct photoluminescence (PL) decays, which were encoded by simple time‐gated (TG) PL intensity detection in three individual temporal detection windows. The well‐defined single‐nanoparticle codes were used for live cell imaging and a one‐measurement distinction of four different cells in a single field of view. This single‐color barcoding strategy opens new opportunities for multiplexed labeling and tracking of cells.     

Application of a Highly Robust and Efficient Fluorescence‐Resonance‐Energy‐Transfer (FRET) System in DNA

We report a feasibility study for the application of our newly developed highly efficient and robust fluorescence‐resonance‐energy‐transfer (FRET) system to DNA. A 2′‐oligodeoxynucleotide, 12 , equipped with a quinolinone derivative as donor and a (bathophenanthroline)ruthenium(II) complex as acceptor and having a single uridine as potential cleavage site under basic conditions revealed an intensive FRET, which almost vanished after cleavage of the oligonucleotide under basic conditions (Fig. 7). Furthermore, in the arrangement of a molecular beacon (MB) DNA (see 13 ), a significant decrease of the FRET was observed after hybridization to a target sequence (Fig. 9). Due to the long decay times of the fluorescence of the Ru‐complex, the system allows for highly sensitive time‐gated measurements.     

Efficient Excitation‐Energy Transfer in Ion‐Based Organic Nanoparticles with Versatile Tunability of the Fluorescence Colours

Organic nanoparticles consisting of 3,3′‐diethylthiacyanine (TC) and ethidium (ETD) dyes are synthesized by ion‐association between the cationic dye mixture (10 % ETD doping) and the tetrakis(4‐fluorophenyl)borate (TFPB) anion, in the presence of a neutral stabilizing polymer, in aqueous solution. Doping with ETD makes the particle size smaller than without doping. Size tuning can also be conducted by varying the molar ratio (ρ) of the loaded anion to the cationic dyes. The fluorescence spectrum of TC shows good overlap with the absorption of ETD in the 450–600 nm wavelength region, so efficient excitation‐energy transfer from TC (donor) to ETD (acceptor) is observed, yielding organic nanoparticles whose fluorescence colours are tunable. Upon ETD doping, the emission colour changes significantly from greenish‐blue to reddish or whitish. This change is mainly dependent on ρ. For the doped nanoparticle sample with ρ=1, the intensity of fluorescence ascribed to ETD is ～150‐fold higher than that from pure ETD nanoparticles (efficient antenna effect). Non‐radiative Förster resonance‐energy transfer (FRET) is the dominant mechanism for the ETD fluorescence enhancement. The organic nanoparticles of a binary dye system fabricated by the ion‐association method act as efficient light‐harvesting antennae, which are capable of transferring light energy to the dopant acceptors in very close proximity to the donors, and can have multi‐wavelength emission colours with high fluorescence quantum yields.     

Highly Efficient,Conjugated‐Polymer‐Based Nano‐Photosensitizers for Selectively Targeted Two‐Photon Photodynamic Therapy and Imaging of Cancer Cells

Two‐photon photodynamic therapy (2P‐PDT) is a promising noninvasive treatment of cancers and other diseases with three‐dimensional selectivity and deep penetration. However, clinical applications of 2P‐PDT are limited by small two‐photon absorption (TPA) cross sections of traditional photosensitizers. The development of folate receptor targeted nano‐photosensitizers based on conjugated polymers is described. In these nano‐photosensitizers, poly{9,9‐bis[6′′‐(bromohexyl)fluorene‐2,7‐ylenevinylene]‐co‐alt‐1,4‐(2,5‐dicyanophenylene)}, which is a conjugated polymer with a large TPA cross section, acts as a two‐photon light‐harvesting material to significantly enhance the two‐photon properties of the doped photosensitizer tetraphenylporphyrin (TPP) through energy transfer. These nanoparticles displayed up to 1020‐fold enhancement in two‐photon excitation emission and about 870‐fold enhancement in the two‐photon‐induced singlet oxygen generation capability of TPP. Surface‐functionalized folic acid groups make these nanoparticles highly selective in targeting and killing KB cancer cells over NIH/3T3 normal cells. The 2P‐PDT activity of these nanoparticles was significantly improved, potentially up to about 1000 times, as implied by the enhancement factors of two‐photon excitation emission and singlet oxygen generation. These nanoparticles could act as novel two‐photon nano‐photosensitizers with combined advantages of low dark cytotoxicity, targeted 2P‐PDT with high selectivity, and simultaneous two‐photon fluorescence imaging capability; these are all required for ideal two‐photon photosensitizers.     

Separation‐free single‐base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites

A separation‐free single‐base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele‐specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5′‐end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite‐converted genomic DNA, and a DNA polymerase. A single base‐extended primer (i.e., SBE product) that was 5′‐Cy3‐ and 3′‐Cy5‐tagged was formed by incorporation of the Cy5‐labeled terminator into the 3′‐end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.     

