Color-Change Photoswitching of an Alkynylpyrene Excimer Dye.

We describe a photoswitchable DNA-based dimeric dye that visibly changes fluorescence from green to blue upon UV irradiation. A novel bis-alkyne-dependent [2+2+2] cycloaddition is proposed as a mechanism for the color change in air. The photoinduced structural switching results in spatial separation of stacked pyrene units, thereby causing selective loss of the excimer emission. We demonstrate and suggest several applications for this novel photoswitch.

Fast Optimization of LiMgMnOx/La2O3 Catalysts for the Oxidative Coupling of Methane.

The development of efficient catalyst for oxidative coupling of methane (OCM) reaction represents a grand challenge in direct conversion of methane into other useful products. Here, we reported that a newly developed combinatorial approach can be used for ultrafast optimization of La2O3-based multicomponent metal oxide catalysts in OCM reaction. This new approach integrated inkjet printing assisted synthesis (IJP-A) with multidimensional group testing strategy (m-GT) tactfully takes the place of conventionally high-throughput synthesis-and-screen experiment. Just within a week, 2048 formulated LiMgMnOx-La2O3 catalysts in a 64·8·8·8·8 = 262 144 compositional space were fabricated by IJP-A in a four-round synthesis-and-screen process, and an optimized formulation has been successfully identified through only 4·8 = 32 times of tests via m-GT screening strategy. The screening process identifies the most promising ternary composition region is Li0-0.48Mg0-6.54Mn0-0.62-La100Ox with an external C2 yield of 10.87% at 700 °C. The yield of C2 is two times as high as the pure nano-La2O3. The good performance of the optimized catalyst formulation has been validated by the manual preparation, which further prove the effectiveness of the new combinatorial methodology in fast discovery of heterogeneous catalyst.

In Vitro Fluorogenic Real-Time Assay of the Repair of Oxidative DNA Damage.

The repair of oxidative damage to DNA is essential to avoid mutations that lead to cancer. Oxidized DNA bases, such as 8-oxoguanine, are a main source of these mutations, and the enzyme 8-oxoguanine glycosylase 1 (OGG1) is the chief human enzyme that excises 8-oxoguanine from DNA. The activity of OGG1 has been linked to human inflammation responses and to cancer, and researchers are beginning to search for inhibitors of the enzyme. However, measuring the activity of the enzyme typically requires laborious gel-based measurements of radiolabeled DNAs. Here we report the design and properties of fluorogenic probes that directly report on the activity of OGG1 (and its bacterial homologue Fpg) in real time as the oxidized base is excised. The probes are short, modified DNA oligomers containing fluorescent DNA bases and are designed to utilize 8-oxoguanine itself as a fluorescence quencher. Screening of combinations of fluorophores and 8-oxoguanine revealed two fluorophores, pyrene and tCo, that are strongly quenched by the damaged base. We tested 42 potential probes containing these fluorophores: the optimum probe, OGR1, yields a 60-fold light-up signal in vitro with OGG1 and Fpg. It can report on oxidative repair activity in mammalian cell lysate and with bacterial cells overexpressing a repair enzyme. Such probes might prove useful in quantifying enzyme activity and performing competitive inhibition assays.

Mix and print: fast optimization of mesoporous CuCeZrO(w) for catalytic oxidation of n-hexane.

Fast optimization of mesoporous ternary metal oxide (CuCeZrO(w)) catalysts for n-hexane oxidation is achieved via a newly developed combinatorial approach based on ink-jet printing assisted synthesis and multi-dimensional group testing.

Pattern-based detection of toxic metals in surface water with DNA polyfluorophores.

Heavy metal contamination of water can be toxic to humans and wildlife; thus the development of methods to detect this contamination is of high importance. Here we describe the design and application of DNA-based fluorescent chemosensors on microbeads to differentiate eight toxic metal ions in water. We developed and synthesized four fluorescent 2'-deoxyribosides of metal-binding ligands. A tetramer-length oligodeoxy-fluoroside (ODF) library of 6561 members was constructed and screened for sequences responsive to metal ions, of which seven sequences were selected. Statistical analysis of the response patterns showed successful differentiation of the analytes at concentrations as low as 100 nM. Sensors were able to classify water samples from 13 varied sites and quantify metal contamination in unknown specimens. The results demonstrate the practical potential of bead-based ODF chemosensors to analyze heavy metal contamination in water samples by a simple and inexpensive optical method.

