Basic Aspects of Absorption and Fluorescence Spectroscopy and Resonance Energy Transfer Methods

Single-Molecule Imaging of Reactive Oxygen Species on a Semiconductor Nano-Heterostructure for Understanding Photocatalytic Heterogeneity in Aqueous

We constructed a single-molecule fluorescence imaging technique to monitor the spatiotemporal distribution of the hydroxyl radical (•OH) on TiO₂-attached multiwalled carbon nanotubes (TiO₂-MWCNTs) in aqueous. We found the heterogeneous distribution of •OH is closely related to the composition and heterostructure of the catalysts. The dynamic •OH production rate was evaluated by counting the single-molecule fluorescent bursts. We further confirmed the production of •OH on TiO₂-MWCNTs mainly occurred via electron reduction during the aqueous photocatalytic process. Our study reveals the mechanism of reactive oxygen species involved photocatalytic reaction and guides the design of advanced semiconductor photocatalysts.

Dose Rate Effects in Fluorescence Chemical Dosimeters Exposed to Picosecond Electron Pulses: An Accurate Measurement of Low Doses at High Dose Rates

The development of ultra-intense electron pulse for applications needs to be accompanied by the implementation of a practical dosimetry system. In this study four different systems were investigated as dosimeters for low doses with a very high-dose-rate source. First, the effects of ultra-short pulses were investigated for the yields of the Fricke dosimeter based on acidic solutions of ferrous sulfate; it was established that the yields were not significantly affected by the high dose rates, so the Fricke dosimeter system was used as a reference. Then, aqueous solutions of three compounds as fluorescence chemical dosimeters were utilized, each operated at a different solution pH: terephthalic acid - basic, trimesic acid - acidic, and coumarin-3- carboxylic acid (C3CA) - neutral. Fluorescence chemical dosimeters offer an attractive alternative to chemical dosimeters based on optical absorption for measuring biologically relevant low doses because of their higher sensitivity. The effects of very intense dose rate (TGy/s) from pulses of fast electrons generated by a picosecond linear accelerator on the chemical yields of fluorescence chemical dosimeters were investigated at low peak doses (<20 Gy) and compared with yields determined under low-dose-rate irradiation from a 60 Co gamma-ray source (mGy/s). For the terephthalate and the trimesic acid dosimeters changes in the yields were not detected within the estimated (∼10%) precision of the experiments, but, due to the complexity of the mechanism of the hydroxyl radical initiated reactions in solutions of the relevant aromatic compounds, significant reductions of the chemical yield (-60%) were observed when the C3CA dosimeter was irradiated with the ultra-short pulses.

In-line UV spectroscopy for the quantification of low-dose active ingredients during the manufacturing of pharmaceutical semi-solid and liquid formulations

UltraViolet (UV) spectroscopy was evaluated as an innovative Process Analytical Technology (PAT) - tool for the in-line and real-time quantitative determination of low-dosed active pharmaceutical ingredients (APIs) in a semi-solid (gel) and a liquid (suspension) pharmaceutical formulation during their batch production process. The performance of this new PAT-tool (i.e., UV spectroscopy) was compared with an already more established PAT-method based on Raman spectroscopy. In-line UV measurements were carried out with an immersion probe while for the Raman measurements a non-contact PhAT probe was used. For both studied formulations, an in-line API quantification model was developed and validated per spectroscopic technique. The known API concentrations (Y) were correlated with the corresponding in-line collected preprocessed spectra (X) through a Partial Least Squares (PLS) regression. Each developed quantification method was validated by calculating the accuracy profile on the basis of the validation experiments. Furthermore, the measurement uncertainty was determined based on the data generated for the determination of the accuracy profiles. From the accuracy profile of the UV- and Raman-based quantification method for the gel, it was concluded that at the target API concentration of 2% (w/w), 95 out of 100 future routine measurements given by the Raman method will not deviate more than 10% (relative error) from the true API concentration, whereas for the UV method the acceptance limits of 10% were exceeded. For the liquid formulation, the Raman method was not able to quantify the API in the low-dosed suspension (0.09% (w/w) API). In contrast, the in-line UV method was able to adequately quantify the API in the suspension. This study demonstrated that UV spectroscopy can be adopted as a novel in-line PAT-technique for low-dose quantification purposes in pharmaceutical processes. Important is that none of the two spectroscopic techniques was superior to the other for both formulations: the Raman method was more accurate in quantifying the API in the gel (2% (w/w) API), while the UV method performed better for API quantification in the suspension (0.09% (w/w) API).

Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes

Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.

Rapid reaction kinetic techniques

Most biochemical processes occur on sub-second time scales. Relaxation and rapid mixing methods allow reactions from microsecond time scales onwards to be monitored in real time. This chapter describes the instrumentation for these techniques and it discusses general topics of sample excitation and signal detection.

Fluorescence and labelling: how to choose and what to do

This chapter provides an overview of fluorescent labelling of different reactants related to the biochemistry of motor proteins. The fluorescent properties of different labels and the advantages and disadvantages of the labelling methods are discussed. This will allow for a careful selection of fluorescent proteins for different applications relating to motor proteins.

Fluorescence to study the ATPase mechanism of motor proteins

This chapter provides an overview of different methodologies to dissect the ATPase mechanism of motor proteins. The use of ATP is fundamental to how these molecular engines work and how they can use the energy to perform various cellular roles. Rapid reaction and single-molecule techniques will be discussed to monitor reactions in real time through the application of fluorescence intensity, anisotropy and FRET. These approaches utilise fluorescent nucleotides and biosensors. While not every technique may be suitable for your motor protein, the different ways to determine the ATPase mechanism should allow a good evaluation of the kinetic parameters.

Fluorescent labeling and modification of proteins

This review provides an outline for fluorescent labeling of proteins. Fluorescent assays are very diverse providing the most sensitive and robust methods for observing biological processes. Here, different types of labels and methods of attachment are discussed in combination with their fluorescent properties. The advantages and disadvantages of these different methods are highlighted, allowing the careful selection for different applications, ranging from ensemble spectroscopy assays through to single-molecule measurements.

Synthesis and spectroscopic characterization of fluorescent boron dipyrromethene-derived hydrazones

Derivatives of 4,4-difluoro-4-bora-3a,4a,diaza-s-indacene (BODIPY® or BDP) that possess a hydrazine substituent on position 5 are potential "turn-on" fluorophores for labeling aldehydes The unnatural amino acid L-3-formyltyrosine can be incorporated into a protein or peptide; thus, these hydrazines are potentially site specific labels for such polymers. In this work, model compounds were synthesized to assess whether the photochemical properties of the BDP-hydrazone would be suitable for protein labeling. Hydrazones were synthesized from the fluorophore 3-chloro-5-hydrazino-BDP and different aldehydes, and the absorption and emission spectra of the products were compared. The hydrazone of an unsubstituted aromatic aldehyde displays absorption and emission maxima (531 nm and 559 nm, respectively in dioxane) that are red shifted relative to those of a hydrazone from an aliphatic aldehyde (513 nm and 543 nm, respectively, in dioxane) and an increased quantum yield (0.21 vs. 0.11, respectively, in dioxane). The presence of a hydroxyl group ortho- to the aldehyde produces a hydrazone in which the absorption and emission maxima are slightly red shifted (528 nm and 564 nm, respectively in dioxane) from the unsubstituted aromatic hydrazone, but the quantum yields of the two hydrazones are equivalent. Thus, an ortho-hydroxy substituted aromatic aldehyde is a suitable electrophile for "turn on" protein labeling using the hydrazino-BDP. The specificity of this labeling reaction for the unnatural amino acid was demonstrated through fluorescent labeling of just the 3-formyltyrosine-containing α-subunit of α,β-tubulin.

Carotenoid fluorescence in Dunaliella salina

Dunaliella salina is a halotolerant green alga that is well known for its carotenoid producing capacity. The produced carotenoids are mainly stored in lipid globules. For various research purposes, such as production and extraction kinetics, we would like to determine and/or localise the carotenoid globules in vivo. In this study, we show that the carotenoid-rich globules emit clear green fluorescence, which can be used in, for example, fluorescence microscopy (e.g. CLSM) to obtain pictures of the cells and their carotenoid content.