Charge transfer as a mechanism for chlorophyll fluorescence concentration quenching

Chlorophyll-Induced Lamellar to Nonlamellar Phase Transitions and Dynamical Heterogeneity in Plant Thylakoid Membranes

Chlorophyll a (CLA) pigments and thylakoid membranes are crucial components of plants for photosynthesis. To understand the effect of CLA on the structure and dynamics of thylakoid membranes, coarse-grained molecular dynamics (CG MD) simulations of thylakoid membranes are performed by varying the numbers of CLA at 293 K using MARTINI-2 force fields. The membrane undergoes a lamellar to nonlamellar phase transition above a critical concentration of CLA. The CLAs dynamically form aggregates of different orders and preferentially fetch the least unsaturated nonbilayer-forming lipids around them, resulting in a nonlamellar phase with fused regions. These fused regions cause a structural arrest of CLA and lipids, inducing dynamic heterogeneity manifested by non-Gaussian parameters and van Hove correlation functions. The lamellar to nonlamellar phase transition of the membrane is associated with a drastic reduction in correlation length of the immobile CLA and lipids governed by the fused topology. Such insights into CLA-induced structural transitions in thylakoid membranes are pertinent for understanding nonphotochemical quenching mechanisms and hold promise for designing future artificial photosynthetic materials and applications in photodynamic therapy.

Evidence for a transfer-to-trap mechanism of fluorophore concentration quenching in lipid bilayers

It is important to understand the behaviors of fluorescent molecules because, firstly, they are often utilized as probes in biophysical experiments and, secondly, they are crucial cofactors in biological processes such as photosynthesis. A phenomenon called "fluorescence quenching" occurs when fluorophores are present at high concentrations, but the mechanisms for quenching are debated. Here, we used a technique called "in-membrane electrophoresis" to generate concentration gradients of fluorophores within a supported lipid bilayer, across which quenching was expected to occur. Fluorescence lifetime imaging microscopy (FLIM) provides images where the fluorescence intensity in each pixel is correlated to fluorescence lifetime: the intensity provides information about the location and concentration of fluorophores and the lifetime reveals the occurrence of energy-dissipative processes. FLIM was used to compare the quenching behavior of three commonly used fluorophores: Texas Red (TR), nitrobenzoaxadiazole (NBD), and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY). FLIM images provided evidence of quenching in regions where the fluorophores accumulated, but the degree of quenching varied between the different fluorophores. The relationship between quenching and concentration was quantified and the "critical radius for trap formation," representing the relative quenching strength, was calculated as 2.70, 2.02, and 1.14 nm, for BODIPY, TR, and NBD, respectively. The experimental data support the theory that quenching takes place via a "transfer-to-trap" mechanism which proposes, firstly, that excitation energy is transferred between fluorophores and may reach a "trap site," resulting in immediate energy dissipation, and, secondly, that trap sites are formed in a concentration-dependent manner. Some previous work suggested that quenching occurs only when fluorophores aggregate, or form long-lived dimers, but our data and this theory argue that traps may be "statistical pairs" of fluorophores that exist only transiently. Our findings should inspire future work to assess whether these traps can be charge-transfer states, excited-state dimers, or something else.

Concentration Quenching of Fluorescence Decay Kinetics of Molecular Systems

Fluorescence concentration quenching occurs when increasing molecular concentration of fluorophores results in a decreasing fluorescence quantum yield. Even though this phenomenon has been studied for decades, its mechanisms and signatures are not yet fully understood. The complexity of the problem arises due to energy migration and trapping in huge networks of molecules. Most of the available theoretical work focuses on integral quantities like fluorescence quantum yield and mean excitation lifetime. In this work, we present a numerical study of the fluorescence decay kinetics of three-dimensional and two-dimensional molecular systems. We investigate the differences arising from the variations in models of trap formations. We also analyze the influence of the molecular orientations to the fluorescence decay kinetics. We compare our results to the well-known analytical models and discuss their ranges of validity. Our findings suggest that the analytical models can provide inspiration for different ways of approximating the fluorescence kinetics, yet more detailed analysis of the experimental data should be done by comparison with numerical simulations.