Combining Electrodeposition and Optical Microscopy for Probing Size‐Dependent Single‐Nanoparticle Electrochemistry

Electrodeposition of nanoparticles (NPs) is a promising route for the preparation of highly electroactive nanostructured electrodes. By taking advantage of progressive electrodeposition, disordered arrays with a wide size distribution of Ag NPs are produced. Combined with surface‐reaction monitoring by using highly sensitive backside absorbing‐layer optical microscopy (BALM), such arrays offer a platform for screening size‐dependent electrochemistry at the single NP level. In particular, this strategy allows rationalizing the electrodeposition dynamics at the single‐NP level (>10 nm), up to the point of quantifying the presence of metal nanoclusters (<2 nm), and probing easier NP oxidation with size decrease, either through electrochemical or galvanic reactions.     

Dual‐Luminophore‐Labeled Gold Nanoparticles with Completely Resolved Emission for the Simultaneous Imaging of MMP‐2 and MMP‐7 in Living Cells under Single Wavelength Excitation

Although considerable effort has been devoted to the design of various nanoprobes for the fluorescent detection of multiple biomarkers in a single assay, they often suffer from emission‐overlapping, owing to small Stokes shifts and wide emission spectra, which results in cross‐talk and inaccurate quantification. Herein, we report the design and synthesis of a new nanoprobe for multienzyme detection with completely resolved emission peaks under single‐wavelength excitation. The probe was assembled by attaching a cleavable peptide spacer, which was comprised from a matrix metalloproteinase‐2 (MMP‐2) substrate and a MMP‐7 substrate, onto the surface of gold nanoparticles (AuNPs) through cysteine residues. A lanthanide complex, BCTOT‐Eu^III (BCTOT=1,10‐bis(5′‐chlorosulfo‐thiophene‐2′‐yl)‐4,4,5,5,6,6,7,7‐octafluorodecane‐1,3,8,10‐tetraone), and 7‐amino‐4‐methylcoumarin (AMC) were attached to the N terminus and the C terminus of the peptide, respectively. In the presence of one or both targeting enzymes, the substrate was cleaved and fluorescence resonance energy transfer (FRET) between the dyes and AuNPs was prohibited, thereby resulting in the dramatic fluorescence emission of dyes. Importantly, there was no emission cross‐talk between the two dyes, thereby ensuring accurate detection of each enzyme. Based on this, the simultaneous fluorescence image of MMP‐2 and MMP‐7 was accomplished in living cells under single wavelength excitation. The apparent differences in the fluorescence imaging indicated distinct differences between the expression levels of MMPs between the human normal liver cells and the human hepatoma cells.     

FRET‐Based Mitochondria‐Targetable Dual‐Excitation Ratiometric Fluorescent Probe for Monitoring Hydrogen Sulfide in Living Cells

Hydrogen sulfide (H₂S) is connected with various physiological and pathological functions. However, understanding the important functions of H₂S remains challenging, in part because of the lack of tools for detecting endogenous H₂S. Herein, compounds Ratio‐H₂S 1/2 are the first FRET‐based mitochondrial‐targetable dual‐excitation ratiometric fluorescent probes for H₂S on the basis of H₂S‐promoted thiolysis of dinitrophenyl ether. With the enhancement of H₂S concentration, the excitation peak at λ≈402 nm of the phenolate form of the hydroxycoumarin unit drastically increases, whereas the excitation band centered at λ≈570 nm from rhodamine stays constant and can serve as a reference signal. Thus, the ratios of fluorescence intensities at λ=402 and 570 nm (I₄₀₂/I₅₇₀) exhibit a drastic change from 0.048 in the absence of H₂S to 0.36 in the presence of 180 μM H₂S; this is a 7.5‐fold variation in the excitation ratios. The favorable properties of the probe include the donor and acceptor excitation bands, which exhibit large excitation separations (up to 168 nm separation) and comparable excitation intensities, high sensitivity and selectivity, and function well at physiological pH. In addition, it is demonstrated that the probe can localize in the mitochondria and determine H₂S in living cells. It is expected that this strategy will lead to the development of a wide range of mitochondria‐targetable dual‐excitation ratiometric probes for other analytes with outstanding spectral features, including large separations between the excitation wavelengths and comparable excitation intensities.     