DNA-polyfluorophore Chemosensors for Environmental Remediation: Vapor-phase Identification of Petroleum Products in Contaminated Soil.

Contamination of soil and groundwater by petroleum-based products is an extremely widespread and important environmental problem. Here we have tested a simple optical approach for detecting and identifying such industrial contaminants in soil samples, using a set of fluorescent DNA-based chemosensors in pattern-based sensing. We used a set of diverse industrial volatile chemicals to screen and identify a set of five short oligomeric DNA fluorophores on PEG-polystyrene microbeads that could differentiate the entire set after exposure to their vapors in air. We then tested this set of five fluorescent chemosensor compounds for their ability to respond with fluorescence changes when exposed to headgas over soil samples contaminated with one of ten different samples of crude oil, petroleum distillates, fuels, lubricants and additives. Statistical analysis of the quantitative fluorescence change data (as Δ(R,G,B) emission intensities) revealed that these five chemosensors on beads could differentiate all ten product mixtures at 1000 ppm in soil within 30 minutes. Tests of sensitivity with three of the contaminant mixtures showed that they could be detected and differentiated in amounts at least as low as one part per million in soil. The results establish that DNA-polyfluorophores may have practical utility in monitoring the extent and identity of environmental spills and leaks, while they occur and during their remediation.

Monitoring eukaryotic and bacterial UDG repair activity with DNA-multifluorophore sensors.

We report the development of simple fluorogenic probes that report on the activity of both bacterial and mammalian uracil-DNA glycosylase (UDG) enzymes. The probes are built from short, modified single-stranded oligonucleotides containing natural and unnatural bases. The combination of multiple fluorescent pyrene and/or quinacridone nucleobases yields fluorescence at 480 and 540 nm (excitation 340 nm), with large Stokes shifts of 140-200 nm, considerably greater than previous probes. They are strongly quenched by uracil bases incorporated into the sequence, and they yield light-up signals of up to 40-fold, or ratiometric signals with ratio changes of 82-fold, on enzymatic removal of these quenching uracils. We find that the probes are efficient reporters of bacterial UDG, human UNG2, and human SMUG1 enzymes in vitro, yielding complete signals in minutes. Further experiments establish that a probe can be used to image UDG activity by laser confocal microscopy in bacterial cells and in a human cell line, and that signals from a probe signalling UDG activity in human cells can be quantified by flow cytometry. Such probes may prove generally useful both in basic studies of these enzymes and in biomedical applications as well.

Genetically encoded multispectral labeling of proteins with polyfluorophores on a DNA backbone.

Genetically encoded methods for protein conjugation are of high importance as biological tools. Here we describe the development of a new class of dyes for genetically encoded tagging that add new capabilities for protein reporting and detection via HaloTag methodology. Oligodeoxyfluorosides (ODFs) are short DNA-like oligomers in which the natural nucleic acid bases are replaced by interacting fluorescent chromophores, yielding a broad range of emission colors using a single excitation wavelength. We describe the development of an alkyl halide dehalogenase-compatible chloroalkane linker phosphoramidite derivative that enables the rapid automated synthesis of many possible dyes for protein conjugation. Experiments to test the enzymatic self-conjugation of nine different DNA-like dyes to proteins with HaloTag domains in vitro were performed, and the data confirmed the rapid and efficient covalent labeling of the proteins. Notably, a number of the ODF dyes were found to increase in brightness or change color upon protein conjugation. Tests in mammalian cellular settings revealed that the dyes are functional in multiple cellular contexts, both on the cell surface and within the cytoplasm, allowing protein localization to be imaged in live cells by epifluorescence and laser confocal microscopy.

Templated chemistry for monitoring damage and repair directly in duplex DNA.