Excitation landscape of the CP43 photosynthetic antenna complex from multiscale simulations

Photosystem II (PSII), the principal enzyme of oxygenic photosynthesis, contains two integral light harvesting proteins (CP43 and CP47) that bind chlorophylls and carotenoids. The two intrinsic antennae play crucial roles in excitation energy transfer and photoprotection. CP43 interacts most closely with the reaction center of PSII, specifically with the branch of the reaction center (D1) that is responsible for primary charge separation and electron transfer. Deciphering the function of CP43 requires detailed atomic-level insights into the properties of the embedded pigments. To advance this goal, we employ a range of multiscale computational approaches to determine the site energies and excitonic profile of CP43 chlorophylls, using large all-atom models of a membrane-bound PSII monomer. In addition to time-dependent density functional theory (TD-DFT) used in the context of a quantum-mechanics/molecular-mechanics setup (QM/MM), we present a thorough analysis using the perturbed matrix method (PMM), which enables us to utilize information from long-timescale molecular dynamics simulations of native PSII-complexed CP43. The excited state energetics and excitonic couplings have both similarities and differences compared with previous experimental fits and theoretical calculations. Both static TD-DFT and dynamic PMM results indicate a layered distribution of site energies and reveal specific groups of chlorophylls that have shared contributions to low-energy excitations. Importantly, the contribution to the lowest energy exciton does not arise from the same chlorophylls at each system configuration, but rather changes as a function of conformational dynamics. An unexpected finding is the identification of a low-energy charge-transfer excited state within CP43 that involves a lumenal (C2) and the central (C10) chlorophyll of the complex. The results provide a refined basis for structure-based interpretation of spectroscopic observations and for further deciphering excitation energy transfer in oxygenic photosynthesis.

Lanthanide-Complex-Enhanced Bioorthogonal Branched DNA Amplification

Fluorescence in situ hybridization (FISH) is a widely used technique for detecting intracellular nucleic acids. However, its effectiveness in detecting low-copy nucleic acids is limited due to its low fluorescence intensity and background autofluorescence. To address these challenges, we present here an approach of lanthanide-complex-enhanced bioorthogonal-branched DNA amplification (LEBODA) with high sensitivity for in situ nuclear acid detection in single cells. The approach capitalizes on two levels of signal amplification. First, it utilizes click chemistry to directly link a substantial number of bridge probes to target-recognizing probes, providing an initial boost in signal intensity. Second, it incorporates high-density lanthanide complexes into each bridge probe, enabling secondary amplifications. Compared to the traditional "double Z" probes used in the RNAscope method, LEBODA exhibits 4 times the single enhancement for RNA detection signal with the click chemistry approach. Using SARS-CoV-2 pseudovirus-infected HeLa cells, we demonstrate the superiority in the detection of viral-infected cells in rare populations as low as 20% infectious rate. More encouragingly, the LEBODA approach can be adapted for DNA-FISH and single-molecule RNA-FISH, as well as other hybridization-based signal amplification methods. This adaptability broadens the potential applications of LEBODA in the sensitive detection of biomolecules, indicating promising prospects for future research and practical use.

Dominant role of excitons in photosynthetic color-tuning and light-harvesting

Photosynthesis is a vital process that converts sunlight into energy for the Earth's ecosystems. Color adaptation is crucial for different photosynthetic organisms to thrive in their ecological niches. Although the presence of collective excitons in light-harvesting complexes is well known, the role of delocalized excited states in color tuning and excitation energy transfer remains unclear. This study evaluates the characteristics of photosynthetic excitons in sulfur and non-sulfur purple bacteria using advanced optical spectroscopic techniques at reduced temperatures. The exciton effects in these bacteriochlorophyll a-containing species are generally much stronger than in plant systems that rely on chlorophylls. Their exciton bandwidth varies based on multiple factors such as chromoprotein structure, surroundings of the pigments, carotenoid content, hydrogen bonding, and metal ion inclusion. The study nevertheless establishes a linear relationship between the exciton bandwidth and Qy singlet exciton absorption peak, which in case of LH1 core complexes from different species covers almost 130 nm. These findings provide important insights into bacterial color tuning and light-harvesting, which can inspire sustainable energy strategies and devices.

Indocyanine Green (ICG) Fluorescence Is Dependent on Monomer with Planar and Twisted Structures and Inhibited by H-Aggregation

The optical properties of indocyanine green (ICG) as a near-infrared (NIR) fluorescence dye depend on the nature of the solvent medium and the dye concentration. In the ICG absorption spectra of water, at high concentrations, there were absorption maxima at 700 nm, implying H-aggregates. With ICG dilution, the main absorption peak was at 780 nm, implying monomers. However, in ethanol, the absorption maximum was 780 nm, and the shapes of the absorption spectra were identical regardless of the ICG concentration, indicating that ICG in ethanol exists only as a monomer without H-aggregates. We found that emission was due to the monomer form and decreased with H-aggregate formation. In the fluorescence spectra, the 820 nm emission band was dominant at low concentrations, whereas at high concentrations, we found that the emission peaks were converted to 880 nm, suggesting a new form via the twisted intramolecular charge transfer (TICT) process of ICG. The NIR fluorescence intensity of ICG in ethanol was approximately 12- and 9-times brighter than in water in the NIR-I and -II regions, respectively. We propose an energy diagram of ICG to describe absorptive and emissive transitions through the ICG structures such as the monomer, H-aggregated, and TICT monomer forms.