Polyfluorophores on a DNA backbone: sensors of small molecules in the vapor phase

Development of a smartphone-based real time cost-effective VOC sensor

Air pollution by various volatile organic compounds (VOC) is a matter of concern for us. So in this regard, designing real-time VOC responsive materials is gaining attention across the scientific community. In this present work, we have developed an inexpensive VOC sensor based on a Meisenheimer complex derived from picric acid and N,N'-dicyclohexylcarbodiimide. The sensor coated TLC plate was used as a sensor of potentially harmful VOCs. The sensor coated TLC plate looks deep red colored and does not show any fluorescence emission under 366 nm UV light. But in the presence of harmful volatile organic compounds like benzene, toluene, xylene, etc the sensor coated TLC plate becomes orange colored and it also shows strong yellow emission under 366 nm UV light. This property was utilized to detect the VOCs by fluorescence spectroscopy. The detection limit for various VOCs was found to be in the range of 0.7-9 ppm. To make the sensor user friendly, we have demonstrated a method where VOCs can be detected using a smartphone in real-time and also the setup is portable.

An electron-rich small AIEgen as a solid platform for the selective and ultrasensitive on-site visual detection of TNT in the solid, solution and vapor states

Promising research on AIEgen (aggregation-induced emission active fluorogens)-based sensors for the detection of explosives (mostly picric acid) is primarily dominated by polymeric molecules. However, herein, we report the ability of a recently developed anthracene-based electron-rich π-conjugate as a small and suitable AIEgen for the selective and sensitive detection of 2,4,6-trinitrotoluene (TNT) through fluorescence (PL) quenching. This fluorophore consists of trimethoxybenzene-linked anthranyl-π-phenothiazine, which is recognized as a significantly electron-rich AIEgen suitable for the selective detection of TNT detection. The detection of TNT was performed in the solid, liquid and vapor states using this AIEgen in the aggregate or solid-state. The detection limit in the solution state was measured to be 3.2 × 10-9 M. When this fluorophore was impregnated on a paper strip for on-site visual detection, TNT was detected up to the 10-14 M level by the naked eye using a 365 nm UV-torch. The paper strip was also successfully used to detect TNT in the vapour state. This application was further extended to detect TNT in field soil. The detection of TNT by replacing trimethoxybenzene in the fluorophore with dimethoxy or monomethoxy was a failure, indicating the requirement of an adequate electron-rich system. Unlike the previous report with static quenching as the main reason for TNT detection, our experimental observations demonstrated the participation of favorable photo-induced electron transfer (PET) between TNT and the fluorophore as the origin of the PL quenching.

Regulation of the Metal Center and Coordinating Anion of Mononuclear Ln(III) Complexes to Promote an Efficient Luminescence Response to Various Organic Solvents

A series of mononuclear lanthanide complexes [Ln(L1)(NO₃)₃], (Ln = Dy(III), 1; Tb(III), 3; and Eu(III), 4; L1 = (N¹E,N²E)-N¹,N²-bis((1-methyl-1H-benzo[d]imidazol-2-yl)methylene)cyclohexane-1,2-diamine) is obtained by reacting N-methylbenzimidazole-2-carbaldehyde (L2) and 1,2-cyclohexanediamine (L3) with Ln(NO₃)₃·6H₂O under solvothermal conditions. L1 ligand is produced via an in situ Schiff base reaction of two molecules of L2 and one molecule of L3. The metal center Ln(III) is in a N₄O₆ environment formed by L1 and NO₃^-. NaSCN is added on the basis of 1 synthesis. One SCN^- replaces one of the three coordinated NO₃^- anions in the 1 structure, and the complex [Dy(L1)(NO₃)₂(SCN)]·CH₃CN (2) is synthesized. The complex 1 shows excellent luminescence response to petroleum ether (PET), an organic solvent. To the best of our knowledge, this study is the first to use a complex for sensing responses to PET. When the metal center is changed, the obtained mononuclear complexes 3 and 4 show an excellent luminescence response to tetrahydrofuran (THF). Lastly, 2 obtained by changing the coordinating anion shows an excellent luminescence response to dichloromethane. Herein, for the first time, we regulate the metal center and coordinating anion of lanthanide complexes to adjust the recognition and response of these complexes to different organic solvents.

