Equilibrium dynamics of spermine-induced plasmid DNA condensation revealed by fluorescence lifetime correlation spectroscopy

An analysis of interactions between three structurally diverse anthocyanidins, as well as their glucosides, and model biological membranes, albumin, and plasmid DNA

The aim of the study is to investigate the differences in the interaction of three structurally diverse anthocyanidins, namely peonidin, petunidin, and delphinidin, as well as their glucosides with model biological membranes, human albumin, and plasmid DNA in order to look into their structure-activity relationships. Fluorimetric studies, as well as ATR-FTIR analyses, were jointly used in order to determine the changes observed in both the hydrophilic and hydrophobic layers of cell-mimic membranes (MM) which reflected the membrane lipid composition of tumour cells and red blood cell membranes (RBCM). Our results showed that anthocyanins and anthocyanidins can cause an increase in the packing order of the polar heads of lipids, as well as interact with their deeper layers by reducing the fluidity of lipid chains. The results presented here indicate that all compounds tested here possessed the ability to bind to human serum albumin (HSA) and the presence of a glucose molecule within the structures formed by anthocyanidin reduces their ability to bind to proteins. Using fluorescence correlation spectroscopy, it was demonstrated that the compounds tested here were capable of forming stable complexes with plasmid DNA and, particularly, strong DNA conformational changes were observed in the presence of petunidin and corresponding glucoside, as well as delphinidin. The results we obtained can be useful in comprehending the anthocyanins therapeutic action as molecular antioxidants and provide a valuable insight into their mechanism of action.

Revealing Explicit Microsecond Carrier Diffusion from One Emission Center to Another in an All-Inorganic Perovskite Nanocrystal

Blinking of freely diffusing CsPbBr₃ nanocrystals (NCs) is studied using fluorescence lifetime correlation spectroscopy (FLCS). Emitted photons from each NCs are assigned to an emission state (exciton or trap) based on their lifetime. Subsequently, an intrastate autocorrelation function (ACF) and an interstate cross-correlation function (CCF) are constructed. Fitting of the AFCs with an analytical model shows that, at low excitation power, the microsecond blinking timescale of the exciton state matches well with that of the trap state. Most interestingly, both of those timescales further correlate with the microsecond growth timescale of the CCF. The strong anti-correlation of the CCF along with the stretched exponential nature of the blinking kinetics confirms the involvement of carrier diffusion and dispersive trap states in NC blinking. At high excitation power, enhanced sample heterogeneity causes a more dispersive blinking. To the best of our knowledge, this is the first report of a NC blinking study using a single-molecule-based FLCS technique.

A high-affinity fluorescence probe for copper(II) ions and its application in fluorescence lifetime correlation spectroscopy

Copper is one of the most important transition metals in many organisms where it catalyzes a manifold of different processes. As a result of copper's redox activity, organisms have to avoid unbound ions, and a dysfunctional copper homeostasis may lead to multifarious pathological processes in cells with very severe ramifications for the affected organisms. In many neurodegenerative diseases, however, the exact role of copper ions is still not completely clarified. In this work, a high-affinity and highly selective copper probe molecule, based on the naturally occurring tetrapeptide DAHK is synthesized. The sensor (log K_D = - 12.8 ± 0.1) is tagged with a fluorescent BODIPY dye whose fluorescence lifetime distinctly decreases from 5.8 ns ± 0.2 ns to 0.4 ns ± 0.1 ns on binding to copper(II) cations. It is shown by using fluorescence lifetime correlation spectroscopy that the concentration of both probe and probe-copper complex can be simultaneously measured even at nanomolar concentration levels. This work presents a possible starting point for a new type of probe and method for future in vivo studies to further reveal the exact role of copper ions in organisms. Graphical abstract.

Quantifying Microsecond Transition Times Using Fluorescence Lifetime Correlation Spectroscopy

Many complex luminescent emitters such as fluorescent proteins exhibit multiple emitting states that result in rapid fluctuations of their excited-state lifetime. Here, we apply fluorescence lifetime correlation spectroscopy (FLCS) to resolve the photophysical state dynamics of the prototypical fluorescence protein enhanced green fluorescent protein (EGFP). We quantify the microsecond transition rates between its two fluorescent states, which have otherwise highly overlapping emission spectra. We relate these transitions to a room-temperature angstrom-scale rotational isomerism of an amino acid next to its fluorescent center. With this study, we demonstrate the power of FLCS for studying the rapid transition dynamics of a broad range of light-emitting systems with complex multistate photophysics, which cannot be easily done by other methods.

