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We recently described the assembly of fluorescent deoxyriboside monomers (“fluorosides”) into DNA-like phosphodiester oligomers (oligodeoxyfluorosides, or ODFs) in which hydrocarbon and heterocyclic aromatic fluorophores interact both physically and electronically. Here we report the identification of a multicolor set of water-soluble ODF dyes that display emission colors across the visible spectrum, and all of which can be simultaneously excited by long-wavelength UV light at 340−380 nm. Multispectral dye candidates were chosen from a library of 4096 tetramer ODFs constructed on PEG-polystyrene beads using a simple long-pass filter to observe all visible colors at the same time. We re-synthesized and characterized a set of 23 ODFs containing one to four individual chromophores, and included 2−3 spacer monomers to increase aqueous solubility and minimize aggregation. Emission maxima of this set range from 376 nm to 633 nm, yielding apparent colors from violet to red, all of which can be visualized directly. The spectra of virtually all ODFs in this set varied considerably from the simple combination of monomer components, revealing extensive electronic interactions between the presumably stacked monomers. In addition, comparisons of anagrams in the set (isomers having the same components in a different sequence) reveal the importance of nearest-neighbor interactions in the emissive behavior. Preliminary experiments with human tumor (HeLa) cells, observing two ODFs by laser confocal microscopy, showed that they can penetrate the outer cellular membrane, yielding cytoplasmic localization. In addition, a set of four distinctly-colored ODFs was incubated with live zebrafish embryos, showing tissue penetration, apparent biostability, and no apparent toxicity. The results suggest that ODF dyes may be broadly useful as labels in biological systems, allowing the simultaneous tracking of multiple species by color, and allowing visualization in moving systems where classical fluorophores fail.

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We demonstrate the use of fluorescent molecular rotors as probes for detecting biomolecular interactions, specifically peptide-protein interactions. Molecular rotors undergo twisted intramolecular charge transfer upon irradiation, relax via the nonradiative torsional relaxation pathway, and have been typically used as viscosity probes. Their utility as a tool for detecting specific biomolecular interactions has not been explored. Using the well characterized p53-Mdm2 interaction as a model system, we designed a 9-(2-carboxy-2-cyanovinyl) julolidine-based p53 peptide reporter, JP1-R, which fluoresces conditionally only upon Mdm2 binding. The reporter was used in a rapid, homogeneous assay to screen a fragment library for antagonists of the p53-Mdm2 interaction, and several inhibitors were identified. Subsequent validation of these hits using established secondary assays suggests increased sensitivity afforded by JP1-R. The fluorescence of molecular rotors contingent upon target binding makes them a versatile tool for detecting specific biomolecular interactions.

Most current approaches to multiantigen fluorescent imaging require overlaying of multiple images taken with separate filter sets as a result of differing dye excitation requirements. This requirement for false-color composite imaging prevents the user from visualizing multiple species in real time and disallows imaging of rapidly moving specimens. To address this limitation, here we investigate the use of oligodeoxyfluoroside (ODF) fluorophores as labels for antibodies. ODFs are short DNA-like oligomers with fluorophores replacing the DNA bases and can be assembled in many colors with excitation at a single wavelength. A DNA synthesizer was used to construct several short ODFs carrying a terminal alkyne group and having emission maxima of 410-670 nm. We developed a new approach to antibody conjugation, using HuisgenSharpless cycloaddition, which was used to react the alkynes on ODFs with azide groups added to secondary antibodies. Multiple ODF-tagged secondary antibodies were then used to mark primary antibodies. The set of antibodies was tested for spectral characteristics in labeling tubulin in HeLa cells and revealed a wide spectrum of colors, ranging from violet-blue to red with excitation through a single filter (340-380 nm). Selected sets of the differently labeled secondary antibodies were then used to simultaneously mark four antigens in fixed cells, using a single image and filter set. We also imaged different surface tumor markers on two live cell lines. Experiments showed that all colors could be visualized simultaneously by eye under the microscope, yielding multicolor images of multiple cellular antigens in real time.bioconjugation | immunofluorescence | multiplex T o understand the complexity and dynamics of the molecular interactions in biological systems, the parallel analysis of multiple species, such as different proteins in a cell or cells in a tissue specimen, is often needed (1, 2). The most common mode of imaging for tracking and labeling such species is fluorescence microscopy. For multispecies imaging, this typically requires the use of various fluorophores having distinct excitation and emission wavelengths. Commonly available organic fluorophores are typically used to tag biomolecules for these purposes (3, 4), which allows the visualization of three, or occasionally more, species via the use of separate excitation and emission filters. Using this strategy, one can label multiple cellular antigens, for example, by use of different commercially available dye-labeled secondary antibodies.Although this approach is widely employed, some nonideal factors still exist. One of the major limiting issues of common organic dyes is that they have widely separated absorption spectra. This fact requires the researcher to use specialized filter sets and take a separate image for each dye; the final multicolor image is then constructed by overlaying false-color single-dye images. This approach enforces some restrictions on the researcher and equipment and places limitations on data acquisition. For ex...