Structural Elucidation and Ultrasensitive Analyses of Volatile Organic Compounds by Paper-Based Nano-Optoelectronic Noses

Paper-based optoelectronic noses (OENs) are being developed based on printing of organic and organometallic reagents on hydrophilic substrates that can visualize the odor of volatiles. In this work, we report for the first time the use of nanoparticles for fabrication of novel paper-based OENs, which represent much higher sensitivity and produce simple but discriminant colorimetric signature of volatile metabolomes. This nano-optoelectronic nose (NOEN) system, which is fabricated by dropping of gold and silver nanoparticles (each synthesized by 8 chemical species) on the paper, gives obvious colorimetric signatures for chemicals having individual or combined functional groups. Owning to their ultrasensitivity, these simple devices need very small amounts of analytes. These devices could detect and discriminate 45 volatile organic compounds in 9 chemical families including phenols, alchohols, ketones, aldehydes, amines, acids, esters, arenes, and hydrocarbons. In addition to excellent discrimination ability, this NOEN sensor shows ultrahigh sensitivity such that could determine volatile compounds with detection limits around or lower than 10 ppb. Moreover, it can be combined with multivariate calibration methods for quantitative analysis of a metabolite in a complex mixture.

Chemistries for DNA Nanotechnology

The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

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.

A single molecular fluorescent probe for selective and sensitive detection of nitroaromatic explosives: A new strategy for the mask-free discrimination of TNT and TNP within same sample

A simple naphthalene based fluorescent probe was first time reported as dual sensing of 2,4,6-trinitrotolune (TNT) and 2,4,6-trinitrophenol (TNP) by distinguishable changes in both solution color change and fluorescence within same sample without any mask agent. Upon addition of TNT and TNP, the strong emission quenching at 412nm and a new emission band at 530nm was observed, respectively. In addition, the sensing mechanism was evaluated by DFT calculations by Gaussian 09 software.

Efficient synthesis of fluorescent alkynyl C-nucleosides via Sonogashira coupling for the preparation of DNA-based polyfluorophores

A facile and general procedure for the preparation of alkynyl C-nucleosides with varied fluorophores is presented. Sonogashira coupling was used as a key reaction to conjugate the dyes to an easily accessible ethynyl functionalized deoxyribose derivative. The new C-nucleosides were used for the preparation of DNA-based polyfluorophores.

Fluorescence based explosive detection: from mechanisms to sensory materials

The detection of explosives is one of the current pressing concerns in global security. In the past few decades, a large number of emissive sensing materials have been developed for the detection of explosives in vapor, solution, and solid states through fluorescence methods. In recent years, great efforts have been devoted to develop new fluorescent materials with various sensing mechanisms for detecting explosives in order to achieve super-sensitivity, ultra-selectivity, as well as fast response time. This review article starts with a brief introduction on various sensing mechanisms for fluorescence based explosive detection, and then summarizes in an exhaustive and systematic way the state-of-the-art of fluorescent materials for explosive detection with a focus on the research in the recent 5 years. A wide range of fluorescent materials, such as conjugated polymers, small fluorophores, supramolecular systems, bio-inspired materials and aggregation induced emission-active materials, and their sensing performance and sensing mechanism are the centerpiece of this review. Finally, conclusions and future outlook are presented and discussed.

DNA-Based Oligochromophores as Light-Harvesting Systems

The chromophores ethynyl pyrene as blue, ethynyl perylene as green and ethynyl Nile red as red emitter were conjugated to the 5-position of 2'-deoxyuridine via an acetylene bridge. Using phosphoramidite chemistry on solid phase labelled DNA duplexes were prepared that bear single chromophore modifications, and binary and ternary combinations of these chromophore modifications. The steady-state and time-resolved fluorescence spectra of all three chromophores were studied in these modified DNA duplexes. An energy-transfer cascade occurs from ethynyl pyrene over ethynyl perylene to ethynyl Nile red and subsequently an electron-transfer cascade in the opposite direction (from ethynyl Nile red to ethynyl perylene or ethynyl pyrene, but not from ethynyl perylene to ethynyl pyrene). The electron-transfer processes finally provide charge separation. The efficiencies by these energy and electron-transfer processes can be tuned by the distances between the chromophores and the sequences. Most importantly, excitation at any wavelength between 350 and 700 nm finally leads to charge separated states which make these DNA samples promising candidates for light-harvesting systems.

Pattern-Based Detection of Anion Pollutants in Water with DNA Polyfluorophores

Many existing irrigation, industrial and chemical storage sites are currently introducing hazardous anions into groundwater, making the monitoring of such sites a high priority. Detecting and quantifying anions in water samples typically requires complex instrumentation, adding cost and delaying analysis. Here we address these challenges by development of an optical molecular method to detect and discriminate a broad range of anionic contaminants with DNA-based fluorescent sensors. A library of 1296 tetrameric-length oligodeoxyfluorosides (ODFs) composed of metal ligand and fluorescence modulating monomers was constructed with a DNA synthesizer on PEG-polystyrene microbeads. These oligomers on beads were incubated with YIII or ZnII ions to provide affinity and responsiveness to anions. Seventeen anions were screened with the library under an epifluorescence microscope, ultimately yielding eight chemosensors that could discriminate 250 μM solutions of all 17 anions in buffered water using their patterns of response. This sensor set was able to identify two unknown anion samples from ten closely-responding anions and could also function quantitatively, determining unknown concentrations of anions such as cyanide (as low as 1 mM) and selenate (as low as 50 μM). Further studies with calibration curves established detection limits of selected anions including thiocyanate (detection limit ~300 μM) and arsenate (~800 μM). The results demonstrate DNA-like fluorescent chemosensors as versatile tools for optically analyzing environmentally hazardous anions in aqueous environments.

