Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates

Fluorescence detection and imaging are vital technologies in the life sciences and clinical diagnostics. The key to obtaining high-resolution images and sensitive detection is to use fluorescent molecules or particles that absorb and emit visible light with high efficiency. We have synthesized supramolecular complexes consisting of a branched DNA template and fluorogenic intercalating dyes. Because dyes can intercalate up to every other base pair, high densities of fluorophores are assembled yet the DNA template keeps them far enough away from each other to prevent self-quenching. The efficiency with which these noncovalent assemblies absorb light is more than 10-fold greater than that of the individual dye molecules. F?rster resonance energy transfer from the intercalated dyes to covalently attached acceptor dyes is very efficient, allowing for wavelength shifting of the emission spectrum. Simple biotinylation of the DNA template allows for labeling of streptavidin-coated synthetic microspheres and mouse T-cells.     

Dual‐Polarization Imaging of a Dual‐Fluorophore Ion Sensor: A Single‐Molecule Study

The fluorescence emission of the dual‐fluorophore Ca²⁺ ion sensor molecule, calcium‐green 2 (CG‐2), has been characterized using dual‐polarization imaging at the single‐molecule level. By comparing the fluorescence intensity of individual CG‐2 molecules in two mutually orthogonal polarization image channels, information about the relative orientation of the two constituent fluorophores in the molecule is obtained. Experimental results from polarization measurements are compared with those predicted from a geometric model based on coupled‐fluorophores that are randomly distributed in space. The results confirm previous optical spectroscopy‐based predictions of the orientation of CG‐2′s fluorophores, and the general applications of this dual‐polarization imaging approach for characterizing the optical properties of molecules containing multiple fluorophores is discussed.     

Fluorescent DNA base replacements: Reporters and sensors for biological systems

We describe the design, synthesis, and properties of nucleoside monomers in which the DNA base is replaced by fluorescent hydrocarbons and heterocycles, and the assembly of these monomers into DNA-like molecules in which the all bases are fluorescent. As monomers, such molecules have useful applications as reporters in the DNA context. The use of fluorescent DNA bases, rather than more traditional fluorophores tethered to the DNA strand, gives a more predictable location and orientation, and yields a more direct response to changes that occur within the helix. In addition to uses as monomers, such compounds can be assembled into polychromophoric oligomers ("oligodeoxyfluorosides" or ODFs). ODFs are water soluble, discrete molecules and are easily arranged into specific sequences by use of a DNA synthesizer. They have displayed a number of properties not readily available in commercial fluorophores, including large Stokes shifts, tunable excitation and emission wavelengths, and sensing responses to physical changes or molecular species in solution. We describe an approach to assembling and screening large sets of oligofluorosides for rapid identification of molecules with desirable properties. Such compounds show promise for applications in biochemistry, biology, environmental and materials applications.     

Modified DNA analogues that sense light exposure with color changes

We report the discovery of a new class of light-sensing molecules. These light sensors are composed of fluorophore oligomers assembled on a DNA backbone. A combinatorial library of tetrafluorophores consisting of over 14 000 compounds was synthesized and screened for rapid responses toward light exposure. Among the most light-sensitive molecules, at least three tetramers were found to respond to light exposure with apparent color changes, rather than simple photobleaching.     

Synthesis and spectral-luminescence properties of stilbene derivatives with two unconjugated fluorophores

Compounds that contain 2,5-diphenyloxazole and 2,5-diphenyl-1,3,4-oxadiazole fluorophore groupings that are not conjugated with one another were obtained by the phosphonate modification of the Wittig reaction from 2-[4 (3)-bromomethylphenyl]-5-(2-tosylaminophenyl)-1,3,4-oxadiazoles and 2-phenyl-5-[4(3)-formylphenyl]-1,3-oxazoles. The absorption and fluorescence spectra of the compounds obtained and the individual fluorophores that constitute the molecules of these compounds were investigated. Intramolecular nonradiating transfer of the electronic excitation energy between the fluorophores that make up the compounds and in binary mixtures of the corresponding luminophores was observed in solutions and in polymeric matrices.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1188–1191, September, 1982.     