The quenching properties of a series of oligodeoxyribosides bearing fluorophore 'bases' is described. Sequences of adjacent, π-stacked pyrenes exhibit stronger electronic interactions visible in both absorbance and emission spectra than pyrenes that are insulated by intervening adenines. Quenching by N, N′-dimethyl-4,4′-bipyridinium dichloride is efficient for excimer-and exciplex-forming oligomers, with Stern-Volmer constants comparable to conjugated polymer "superquenching" schemes.Fluorescence quenching-based strategies have recently become broadly useful in nucleic acidbased biotechnologies. Quencher-fluorophore pairs are widely employed in DNA sequence reporting, and are found in multiple formats such as PNA beacons, 1 varied classes of molecular beacons, 2 quenched autoligation probes, 3 and "Scorpion" 4 and "Pacman" 5 probes. Removal of a quencher from a fluorescent label results in an increase in emission, thus yielding a clear and simple signal for the presence of a genetic sequence. However, the sensitivity of such methods depends heavily on the efficiency of quenching, and as a result there has been a substantial amount of research recently on design of new quenchers for existing labels, 6 and on careful matching of specific quenchers with known fluorophores. 7 Even with this optimization, the degree of quenching using discrete labels is often limiting in nucleic acid sequence reporting. Importantly, recent studies of conjugated luminescent polymers have shown exceptionally high quenching efficiencies, due to the mobility of the exciton in a given polymer chain. 8 This has led to their recent application in aggregate-based DNA assays. 9 However, such strategies have not found application in labeledd nucleic acid probes, possibly because of the large size and inhomogeneity of such polymers, and because it would be difficult to conjugate them to synthetic DNA probes.Here we describe the finding of highly efficient quenching in a different class of oligomeric reporters in which the fluorophores are assembled on a DNA backbone. The molecules are well-defined, relatively small, water-soluble oligomers and are trivial to conjugate to DNA. We find that they can display quenching efficiencies that are unprecedented for discrete organic molecules, and rival values previously seen only for conjugated polymeric systems.We have recently studied these DNA-like fluorophores (oligodeoxyfluorosides (ODFs)) as a new class of reporters and sensors. 10 They display highly diverse and tunable properties kool@stanford.edu. NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript depending on length, composition, and sequence. To begin to explore the quenching properties of such fluorophores, we constructed a simple oligomer series containing pyrene nucleoside monomers (see structures) to explore the effect of chain length on the optical properties. It is known that pyrene molecules can interact, depending on their orientation and proximity, exhibiting spectral changes both in th...

We describe studies aimed at testing whether oligomeric exciplex-and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Förster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3' end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Förster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single wavelength; thus, ODFs may be candidates as "universal FRET donors", thus allowing multicolor FRET of multiple species to be carried out with one excitation.

DNA-scaffolded oligodeoxyriboside fluorophores (ODFs) were used as the reporters in turn-on sensing of enzymatic bond-cleaving activity. A tetramer ODF of pyrene deoxynucleosides displayed high quenching efficiency when conjugated via ester linkages with a dabcyl quencher, and yielded large signal increases with several enzymes in vitro and in intact human cells.