A cyanine dye probe for K+ detection based on DNA construction of G-quadruplex

Potassium ion (K⁺) plays an important role in the maintenance of cellular biological process for human health. Thus, the detection of K⁺ is very important. Here, based on the interaction between thiamonomethinecyanine dye and G-quadruplex formation sequence (PW17), K⁺ detection spectrum was characterized by UV-Vis spectrometry. The single-stranded sequence of PW17 can fold into G-quadruplex in the presence of K⁺. PW17 can induce a dimer-to-monomer transition of the absorption spectrum of cyanine dyes. This method shows high specificity against some other alkali cations, even at high concentrations of Na⁺. Further, this detection strategy can realize the detection of K⁺ in tap water.

Synthetic Access to Benzimidacarbocyanine Dyes to Tailor Their Aggregation Properties

Developing structure-aggregation relationships of cyanine dyes is crucial for controlling their optical properties for various uses. This study develops a synthetic route and the structure-dependent self-assembly of a family of benzimidacarbocyanine dyes for J- or H-aggregation properties. It was found that both the presence and placement of halogen atoms play a defining role in the resulting supramolecular interactions of these compounds.

Multiple-Labeled Antibodies Behave Like Single Emitters in Photoswitching Buffer

The degree of labeling (DOL) of antibodies has so far been optimized for high brightness and specific and efficient binding. The influence of the DOL on the blinking performance of antibodies used in direct stochastic optical reconstruction microscopy (dSTORM) has so far attained limited attention. Here, we investigated the spectroscopic characteristics of IgG antibodies labeled at DOLs of 1.1-8.3 with Alexa Fluor 647 (Al647) at the ensemble and single-molecule level. Multiple-Al647-labeled antibodies showed weak and strong quenching interactions in aqueous buffer but could all be used for dSTORM imaging with spatial resolutions of ∼20 nm independent of the DOL. Single-molecule fluorescence trajectories and photon antibunching experiments revealed that individual multiple-Al647-labeled antibodies show complex photophysics in aqueous buffer but behave as single emitters in photoswitching buffer independent of the DOL. We developed a model that explains the observed blinking of multiple-labeled antibodies and can be used for the development of improved fluorescent probes for dSTORM experiments.

Influence of the interaction with DNA on the spectral-fluorescent and photochemical properties of some meso-substituted polymethine dyes

Spectral-fluorescent and photochemical properties of meso-substituted thiacarbocyanine dyes 3,3'-dimethyl-9-phenylthiacarbocyanine and 3,3'-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine in solutions and their interaction with DNA were studied. The dyes form noncovalent complexes with DNA, which is accompanied by changes in the absorption spectra and an increase in the fluorescence intensity of the dyes. The data obtained suggest that the dyes are in the form of trans-isomers both in solvents of different polarity and in complexes with DNA. It was shown that the interaction of the dyes with DNA is a complex process involving monomeric dye molecules and aggregates of the dyes. The primary photochemical processes of the dyes in solutions and in complexes with DNA were studied by flash photolysis technique. Upon flash photoexcitation in solutions, the formation and decay of the photoisomers of the dyes were observed, with no generation of the triplet states. In the complex with DNA, no signal of photoisomers was detected; in the absence of oxygen, the formation of the triplet state of the dyes was observed. The decay kinetics of the triplet state of the dyes were two-exponential. The process of quenching of the triplet state of the dyes by oxygen in a complex with DNA was studied, the respective quenching rate constants were estimated, being lower than the diffusion-controlled value.

The Effect of Fluorophore Conjugation on Antibody Affinity and the Photophysical Properties of Dyes

Because the degree of labeling (DOL) of cell-bound antibodies, often required in quantitative fluorescence measurements, is largely unknown, we investigated the effect of labeling with two different fluorophores (AlexaFluor546, AlexaFluor647) in a systematic way using antibody stock solutions with different DOLs. Here, we show that the mean DOL of the cell-bound antibody fraction is lower than that of the stock using single molecule fluorescence measurements. The effect is so pronounced that the mean DOL levels off at approximately two fluorophores/IgG for some antibodies. We developed a method for comparing the average DOL of antibody stocks to that of the isolated, cell-bound fraction based on fluorescence anisotropy measurements confirming the aforementioned conclusions. We created a model in which individual antibody species with different DOLs, present in an antibody stock solution, were assumed to have distinct affinities and quantum yields. The model calculations confirmed that a calibration curve constructed from the anisotropy of antibody stocks can be used for determining the DOL of the bound fraction. The fluorescence intensity of the cell-bound antibody fractions and of the antibody stocks exhibited distinctly different dependence on the DOL. The behavior of the two dyes was systematically different in this respect. Fitting of the model to these data revealed that labeling with each dye affects quantum yield and antibody affinity differentially. These measurements also implied that fluorophores in multiply labeled antibodies exhibit self-quenching and lead to decreased antibody affinity, conclusions directly confirmed by steady-state intensity measurements and competitive binding assays. Although the fluorescence lifetime of antibodies labeled with multiple fluorophores decreased, the magnitude of this change was not sufficient to account for self-quenching indicating that both dynamic and static quenching processes occur involving H-aggregate formation. Our results reveal multiple effects of fluorophore conjugation, which must not be overlooked in quantitative cell biological measurements.