We report the fluorogenic detection of the product of base excision repair (an abasic site) in a specific sequence of duplex DNA. This is achieved by DNA-templated chemistry, employing triple helix-forming probes that contain unnatural nucleobases designed to selectively recognize the site of a missing base. Light-up signals of up to 36-fold were documented, and probes could be used to monitor enzymatic removal of a damaged base.

DNA polyfluorophores for real-time multicolor tracking of dynamic biological systems.

Dye-ing to live: Spectral limitations of common organic dyes make it difficult or impossible to visualize and follow multiple biological components in rapidly moving systems. The development of a multispectral set of improved DNA-scaffolded fluorophores is described. Their use in multicolor cellular imaging (see scheme) and in tracking of biological motions on the subsecond timescale is demonstrated.

Fluorescent DNA chemosensors: identification of bacterial species by their volatile metabolites.

Polyfluorophores built on a DNA scaffold (ODFs) were synthesized and tested for fluorescence responses to the volatiles from M. tuberculosis, E. coli and P. putida in closed Petri dishes. Two sensors in a pattern-based response could distinguish the bacterial strains accurately, suggesting the use of ODFs in rapid identification of infectious agents.

Combinatorial synthesis of galactosyl-1,3,5-triazines as novel nucleoside analogues.

Herein we report a parallel solid-phase synthesis of 1,3,5-triazine based nucleoside analogues by a three-step substitution, starting from 2,4,6-trichloro-1,3,5-triazine. A library of 80 galactosyl-1,3,5-triazine compounds was prepared in high purity without extensive reaction conditions or tedious purification, suggesting the generality of this method.

Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging.

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 Huisgen-Sharpless 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.

Diversity-oriented fluorescence library approach (DOFLA) to the discovery of chymotrypsin sensor.

The diversity-oriented fluorescence library approach (DOFLA) has emerged and found applications in various fields to meet the acute demands for novel fluorescence sensors. The power of this approach has been demonstrated with the impressive discoveries of novel sensors for polymers such as DNA and heparin or for small molecules such as GTP and glutathione ( J. Am. Chem. Soc. 2003, 125, 1130- 1131 ; J. Am. Chem. Soc. 2006, 128, 10380- 10381 ; J. Am. Chem. Soc. 2007, 129, 4510- 4511 ; Chem. Commun. [Online early access]. DOI: 10.1039/b717058k. Published online Dec 11, 2008. http://www.rsc.org/publishing/journals/CC/article.asp?doi=b717058k ). Herein we report the application of this approach on quinaldinium fluorescent dye library synthesis on solid support and novel chymotrypsin sensor discovery. The new sensors are not only selective to chymotrypsin over other proteins but also only to the active conformation of chymotrypsin.

Discovery of heparin chemosensors through diversity oriented fluorescence library approach.

Two novel heparin sensors, Heparin Orange and Heparin Blue, were developed by a diversity oriented fluorescence library approach (DOFLA) from a benzimidazolium library; the discovered compounds showed remarkable properties and have the potential to be applied to monitoring heparin levels in clinical plasma samples for point-of-care detection.

Combinatorial synthesis of benzimidazolium dyes and its diversity directed application toward GTP-selective fluorescent chemosensors.

Highly selective fluorescence turn-on GTP sensor, GTP Green, was discovered by a diversity directed sensor approach, combined by solid-phase combinatorial synthesis of a benzimidazolium library and high-throughput screening.

Tools for target identification and validation.

Reliable technologies for addressing target identification and validation are the foundation of successful drug development. Microarrays have been well utilized in genomics/proteomics approaches for gene/protein expression profiling and tissue/cell-scale target validation. Besides being used as an essential step in analyzing high-throughput experiments such as those involving microarrays, bioinformatics can also contribute to the processes of target identification and validation by providing functional information about target candidates and positioning information to biological networks. Antisense technologies (including RNA interference technology, which is recently very 'hot') enable sequence-based gene knockdown at the RNA level. Zinc finger proteins are a DNA transcription-targeting version of knockdown. Chemical genomics and proteomics are emerging tools for generating phenotype changes, thus leading to target and hit identifications. NMR-based screening, as well as activity-based protein profiling, are trying to meet the requirement of high-throughput target identification.