New Anthracene Derivatives as Triplet Acceptors for Efficient Green‐to‐Blue Low‐Power Upconversion

Three new anthracene derivatives [2‐chloro‐9,10‐dip‐tolylanthracene (DTACl), 9,10‐dip‐tolylanthracene‐2‐carbonitrile (DTACN), and 9,10‐di(naphthalen‐1‐yl)anthracene‐2‐carbonitrile (DNACN)] were synthesized as triplet acceptors for low‐power upconversion. Their linear absorption, single‐photon‐excited fluorescence, and upconversion fluorescence properties were studied. The acceptors exhibit high fluorescence yields in DMF. Selective excitation of the sensitizer Pd^IIoctaethylporphyrin (PdOEP) in solution containing DTACl, DTACN, or DNA‐CN at 532 nm with an ultralow excitation power density of 0.5 W cm^?2 results in anti‐Stokes blue emission. The maximum upconversion quantum yield (Φ_UC=17.4 %) was obtained for the couple PdOEP/DTACl. In addition, the efficiency of the triplet–triplet energy transfer process was quantitatively studied by quenching experiments. Experimental results revealed that a highly effective acceptor for upconversion should combine high fluorescence quantum yields with efficient quenching of the sensitizer triplet.     

Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically‐Encoded Probes for DNA‐PAINT

The nuclear pore complex (NPC) is one of the largest and most complex protein assemblies in the cell and, among other functions, serves as the gatekeeper of nucleocytoplasmic transport. Unraveling its molecular architecture and functioning has been an active research topic for decades with recent cryogenic electron microscopy and super‐resolution studies advancing our understanding of the architecture of the NPC complex. However, the specific and direct visualization of single copies of NPC proteins is thus far elusive. Herein, we combine genetically‐encoded self‐labeling enzymes such as SNAP‐tag and HaloTag with DNA‐PAINT microscopy. We resolve single copies of nucleoporins in the human Y‐complex in three dimensions with a precision of circa 3 nm, enabling studies of multicomponent complexes on the level of single proteins in cells using optical fluorescence microscopy.     

Multilayer Microcapsules for FRET Analysis and Two‐Photon‐Activated Photodynamic Therapy

Microcapsules obtained by layer‐by‐layer assembly provide a good platform for biological analysis owing to their component diversity, multiple binding sites, and controllable wall thickness. Herein, different assembly species were obtained from two‐photon dyes and traditional photosensitizers, and further assembled into microcapsules. Fluorescence resonance energy transfer (FRET) was shown to occur between the two‐photon dyes and photosensitizers. Confocal laser scanning microscopy (CLSM) with one‐ and two‐photon lasers, fluorescence lifetime imaging microscopy (FLIM), and time‐resolved fluorescence spectroscopy were used to analyze the FRET effects in the microcapsules. The FRET efficiency could easily be controlled through changing the assembly sequence. Furthermore, the capsules are phototoxic upon one‐ or two‐photon excitation. These materials are thus expected to be applicable in two‐photon‐activated photodynamic therapy for deep‐tissue treatment.     

Near‐Infrared‐Light‐Driven Artificial Photosynthesis by Nanobiocatalytic Assemblies

Artificial photosynthesis in nanobiocatalytic assemblies aims to reconstruct man‐made photosensitizers, electron mediators, electron donors, and redox enzymes for solar synthesis of valuable chemicals through photochemical cofactor regeneration. Herein, we report, for the first time, on nanobiocatalytic artificial photosynthesis in near‐infrared (NIR) light, which constitutes over 46% of the solar energy. For NIR‐light‐driven photoenzymatic synthesis, we synthesized silica‐coated upconversion nanoparticles, Si‐NaYF4:Yb,Er and Si‐NaYF4:Yb,Tm, for efficient photon‐conversion through Förster resonance energy transfer (FRET) with rose bengal (RB), a photosensitizer. We observed NIR‐induced electron transfer by using linear sweep voltammetric analysis; this indicates that photoexcited electrons of RB/Si‐NaYF4:Yb,Er are transferred to NAD+ through a Rh‐based electron mediator. RB/Si‐NaYF4:Yb,Er nanoparticles, which exhibit higher FRET efficiency due to more spectral overlap than RB/Si‐NaYF4:Yb,Tm, perform much better in the photoenzymatic conversion.     

Dimension‐Matched Zinc Phthalocyanine/BiVO4 Ultrathin Nanocomposites for CO2 Reduction as Efficient Wide‐Visible‐Light‐Driven Photocatalysts via a Cascade Charge Transfer

Cascade charge transfer was realized by a H‐bond linked zinc phthalocyanine/BiVO₄ nanosheet (ZnPc/BVNS) composite, which subsequently works as an efficient wide‐visible‐light‐driven photocatalyst for converting CO₂ into CO and CH₄, as shown by product analysis and ¹³C isotopic measurement. The optimized ZnPc/BVNS nanocomposite exhibits a ca. 16‐fold enhancement in the quantum efficiency compared with the reported BiVO₄ nanoparticles at the excitation of 520 nm with an assistance of 660 nm photons. Experimental and theoretical results show the exceptional activities are attributed to the rapid charge separation by a cascade Z‐scheme charge transfer mechanism formed by the dimension‐matched ultrathin (ca. 8 nm) heterojunction nanostructure. The central Zn²⁺ in ZnPc could accept the excited electrons from the ligand and then provide a catalytic function for CO₂ reduction. This Z‐scheme is also feasible for other MPc, such as FePc and CoPc, together with BVNS.     