New cytotoxic butyltin complexes with 2-sulfobenzoic acid: Molecular interaction with lipid bilayers and DNA as well as in vitro anticancer activity

New butyltin complexes with 2-sulfobenzoic acid: [Sn(C4H9)2{O3SC6H4COO-2}(H2O)]·(C2H5OH) (DBTsbz), [Sn(C4H9)3{O3SC6H4COOH-2}] (TBTsbz) and [Sn2(C4H9)6{μ-O3SC6H4COO-2}] (DTBTsbz) are very effective cytotoxic agents against tumor cells. The molecular interaction of these complexes with lipid membranes and DNA has been investigated. The IR spectra and changes of (1)H, (13)C chemical shifts suggest that SO3 and COO groups of 2-sulfobenzoato ligand interact with O atom of glycerin fragment of DPPC. Moreover, the compounds form Sn-OP bonds with phosphate groups of DPPC, which was shown by the lower frequency shift of the νs(PO2(-)) and νas(PO2(-)) band, by change of (31)P NMR signals and by DFT calculation. Another possibility is the interaction of the phosphate group of DPPC owing to formation of hydrogen bond O-H…O-P between water molecule coordinated to Sn and oxygen atom from the phosphate group. Using TCSPC-FCS we characterized DNA supramolecular assemblies' formation upon increasing TBTsbz, DTBTsbz and DBTsbz concentration. Diffusion time, lifetime and particle number changes are altered systematically with increasing Ccomp/CDNAbp ratio in following effectiveness order DBTsbz > TBTsbz > DTBTsbz. From those parameters we can conclude that all these compounds lead to a change of DNA winding, strand but not to DNA compaction. Investigated compounds show very high cytotoxic activity against cancer cell lines. All compounds exhibit efficient in vitro antitumor activity toward Jurkat (T-cell leukemia), CL-1 (T-lymphoblastoid cell line), GL-1 (B cell lymphoma cell line) and D-17 (canine osteosarcoma). The DBTsbz is more effective then carboplatin against canine osteosarcoma.

New gluconamide-type cationic surfactants: Interactions with DNA and lipid membranes

New linear cationic surfactants - 2-(alkyldimethylammonio)ethylgluconamide bromides, denoted as CnGAB, n=10, 12, 14 and 16 - were synthesized from natural resources and characterized with respect to their potential as gene-delivery agents in gene therapy applications. Interactions with plasmid DNA and with model membranes were studied both experimentally and theoretically. The compounds with n=12, 14 and 16 show exponentially increasing ability to fully condense DNA. C16GAB condenses DNA at 1:1 surfactant to nucleotide molar ratio. Furthermore, CnGABs interact with model membrane, slightly lowering the temperature of the main phase transition Tm of the DPPC bilayer. C10GAB is found to interact only at the membrane surface. C16GAB reduces Tm less than C12GAB and C14GAB, and forms domains in the bilayer at the surfactant/DPPC molar ratio of 0.1 and higher. The results suggest that C16GAB can be a promising candidate for building gene-delivery carrier systems.

Fluorescence Lifetime Correlation Spectroscopy (FLCS): concepts, applications and outlook

Fluorescence Lifetime Correlation Spectroscopy (FLCS) is a variant of fluorescence correlation spectroscopy (FCS), which uses differences in fluorescence intensity decays to separate contributions of different fluorophore populations to FCS signal. Besides which, FLCS is a powerful tool to improve quality of FCS data by removing noise and distortion caused by scattered excitation light, detector thermal noise and detector afterpulsing. We are providing an overview of, to our knowledge, all published applications of FLCS. Although these are not numerous so far, they illustrate possibilities for the technique and the research topics in which FLCS has the potential to become widespread. Furthermore, we are addressing some questions which may be asked by a beginner user of FLCS. The last part of the text reviews other techniques closely related to FLCS. The generalization of the idea of FLCS paves the way for further promising application of the principle of statistical filtering of signals. Specifically, the idea of fluorescence spectral correlation spectroscopy is here outlined.

Early amyloidogenic oligomerization studied through fluorescence lifetime correlation spectroscopy

Amyloidogenic protein aggregation is a persistent biomedical problem. Despite active research in disease-related aggregation, the need for multidisciplinary approaches to the problem is evident. Recent advances in single-molecule fluorescence spectroscopy are valuable for examining heterogenic biomolecular systems. In this work, we have explored the initial stages of amyloidogenic aggregation by employing fluorescence lifetime correlation spectroscopy (FLCS), an advanced modification of conventional fluorescence correlation spectroscopy (FCS) that utilizes time-resolved information. FLCS provides size distributions and kinetics for the oligomer growth of the SH3 domain of α-spectrin, whose N47A mutant forms amyloid fibrils at pH 3.2 and 37 °C in the presence of salt. The combination of FCS with additional fluorescence lifetime information provides an exciting approach to focus on the initial aggregation stages, allowing a better understanding of the fibrillization process, by providing multidimensional information, valuable in combination with other conventional methodologies.

DNA Binding Hydroxyl Radical Probes

The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA.