Effect of chain length on the assembly of mercaptoalkanoic acid multilayer films ligated through divalent Cu ions

The structural stability of alkenthiolate monolayers assembled on gold surfaces is a result of the well-defined organization of the individual molecules within the film. The formation of three-dimensional films assembled by stacking multiple molecular monolayers is substantially more challenging because the correct organization of the molecular components is required not only within the individual monolayers but also between the monolayers of the film. In this paper we examine the structure of multilayer films based on mercaptoalkanoic acid monolayers in which ligation between adjacent monolayers is achieved using the interaction of carboxylic acid and thiol groups with a divalent Cu ion. Using contact angle analysis and atomic force microscopy, we show that the use of Cu(2+) has profound implications on the properties and structure of the multilayer film. In particular, the divalent ions effectively prohibit the complete assembly of the next monolayer. For multilayer SAMs assembled from short alkane chains with six methylene groups, we find that molecules in the incomplete adlayer organize themselves randomly over the underlying monolayer. However, as the number of methylene groups increases (11 and 16 methylene groups), the upper layer tends to fracture into discrete islands which cover around 50% of the surface. The height of these islands is found to be equal to that expected for a complete, well-ordered monolayer assembled from the equivalent mercaptoalkanoic acid molecules. This relationship between chain length and island growth results from the migration of molecules into ordered aggregates driven by the reduction of free energy associated with maximizing intermolecular interactions.     

Subdiffraction‐Resolution Fluorescence Microscopy of Myosin–Actin Motility

Subdiffraction‐resolution imaging by subsequent localization of single photoswitchable molecules can achieve a spatial resolution in the range of ～20 nm with moderate excitation intensities, but have so far been too slow for imaging faster dynamics in biology. Herein, we introduce a novel approach for video‐like subdiffraction microscopy based on rapid and reversible photoswitching of commercially available organic carbocyanine fluorophores. With the present concept, we demonstrate in vitro studies on the motility of fluorophore‐labeled actin filaments along myosin II. Actin filaments were densely labeled with carbocyanine fluorophores, and the gliding velocity adjusted by the concentration of ATP. At imaging frame rates of ～100 Hz, only 100 consecutive frames are sufficient to generate a single high‐resolution image of moving actin filaments with a lateral resolution of ～30 nm. A video‐like sequence is generated from individual reconstructed images by additionally applying a sliding window algorithm. We measured velocities of individual actin filaments of up to ～0.18 μm s^?1, observed strong bending and disruption of filaments as well as locally immobile fragments.     

Phosphorylation-driven protein-protein interactions: a protein kinase sensing system

A highly flexible protein kinase sensing system is described that furnishes severalfold changes in fluorescence in response to phosphorylation. A library of Src kinase peptide substrates was prepared that contained different environmentally sensitive fluorophores positioned at various sites on the active site directed sequence. Robust changes in fluorescent intensity were observed in the presence of a phosphotyrosine binding domain protein (Lck SH2 domain), which furnishes a hydrophobic environment for the fluorophore. This protein kinase sensing system has the advantages that the fluorescent indicator can be unobtrusively positioned on the peptide substrate, and that different environmentally sensitive fluorophores with distinct photophysical properties can be employed.     

Efficient White‐Light Generation from Ionically Self‐Assembled Triply‐Fluorescent Organic Nanoparticles

Low cost, simple, and environmentally friendly strategies for white‐light generation which do not require rare‐earth phosphors or other toxic or elementally scare species remain an essentially unmet challenge. Progress in the area of all‐organic approaches is highly sought, single molecular systems remaining a particular challenge. Taking inspiration from the designer nature of ionic‐liquid chemistry, we now introduce a new strategy toward white‐light emission based on the facile generation of nanoparticles comprising three different fluorophores assembled in a well‐defined stoichiometry purely through electrostatic interactions. The building blocks consist of the fluorophores aminopyrene, fluorescein, and rhodamine 6G which represent blue, green, and red‐emitting species, respectively. Spherical nanoparticles 16(±5) nm in size were prepared which display bright white‐light emission with high fluorescence quantum efficiency (26 %) and color coordinate at (0.29, 0.38) which lie in close proximity to pure white light (0.33, 0.33). It is noteworthy that this same fluorophore mixture in free solution yields only blue emission. Density functional theory calculations reveal H‐bond and ground‐state proton transfer mediated absolute non‐parallel orientation of the constituent units which result in frustrated energy transfer, giving rise to emission from the individual centers and concomitant white‐light emission.     

Fluorescence images of DNA-bound YOYO between coupled silver particles

Oligonucleotide-bound silver particles were coupled through hybridization with target complementary oligonucleotides. YOYO molecules were intercalated into DNA duplexes bound between the coupled metal particles. Fluorescence images of YOYO molecules were monitored by scanning confocal microscopy. Relative to the free single YOYO, the emission brightness of the image was enhanced 80-fold after intercalating the fluorophores into the DNA duplexes between the coupled silver particles. Some images of the labeled metal particle dimers were observed to be dumbbell-shaped, suggesting that the stretching of intercalated YOYO molecules was restricted because of the orientation effect of fluorophores. The shortened lifetime of YOYO molecules between the coupled metal particles indicated that the fluorescence was enhanced via a near-field interaction mechanism between the fluorophore and the metal nanoparticle.     