Fluorescence resonance energy transfer between green fluorescent protein and doxorubicin enabled by DNA nanotechnology

DNA nanotechnology is a rapidly growing research area, where DNA may be used for wide range of applications such as construction of nanodevices serving for large scale of diverse purposes. Likewise a panel of various purified fluorescent proteins is investigated for their ability to emit their typical fluorescence spectra under influence of particular excitation. Hence these proteins may form ideal donor molecules for assembly of fluorescence resonance emission transfer (FRET) constructions. To extend the application possibilities of fluorescent proteins, while using DNA nanotechnology, we developed nanoconstruction comprising green fluorescent protein (GFP) bound onto surface of surface active nanomaghemite and functionalized with gold nanoparticles. We took advantage of natural affinity between gold and thiol moieties, which were modified to bind DNA fragment. Finally we enclosed doxorubicin into fullerene cages. Doxorubicin intercalated in DNA fragment bound on the particles and thus we were able to connect these parts together. Because GFP behaved as a donor and doxorubicin as an acceptor using excitation wavelength for GFP (395 nm) in emission wavelength of doxorubicin (590 nm) FRET was observed. This nanoconstruction may serve as a double‐labeled transporter of doxorubicin guided by force of external magnetic force owing to the presence of nanomaghemite. Further nanomaghemite offers the possibility of using this technology for thermotherapy.     

Calix[4]arene‐Functionalised Silver Nanoparticles as Hosts for Pyridinium‐Loaded Gold Nanoparticles as Guests

A series of lipophilic gold nanoparticles (AuNPs) circa 5 nm in diameter and having a mixed organic layer consisting of 1‐dodecanethiol and 1‐(11‐mercaptoundecyl) pyridinium bromide was synthesised by reacting tetraoctylammonium bromide stabilised AuNPs in toluene with different mixtures of the two thiolate ligands. A bidentate ω‐alkylthiolate calix[4]arene derivative was instead used as a functional protecting layer on AgNPs of approximately 3 nm. The functionalised nanoparticles were characterised by transmission electron microscopy (TEM), and by UV/Vis and X‐ray photoelectron spectroscopy (XPS). Recognition of the pyridinium moieties loaded on the AuNPs by the calix[4]arene units immobilised on the AgNPs was demonstrated in solution of weakly polar solvents by UV/Vis titrations and DLS measurements. The extent of Au‐AgNPs aggregation, shown through the low‐energy shift of their surface plasmon bands (SPB), was strongly dependent on the loading of the pyridinium moieties present in the organic layer of the AuNPs. Extensive aggregation between dodecanethiol‐capped AuNPs and the Ag calix[4]arene‐functionalised NPs was also promoted by the action of a simple N‐octyl pyridinium difunctional supramolecular linker. This linker can interdigitate through its long fatty tail in the organic layer of the dodecanethiol‐capped AuNPs, and simultaneously interact through its pyridinium moiety with the calix[4]arene units at the surface of the modified AgNPs.     

Non‐Aqueous Sol–Gel Synthesis of Ultra Small Persistent Luminescence Nanoparticles for Near‐Infrared In Vivo Imaging

Ultra‐small ZnGa₂O₄:Cr³⁺ nanoparticles (6 nm) that exhibit near‐infrared (NIR) persistent luminescence properties are synthesized by using a non‐aqueous sol–gel method assisted by microwave irradiation. The nanoparticles are pegylated, leading to highly stable dispersions under physiological conditions. Preliminary in vivo studies show the high potential for these ultra‐small ZnGa₂O₄:Cr³⁺ nanoparticles to be used as in vivo optical nanotools as they emit without the need for in situ excitation and, thus, avoid the autofluorescence of tissues.     

Toehold‐Mediated Displacement of an Adenosine‐Binding Aptamer from a DNA Duplex by its Ligand

DNA is increasingly used to engineer dynamic nanoscale circuits, structures, and motors, many of which rely on DNA strand‐displacement reactions. The use of functional DNA sequences (e.g., aptamers, which bind to a wide range of ligands) in these reactions would potentially confer responsiveness on such devices, and integrate DNA computation with highly varied molecular stimuli. By using high‐throughput single‐molecule FRET methods, we compared the kinetics of a putative aptamer–ligand and aptamer–complement strand‐displacement reaction. We found that the ligands actively disrupted the DNA duplex in the presence of a DNA toehold in a similar manner to complementary DNA, with kinetic details specific to the aptamer structure, thus suggesting that the DNA strand‐displacement concept can be extended to functional DNA–ligand systems.