How environmental solution conditions determine the compaction velocity of single DNA molecules

Understanding the mechanisms of DNA compaction is becoming increasingly important for gene therapy and nanotechnology DNA applications. The kinetics of the compaction velocity of single DNA molecules was studied using two non-protein condensation systems, poly(ethylene glycol) (PEG) with Mg²⁺ for the polymer-salt-induced condensation system and spermine for the polyamine condensation system. The compaction velocities of single tandem λ-DNA molecules were measured at various PEG and spermine concentrations by video fluorescent microscopy. Single DNA molecules were observed using a molecular stretching technique in the microfluidic flow. The results show that the compaction velocity of a single DNA molecule was proportional to the PEG or spermine concentration to the power of a half. Theoretical considerations indicate that the compaction velocity is related to differences in the free energy of a single DNA molecule between the random coil and compacted states. In the compaction kinetics with PEG, acceleration of the compaction velocity occurred above the overlap concentration while considerable deceleration occurred during the coexistence state of the random coil and the compacted conformation. This study demonstrates the control factors of DNA compaction kinetics and contributes toward the understanding of the compaction mechanisms of non-protein DNA interactions as well as DNA–protein interactions in vivo.

Resolving inhomogeneity using lifetime-weighted fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) was extended by incorporating information of the fluorescence lifetime. This new experimental approach, called lifetime-weighted FCS, enables us to observe fluorescence lifetime fluctuations in the nano- to millisecond time region. The potential of this method for resolving inhomogeneity in complex systems was demonstrated. First, by measuring a mixture of two dye molecules having different fluorescence lifetimes, it was shown that the lifetime-weighted correlation deviates from the ordinary intensity correlation only when the system is inhomogeneous. This demonstrated that lifetime-weighted FCS is capable of detecting inhomogeneity in an ensemble-averaged fluorescence decay profile without any a priori knowledge about the system. Second, we applied this method to a dye-labeled polypeptide, a prototypical model of complex biopolymers. It was found that the ratio between the lifetime-weighted and ordinary intensity correlation changes with change of the environment around the polypeptide. This result was interpreted in terms of environment-dependent conformational inhomogeneity of the polypeptide. Delay time dependence of the ratio was found to be constant from ∼1 μs to several milliseconds, indicating that the observed inhomogeneity is persistent in the measured time scale. In combination with fluorescence intensity correlation, lifetime-weighted FCS allows us to examine conformational fluctuations of complex systems in the time region from nano- to milliseconds, being free from the translational diffusion signal.

FRET fluctuation spectroscopy of diffusing biopolymers: contributions of conformational dynamics and translational diffusion

The use of fluorescence correlation spectroscopy (FCS) to study conformational dynamics in diffusing biopolymers requires that the contributions to the signal due to translational diffusion are separated from those due to conformational dynamics. A simple approach that has been proposed to achieve this goal involves the analysis of fluctuations in fluorescence resonance energy transfer (FRET) efficiency. In this work, we investigate the applicability of this methodology by combining Monte Carlo simulations and experiments. Results show that diffusion does not contribute to the measured fluctuations in FRET efficiency in conditions where the relaxation time of the kinetic process is much shorter than the mean transit time of the molecules in the optical observation volume. However, in contrast to what has been suggested in previous work, the contributions of diffusion are otherwise significant. Neglecting the contributions of diffusion can potentially lead to an erroneous interpretation of the kinetic mechanisms. As an example, we demonstrate that the analysis of FRET fluctuations in terms of a purely kinetic model would generally lead to the conclusion that the system presents complex kinetic behavior even for an idealized two-state system.

Lipopolythiourea/DNA interaction: a biophysical study

Lipopolythioureas (LPT) are original non cationic systems representing an alternative to cationic lipids. Their high transfection efficiency prompted us to investigate further their biophysical properties, and in particular how thiourea lipids interact with DNA. The interaction of lipopolythiourea with DNA was investigated by fluorescence correlation microscopy (FCS). Influence of the lipid length and nature of the thiourea head on the thiourea/DNA interaction were studied. FCS revealed a strong interaction between lipopolythiourea and DNA, occurring at 1 equivalent of a thiourea lipid by a DNA phosphate group, and leading to a condensed plasmid state. From previous in vitro experiments, we could conclude that the lipid leading to the more condensed state of DNA was also the more efficient to transfect cells.

Recent developments in fluorescence correlation spectroscopy for diffusion measurements in planar lipid membranes

Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as 2-focus, Z-scan or scanning FCS, which overcome most of the artefacts and limitations of standard FCS. We focus on diffusion measurements of lipids and proteins in planar lipid membranes and review the contributions of FCS to elucidating membrane dynamics and the factors influencing it, such as membrane composition, ionic strength, presence of membrane proteins or frictional coupling with solid support.