Control of Circularly Polarized Luminescence by Orientation of Stacked π‐Electron Systems

Planar chiral building blocks based on 4,7,12,15‐tetrasubstituted [2.2]paracyclophanes were obtained via a synthetic route involving an optical resolution step. Planar chiral enantiomers, comprising two fluorophores that were stacked to form a V‐shaped higher‐ordered structure, were synthesized from these building blocks. The V‐shaped molecules emitted intense circularly polarized luminescence (CPL). Their chiroptical properties were compared with those of X‐shaped molecules bearing the same two fluorophores stacked together. The CPL sign of the X‐shaped molecule was opposite to that of the V‐shaped molecule, which is supported by the theoretical results, indicating that the CPL sign can be controlled by the orientation of the stacked fluorophores.     

Enhanced fluorescence images for labeled cells on silver island films

Silver island films (SIFs) were deposited on glass substrates to serve as supports. T-Lymphocytic (PM1) cell lines were labeled by Alexa Fluor 680-dextran conjugates on the membranes or by YOYO in the nuclei. The fluorescence images of the cell lines were recorded in the emission intensity and lifetime using scanning confocal microscopy. The fluorescence signals by the fluorophores bound on the cell membranes were enhanced significantly by SIF supports as compared with those on the glass. In addition to the increase in the intensity, there was a dramatic shortening of the emission lifetime. In contrast to the Alexa Fluor 680 fluorophores on the membranes, the YOYO fluorophores intercalated in the cell nuclei were not influenced significantly by the silver islands. This result can be interpreted by an effect of the distance on coupling between the fluorophores and metal particles: the fluorophores on the cell membranes are localized within, but the fluorophores in the cell nuclei are beyond the region of metal-enhanced fluorescence. Thus, the metal supports can be used to improve the detection sensitivity for target molecules on cell surfaces when they are fluorescently labeled.     

Deconvolution of fluorescence spectra: contribution to the structural analysis of complex molecules

Fluorescence spectroscopy is a sensitive analytical tool in the studies of both simple and complex molecular structures. In complex molecules, however, determining the number and position of components may give a specific insight into the structure, complementary to the other analytical techniques. We applied log–normal model to analyze fluorescence of simple monofluorophore molecule. In order to analyze spectra where both fluorophores and Raman emission bands were present, we developed a method obtained by combination of the symmetric, Gaussian, for Raman and asymmetric, log–normal model, for fluorescence, applicable to the molecules of different complexity. Technically, for each sample we varied excitation wavelength with 5 nm step and recorded the corresponding emission spectra. They were subsequently used for component analysis. Position of each component was plotted against the excitation wavelength. Applying this approach we could identify minimal number of components having stable positions, while their approximate probability density (APD) in a spectral series was correlated with the probable number of fluorophores in the molecule. The method was tested on molecules containing different number of fluorophores: monomers involved in the synthesis of plant polymer lignin—coniferyl alcohol (one fluorophore), ferulic acid (two fluorophores) and on lignin model compound produced from these monomers (many fluorophores). All investigated species belong to benzene-substituted class of compounds, and it is reasonable to assume that they have similar fluorescence band contour. We also report the results of environmental scanning electron microscopy (ESEM) studies showing multilayered dehydrogenative polymer (DHP) structure, in order to show complexity of the polymer. Our results present complementarity of these two approaches in the structural studies of the lignin model compound.     

Probing the Limits of Selectivity in a Recognition‐Mediated Reaction Network Embedded within a Dynamic Covalent Library

Two recognition‐mediated reaction processes operating through reactive binary complexes drive resolution of a 24‐component dynamic covalent library, assembled from individual aldehydes and nucleophiles. The effectiveness of the library resolution and selective amplification of one recognition‐enabled species over another is limited by the difference in the rates of the recognition‐mediated reactive processes and the strength of the recognition processes employed in the dynamic system.     

Enhanced fluorescence of Cy5-labeled oligonucleotides near silver island films: a distance effect study using single molecule spectroscopy

We investigated fluorescence enhancements and lifetime reductions of Cy5 probe molecules at various distances from the deposited silver island film surface using single molecule spectroscopic methods. The proximity of fluorophore molecules to the surface was controlled by alternating layers of biotinylated bovine serum albumin (BSA-biotin) and avidin, followed by binding of Cy5-labeled oligonucleotides to the top of a BSA-biotin layer structure. We observed dramatically varied brightness of fluorophores with distances from metal structures as well with reduced blinking in the presence of silver island films. In addition, distributions of fluorescence lifetimes and apparent emission intensities from individual molecules indicate an inhomogeneous nature of local matrix surface near metallic nanostructures. These studies illustrate the exclusive information that is otherwise hidden in ensemble measurements.     