Rational design of a fluorescent poly(N-aryleneindole ether sulfone) switch by cation–π interactions

A fluorescence emission on–off switch is achieved by adjusting the assembly of poly(N-aryleneindole ether sulfone) (PESIN) and pyridine hydrochloride via the cation–π interactions.

Synthesis and systematic evaluation of dark resonance energy transfer (DRET)-based library and its application in cell imaging

In this paper, we report a new strategy for constructing a dye library with large Stokes shifts. By coupling a dark donor with BODIPY acceptors of tunable high quantum yield, a novel dark resonance energy transfer (DRET)-based library, named BNM, has been synthesized. Upon excitation of the dark donor (BDN) at 490 nm, the absorbed energy is transferred to the acceptor (BDM) with high efficiency, which was tunable in a broad range from 557 nm to 716 nm, with a high quantum yield of up to 0.8. It is noteworthy to mention that the majority of the non-radiative energy loss of the donor was converted into the acceptor's fluorescence output with a minimum leak of donor emission. Fluorescence imaging tested in live cells showed that the BNM compounds are cell-permeable and can also be employed for live-cell imaging. This is a new library which can be excited through a dark donor allowing for strong fluorescence emission in a wide range of wavelengths. Thus, the BNM library is well suited for high-throughput screening or multiplex experiments in biological applications by using a single laser excitation source.

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 gold nanoparticle nanocomposite films for chemiresistive vapor sensing

Chemiresistive vapor sensors combining functionalized gold nanoparticles and single-stranded DNA oligomers are investigated to enhance specificity in chemical sensing. Sensors are made by depositing DNA-functionalized gold nanoparticles onto microfabricated electrodes using four distinct sequences. Sensor performance is evaluated for response to relative humidity and exposure to vapor analytes including ethanol, methanol, hexane, dimethyl methylphosphonate, and toluene under different relative humidity. It is found that sensors display a nonmonotonic resistance change toward increasing humidity due to the combined effects of hydration induced swelling and ionic conduction. Responses to vapor analytes show sequence-dependent patterns as well as a strong influence of humidity. Overall, the findings are encouraging for using DNA oligomers to enhance specificity in chemical sensing.

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.

Syntheses and photophysical properties of 5'-6-locked fluorescent nucleosides

Nine fluorescent 5'-6-locked nucleosides were synthesized by condensation of various 1,2-diketones with 5-amino-2'-deoxycytidine. The nucleosides have different substituents on the pyrazine core structure, ranging from two methyl groups to polyaromatic rings. The photophysical properties of each nucleoside were determined, with the nucleosides displaying diverse absorption and emission maxima, extinction coefficients and quantum yields. The nucleoside with the highest fluorescence brightness was phosphitylated and incorporated into an oligonucleotide by means of automated oligonucleotide synthesis. The labelled oligonucleotide in aqueous buffer exhibited a substantially lowered extinction coefficient and quantum yield compared to the nucleoside in THF. The photophysical properties of the nucleoside were also compared in different DNA structural contexts, a single strand, a 14-mer duplex, a 14-mer duplex with an 11-mer overhang, and a 25-mer nicked duplex labelled at the nick site. Circular dichroism and melting temperature studies verified that the nucleoside did not perturb or destabilize the DNA helixes. In fact, when incorporated at the nick site, the nucleoside was found to stabilize the nicked duplex notably compared to its unmodified counterpart. The brightness of the fluorescent nucleoside in DNA increased as the polarity of its surroundings decreased, being highest in the 25-mer nicked duplex where exposure to the polar solvent is minimized by stacking to the adjacent bases on both the 3'- and 5'-side. The nucleosides brightness in the nicked duplex was also found to increase with lowered temperature, in accordance with expected temperature-dependent changes in the stacked-unstacked equilibrium at the nick site.

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.

Preoxidation for colorimetric sensor array detection of VOCs

A disposable preoxidation technique that dramatically improves the detection and identification of volatile organic compounds (VOCs) by a colorimetric sensor array is reported. Passing a vapor stream through a tube packed with chromic acid on silica immediately before the colorimetric sensor array substantially increases the sensitivity to less-reactive VOCs and improves the limits of detection (LODs) ~300-fold, permitting the detection, identification, and discrimination of 20 commonly found indoor VOC pollutants at both their immediately dangerous to life or health (IDLH) and permissible exposure limit (PEL) concentrations. The LODs of these pollutants were on average 1.4% of their respective PELs.

