Ultrafast fluorescence quenching dynamics of Atto655 in the presence of N-acetyltyrosine and N-acetyltryptophan in aqueous solution: proton-coupled electron transfer versus electron transfer

Carbon quantum dots-Annexin V probe: photoinduced electron transfer mechanism, phosphatidylserine detection, and apoptotic cell imaging

An annexin V-based probe is designed and fabricated using carbon quantum dot as highly stable and biocompatible fluorescent crystals for real-time fluorescence imaging of apoptotic cells. Carbon quantum dots were synthesized, characterized, and conjugated to annexin V. The fluorescence of CQDs at 450 nm (excitation at 350 nm) is quenched due to the photoinduced electron transfer between "carbon quantum dots" and two amino acids (tyrosine and tryptophan) in the annexin structure as quencher. The probe shows very strong and bright fluorescence emission in the presence of phosphatidylserine on the outer layer of the apoptotic cell membrane. It was shown that using fluorescence spectroscopy, the probe can be applied to sensitive phosphatidylserine determination and using fluorescence microscopy, it is possible to monitor cell apoptosis in real time.

A Quenched Annexin V-Fluorophore for the Real-Time Fluorescence Imaging of Apoptotic Processes In Vitro and In Vivo

Annexin-based probes have long been used to study apoptotic cell death, which is of key importance to many areas of biological research, drug discovery, and clinical applications. Although apoptosis is a dynamic biological event with cell-to-cell variations, current annexin-based probes are impractical for monitoring apoptosis in real-time. Herein, a quenched annexin V-near-infrared fluorophore conjugate (Q-annexin V) is reported as the first OFF-ON annexin protein-based molecular sensor for real-time near-infrared fluorescence imaging of apoptosis. Q-annexin V is non-fluorescent in the extracellular region, due to photoinduced electron transfer interactions between the conjugated dye and amino acid quenchers (tryptophan and tyrosine). The probe becomes highly fluorescent when bound to phosphatidylserines on the outer layer of cell membranes during apoptosis, thereby enabling apoptosis to be monitored in real-time in 2D and 3D cell structures. In particular, Q-annexin V shows superior utility for in vivo apoptosis fluorescence imaging in animal models of cisplatin-induced acute kidney injury and cancer immune therapy, compared to the conventional polarity-sensitive pSIVA-IANBD or annexin V-Alexa647 conjugates.

Photon induced quantum yield regeneration of cap-exchanged CdSe/CdS quantum rods for ratiometric biosensing and cellular imaging

Full water-dispersion of commercial hydrophobic CdSe/CdS core/shell quantum rods (QRs) was achieved by cap-exchange using a dihydrolipoic acid zwitterion ligand at a low ligand:QR molar ratio (LQMR) of 1000. However, this process almost completely quenched the QR fluorescence, greatly limiting its potential in downstream fluorescence based applications. Fortunately, we found that the QR fluorescence could be recovered by exposure to near ultra-violet to blue light radiation (e.g. 300-450 nm). These "reborn" QRs were found to be compact, bright, and stable, and were resistant to non-specific adsorption, which make them powerful fluorescent probes in broad biomedical applications. We demonstrated their potential in two model applications: first, the QRs were conjugated with His₈-tagged small antibody mimetic proteins (also known as Affimers) for the sensitive detection of target proteins via a Förster resonance energy transfer (FRET) readout strategy and second, the QR surface was functionalized with biotins for targeted imaging of cancer cells.

Photon Antibunching Reveals Static and Dynamic Quenching Interaction of Tryptophan with Atto-655

Fluorescence correlation spectroscopy (FCS) of photoinduced electron transfer (PET) between the dye Atto-655 and the amino acid tryptophan has been extensively used for studying fast conformational dynamics of small disordered peptides and proteins. However, a precise understanding of the quenching mechanism and its exact rates that would explain ensemble as well as single-molecule spectroscopy results is still lacking. In this contribution, a general unified model for intermolecular PET between Atto-655 and tryptophan is developed, which involves ground-state complex formation, quenching sphere of action, and dynamic quenching at the single-molecule level. We present measurements of fluorescence antibunching, fluorescence lifetime, and steady-state fluorescence intensity and absorbance and demonstrate that our model is capable to describe all results in a global and coherent manner.

Covalent dye attachment influences the dynamics and conformational properties of flexible peptides

Fluorescence spectroscopy techniques like Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) have become important tools for the in vitro and in vivo investigation of conformational dynamics in biomolecules. These methods rely on the distance-dependent quenching of the fluorescence signal of a donor fluorophore either by a fluorescent acceptor fluorophore (FRET) or a non-fluorescent quencher, as used in FCS with photoinduced electron transfer (PET). The attachment of fluorophores to the molecule of interest can potentially alter the molecular properties and may affect the relevant conformational states and dynamics especially of flexible biomolecules like intrinsically disordered proteins (IDP). Using the intrinsically disordered S-peptide as a model system, we investigate the impact of terminal fluorescence labeling on the molecular properties. We perform extensive molecular dynamics simulations on the labeled and unlabeled peptide and compare the results with in vitro PET-FCS measurements. Experimental and simulated timescales of end-to-end fluctuations were found in excellent agreement. Comparison between simulations with and without labels reveal that the π-stacking interaction between the fluorophore labels traps the conformation of S-peptide in a single dominant state, while the unlabeled peptide undergoes continuous conformational rearrangements. Furthermore, we find that the open to closed transition rate of S-peptide is decreased by at least one order of magnitude by the fluorophore attachment. Our approach combining experimental and in silico methods provides a benchmark for the simulations and reveals the significant effect that fluorescence labeling can have on the conformational dynamics of small biomolecules, at least for inherently flexible short peptides. The presented protocol is not only useful for comparing PET-FCS experiments with simulation results but provides a strategy to minimize the influence on molecular properties when chosing labeling positions for fluorescence experiments.

The interaction of amino acids with macrocyclic pH probes of pseudopeptidic nature

The fluorescence quenching, by a series of amino acids, of pseudopeptidic compounds acting as probes for cellular acidity has been investigated.