Exploring Fluorescent Dyes at Biomimetic Interfaces with Second Harmonic Generation and Molecular Dynamics

The adsorption of a DNA fluorescent probe belonging to the thiazole orange family at the dodecane/water and dodecane/phospholipid/water interfaces has been investigated using a combination of surface second harmonic generation (SSHG) and all-atomistic molecular dynamics (MD) simulations. Both approaches point to a high affinity of the cationic dye for the dodecane/water interface with a Gibbs free energy of adsorption on the order of -45 kJ/mol. Similar affinity was observed with a monolayer of negatively charged DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol)) lipids. On the other hand, no significant adsorption could be found with the zwitterionic DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) lipids. This was rationalized in terms of Coulombic interactions between the monolayer surface and the cationic dye. The similar affinity for the interface with and without DPPG, despite the favorable Coulombic attraction in the latter case, could be explained after investigating the interfacial orientation of the dye. In the absence of a monolayer, the dye adsorbs with its molecular plane almost flat at the interface, whereas in the presence of DPPG it has to intercalate into the monolayer and adopt a significantly different orientation to benefit from the electrostatic stabilization.

Achieving effective terminal exciton delivery in quantum dot antenna-sensitized multistep DNA photonic wires

Assembling DNA-based photonic wires around semiconductor quantum dots (QDs) creates optically active hybrid architectures that exploit the unique properties of both components. DNA hybridization allows positioning of multiple, carefully arranged fluorophores that can engage in sequential energy transfer steps while the QDs provide a superior energy harvesting antenna capacity that drives a Förster resonance energy transfer (FRET) cascade through the structures. Although the first generation of these composites demonstrated four-sequential energy transfer steps across a distance >150 Å, the exciton transfer efficiency reaching the final, terminal dye was estimated to be only ~0.7% with no concomitant sensitized emission observed. Had the terminal Cy7 dye utilized in that construct provided a sensitized emission, we estimate that this would have equated to an overall end-to-end ET efficiency of ≤ 0.1%. In this report, we demonstrate that overall energy flow through a second generation hybrid architecture can be significantly improved by reengineering four key aspects of the composite structure: (1) making the initial DNA modification chemistry smaller and more facile to implement, (2) optimizing donor-acceptor dye pairings, (3) varying donor-acceptor dye spacing as a function of the Förster distance R0, and (4) increasing the number of DNA wires displayed around each central QD donor. These cumulative changes lead to a 2 orders of magnitude improvement in the exciton transfer efficiency to the final terminal dye in comparison to the first-generation construct. The overall end-to-end efficiency through the optimized, five-fluorophore/four-step cascaded energy transfer system now approaches 10%. The results are analyzed using Förster theory with various sources of randomness accounted for by averaging over ensembles of modeled constructs. Fits to the spectra suggest near-ideal behavior when the photonic wires have two sequential acceptor dyes (Cy3 and Cy3.5) and exciton transfer efficiencies approaching 100% are seen when the dye spacings are 0.5 × R0. However, as additional dyes are included in each wire, strong nonidealities appear that are suspected to arise predominantly from the poor photophysical performance of the last two acceptor dyes (Cy5 and Cy5.5). The results are discussed in the context of improving exciton transfer efficiency along photonic wires and the contributions these architectures can make to understanding multistep FRET processes.

Characterization of the triplet state of hybridization-sensitive DNA probe by using fluorescence correlation spectroscopy

The nonradiative relaxation mechanism of the newly synthesized hybridized-sensitive DNA probe has not been fully understood until now. In this study, the transient dark state of the probe, which is a double fluorescent dye attached to a specific DNA sequence, was investigated using a fluorescence correlation spectroscopy (FCS). The transient dark state was measured in various solvents that are known to affect the intersystem crossing or photoisomerization of the DNA probe. On the basis of the experimental results, a simplified two energy state model of the probe was constructed, and this model provides an insight into the nonradiative relaxation mechanism of the fluorophore and the applications for DNA and RNA detection. The transient dark state that was measured in a time scale of a few microseconds is a triplet state and is related to photoisomerization, viscosity, oxygen concentration, and hybridization, all of which are important parameters for cellular microscopy. The transient dark state in a time scale of a sub-microseconds is sensitively changed after the addition of target DNA. The characterization can improve the probe's capability to identify target DNA/RNA by using FCS since the triplet state that occurred after hybridization is distinctive in the time scale with that occurred before hybridization.