Chemistry of nucleic acids: impacts in multiple fields

Research in nucleic acids has made major advances in the past decade in multiple fields of science and technology. Here we discuss some of the most important findings in DNA and RNA research in the fields of biology, chemistry, biotechnology, synthetic biology, nanostructures and optical materials, with emphasis on how chemistry has impacted, and is impacted by, these developments. Major challenges ahead include the development of new chemical strategies that allow synthetically modified nucleic acids to enter into, and function in, living systems.

A simple and sensitive fluorescent sensing platform for Hg²+ ions assay based on G-quenching

In this work, a novel fluorescence biosensor was demonstrated for detection of Hg(2+) ions with relatively high selectivity and sensitivity. The sensing scheme was based on G-quenching induced by Hg(2+) ions. In the presence of Hg(2+) ions, the single-stranded signal probe which has carboxylfluorescein (FAM) and guanine segment at its 5' and 3' ends, respectively, folded into duplex-like structure via the Hg(2+)-mediated coordination of T-Hg(2+)-T base pairs. It brought guannine segment close to the dye and caused a remarkable decrease of fluorescence signal. The sensor showed a sensitive response to Hg(2+) ions in a concentration range from 0.5 to 10 μM, and a detection limit of 0.5 nM was given. This homogeneous system required only a single-labeled oligonucleotide, operated by concise procedures, and possessed comparable sensitivity as previous approaches. Furthermore, the sensor exhibits a great perspective for future practical applications.

Differentiating between fluorescence-quenching metal ions with polyfluorophore sensors built on a DNA backbone

A common problem in detecting metal ions with fluorescentchemosensors is the emission-suppressing effects of fluorescence-quenching metal ions. This quenching tendency makes it difficult to design sensors with turn-on signal, and differentiate between several metal ions that may yield a strong quenching response. To address these challenges, we investigate a new sensor design strategy, incorporating fluorophores and metal ligands as DNA base replacements in DNA-like oligomers, for generating a broader range of responses for quenching metal ions. The modular molecular design enabled rapid synthesis and discovery of sensors from libraries on PEG-polystyrene beads. Using this approach, water-soluble sensors 1-5 were identified as strong responders to a set of eight typically quenching metal ions (Co(2+), Ni(2+), Cu(2+), Hg(2+), Pb(2+), Ag(+), Cr(3+), and Fe(3+)). They were synthesized and characterized for sensing responses in solution. Cross-screening with the full set of metal ions showed that they have a wide variety of responses, including emission enhancements and red- and blue-shifts. The diversity of sensor responses allows as few as two sensors (1 and 2) to be used together to successfully differentiate these eight metals. As a test, a set of unknown metal ion solutions in blind studies were also successfully identified based on the response pattern of the sensors. The modular nature of the sensor design strategy suggests a broadly applicable approach to finding sensors for differentiating many different cations by pattern-based recognition, simply by varying the sequence and composition of ligands and fluorophores on a DNA synthesizer.

Differentiating a diverse range of volatile organic compounds with polyfluorophore sensors built on a DNA scaffold

Oligodeoxyfluorosides (ODFs) are short DNA-like oligomers in which DNA bases are replaced with fluorophores. A preliminary study reported that some sequences of ODFs were able to respond to a few organic small molecules in the vapor phase, giving a change in fluorescence. Here, we follow up on this finding by investigating a larger range of volatile organic analytes, and a considerably larger set of sensors. A library of tetramer ODFs of 2401 different sequences was prepared by using combinatorial methods, and was screened in air for fluorescence responses to a set of ten different volatile organics, including multiple aromatic and aliphatic compounds, acids and bases, varied functional groups, and closely related structures. Nineteen responding sensors were selected and characterized. These sensors were cross-screened against all ten analytes, and responses were measured qualitatively (by changes in color and intensity) and quantitatively (by measuring ΔR, ΔG, and ΔB values averaged over five to six sensor beads; R=red, G=green, B=blue). The results show that sensor responses were diverse, with a single sensor responding differently to as many as eight of the ten analytes; multiple classes of responses were seen, including quenching, lighting-up, and varied shifts in wavelength. Responses were strong, with raw ΔR, ΔG, and ΔB values of as high as >200 on a 256-unit scale and unamplified changes in many cases apparent to the naked eye. Sensors were identified that could distinguish clearly between even very closely related compounds such as acrolein and acrylonitrile. Statistical methods were applied to select a small set of four sensors that, as a pattern response, could distinguish between all ten analytes with high confidence. Sequence analysis of the full set of sensors suggested that sequence/order of the monomer components, and not merely composition, was highly important in the responses.