有组织介质中的偶合反应Ⅰ.油溶性成色剂的偶合活性

本文采用连续流动装置测量,并配合数值模拟法得到表征五种油珠分散状叔戊酰苯胺型成色剂的油珠偶合活性的偶合反应比速率常数和表观偶合速率常数,同时测定了叔戊酰苯胺型成色剂油珠在胶片层中的照相活性以及表征它们在非水溶液中分子偶合活性的解离常数pKa值,并且比较了上述结果。研究表明,油珠状成色剂的反应规律与分子状成色剂的反应规律是不相同的,这是由于经过“分子组装”后的成色剂油珠在反应时不再以分子为反应单元而是以分子组装体为单元。     

Organized arrays of individual DNA molecules tethered to supported lipid bilayers

An unappreciated aspect of many single-molecule techniques is the need for an inert surface to which individual molecules can be anchored without compromising their biological integrity. Here, we present new methods for tethering large DNA molecules to the surface of a microfluidic sample chamber that has been rendered inert by the deposition of a supported lipid bilayer. These methods take advantage of the "bio-friendly" environment provided by zwitterionic lipids, but still allow the DNA molecules to be anchored at fixed positions on the surface. We also demonstrate a new method for constructing parallel arrays of individual DNA molecules assembled at defined positions on a bilayer-coated, fused silica surface. By using total internal reflection fluorescence microscopy to visualize the arrays, it is possible to simultaneously monitor hundreds of aligned DNA molecules within a single field-of-view. These molecular arrays will significantly increase the throughput capacity of single-molecule, fluorescence-based detection methods by allowing parallel processing of multiple individual reaction trajectories.     

Latent fluorophore based on the trimethyl lock

Fluorescent molecules are essential for basic research in the biological sciences and have numerous practical applications. Herein is described the synthesis and use of a new class of latent fluorophores based on a novel design element, the trimethyl lock, that confers distinct advantages over extant fluorophores and pro-fluorophores. A diacetyl version of the latent fluorophore is stable in a biological environment, but rapidly yields rhodamine 110 upon acetyl-group hydrolysis by pig liver esterase or endogenous esterases in the cytosol and lysosomes of human cells. This design element is general and, hence, provides access to an ensemble of useful latent fluorophores.     

A facile combinatorial approach to construct a ratiometric fluorescent sensor: application for the real-time sensing of cellular pH changes

Realtime monitoring of the cellular environment, such as the intracellular pH, in a defined cellular space provides a comprehensive understanding of the dynamics processes in a living cell. Considering the limitation of spatial resolution in conventional microscopy measurements, multiple types of fluorophores assembled within that space would behave as a single fluorescent probe molecule. Such a character of microscopic measurements enables a much more flexible combinatorial design strategy in developing fluorescent probes for given targets. Nanomaterials with sizes smaller than the microscopy spatial resolution provide a scaffold to assemble several types of fluorophores with a variety of optical characteristics, therefore providing a convenient strategy for designing fluorescent pH sensors. In this study, fluorescein (CF) and tetramethylrhodamine (CR) were assembled on a DNA nanostructure with controlling the number of each type of fluorophore. By taking advantage of the different responses of CF and CR emissions to the pH environment, an appropriate assembly of both CF and CR on DNA origami enabled a controlled intensity of fluorescence emission and ratiometric pH monitoring within the space defined by DNA origami. The CF and CR-assembled DNA origami was successfully applied for monitoring the intracellular pH changes.

A combinatorial assembly of two types of intensity-based fluorophores on a DNA nanostructure provided a ratiometric pH probe with high emission intensity for monitoring intracellular pH changes.     

Parallel factor analysis of spider fluorophores

Fluorophores from the hemolymph of yellow sac spiders (Cheiracanthium mildei) have been characterized using excitation emission matrix (EEM) fluorescence spectroscopy. This approach provides characterization of fluorophores present in the organism without having to isolate pure samples. Minimal variation occurs between individual samples and each EEM has two distinct peaks, suggesting two fluorophores may be present in the hemolymph. Parallel factor analysis reveals that three fluorophores (with excitation and emission maxima at 270/319, 330/389, and 350/465 nm) best explains the sample to sample variation. By comparing the spectra of the three individual components to fluorophores found in scorpions it is shown that these spiders possess different fluorophores than scorpions. Furthermore, the fluorescence observed is not consistent with beta-carboline or 4-methyl-7-hydroxycoumarin, two compounds previously described in scorpions.