Homotransfer of FRET Reporters for Live Cell Imaging

Functionalizing Surfaces by Physical Vapor Deposition To Measure the Degree of Nanoscale Contact Using FRET

Adhesion between solid materials is caused by intermolecular forces that only take place if the adhering surfaces are at nanoscale contact (NSC) (i.e., 0.1-0.4 nm. To study adhesion, NSC can be evaluated with Förster Resonance Energy Transfer (FRET). FRET uses the interaction of compatible fluorescence molecules to measure the nanometer distance between bonded surfaces. For this, each surface is labeled with one fluorescence dye, named the Donor or Acceptor. If these molecules are in NSC, a nonradiative Donor-Acceptor energy transfer will occur and can be detected using FRET spectroscopy. Here, for the first time, we introduce an innovative concept of a FRET-based NSC measurement employing dye-nanolayer films prepared by a physical vapor deposition (PVD). The dye nanolayers were prepared by PVD from the vaporization of the Donor and Acceptor molecules separately. The selected molecules, 7-Amino-4-methyl-cumarin (C120) and 5(6)-Carboxy-2',7'-dichlor-fluorescein (CDCF), present high quantum yields (QY, QYD = 0.91 and QYA = 0.64) and a low FRET distance range of 0.6-2.2 nm, adequate for the study of NSC. The produced dye-nanolayer films exhibit a uniform dye distribution (verified by atomic force microscopy) and suitable fluorescence intensities. To validate the NSC measurements, FRET spectroscopy experiments were performed with bonded dye-nanolayer films prepared under different loads (from 1.5 to 140 bar), thus creating different degrees of NSC. The results show an increase in FRET intensity (R 2 = 0.95) with the respective adhesion energy between the films, which is directly related to the degree of NSC. Hence, this work establishes FRET as an experimental technique for the measurement of NSC, and its relation to surface adhesion. Additionally, thanks to the FRET dye-nanolayer approach, the method can be employed on arbitrary surfaces. Essentially, any sufficiently transparent substrate can be functionalized with FRET compatible dyes to evaluate NSC, which represents a breakthrough in contact mechanics investigations of soft and hard solid materials.

Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy

The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.

Beads on a Chain Fluorescent Oligomeric Materials: Interactions of Conjugated Organic Cross-Linkers with Silsesquioxane Cages

Organic electronic materials have advantages over inorganics in terms of versatility, cost, and processability. Recent advancements in organic materials for light-emitting diodes (OLED), field effect transistors (OFET), and photovoltaics have engendered extensive innovation potential on this field. In this research, we focus on synthesizing SQ (silsesquioxane) based oligomers cross-linked by dibromo-aromatic linkers and explore how the cross-linker influences their photophysical properties. Bis-trialkoxy silyl (linker) model compounds were synthesized to compare noncage photophysical properties with the oligomers. Several techniques such as UV/vis, fluorescence, FTIR, and thermal gravimetric analysis (TGA) have been used to characterize the systems. Time-resolved fluorescence and femtosecond transient absorption spectroscopy were used to understand the excited state dynamics of these materials. Studies were carried out to understand the differences between monomers and oligomers and potential energy transfer and charge transfer between the cages and cross-linking chromophores. Transient absorption showed lower energy absorption from the excited states, suggesting short-range communication between moieties. Single photon counting studies have shown distinct lifetime differences between most linkers and cages display possible excitation energy transfer through these materials. Transient absorption anisotropy measurements have shown signatures for excitation energy transfer between linker chromophores for oligomeric compounds. The silsesquioxane (SQ) backbone of the oligomers gives substantial thermal stability as well as solution processability, giving better flexibility for achieving energy transfer between linking chromophores.

Fluorescence depolarization dynamics of ionic strength sensors using time-resolved anisotropy

Eukaryotic cells exploit dynamic and compartmentalized ionic strength to impact a myriad of biological functions such as enzyme activities, protein-protein interactions, and catalytic functions. Herein, we investigated the fluorescence depolarization dynamics of recently developed ionic strength biosensors (mCerulean3-linker-mCitrine) in Hofmeister salt (KCl, NaCl, NaI, and Na₂SO₄) solutions. The mCerulean3-mCitrine acts as a Förster resonance energy transfer (FRET) pair, tethered together by two oppositely charged α-helices in the linker region. We developed a time-resolved fluorescence depolarization anisotropy approach for FRET analyses, in which the donor (mCerulean3) is excited by 425-nm laser pulses, followed by fluorescence depolarization analysis of the acceptor (mCitrine) in KE (lysine-glutamate), arginine-aspartate, and arginine-glutamate ionic strength sensors with variable amino acid sequences. Similar experiments were carried out on the cleaved sensors as well as an E6G2 construct, which has neutral α-helices in the linker region, as a control. Our results show distinct dynamics of the intact and cleaved sensors. Importantly, the FRET efficiency decreases and the donor-acceptor distance increases as the environmental ionic strength increases. Our chemical equilibrium analyses of the collapsed-to-stretched conformational state transition of KE reveal that the corresponding equilibrium constant and standard Gibbs free energy changes are ionic strength dependent. We also tested the existing theoretical models for FRET analyses using steady-state anisotropy, which reveal that the angle between the dipole moments of the donor and acceptor in the KE sensor are sensitive to the ionic strength. These results help establish the time-resolved depolarization dynamics of these genetically encoded donor-acceptor pairs as a quantitative means for FRET analysis, which complement traditional methods such as time-resolved fluorescence for future in vivo studies.

A Guide to Fluorescence Lifetime Microscopy and Förster's Resonance Energy Transfer in Neuroscience

Fluorescence lifetime microscopy (FLIM) and Förster's resonance energy transfer (FRET) are advanced optical tools that neuroscientists can employ to interrogate the structure and function of complex biological systems in vitro and in vivo using light. In neurobiology they are primarily used to study protein-protein interactions, to study conformational changes in protein complexes, and to monitor genetically encoded FRET-based biosensors. These methods are ideally suited to optically monitor changes in neurons that are triggered optogenetically. Utilization of this technique by neuroscientists has been limited, since a broad understanding of FLIM and FRET requires familiarity with the interactions of light and matter on a quantum mechanical level, and because the ultra-fast instrumentation used to measure fluorescent lifetimes and resonance energy transfer are more at home in a physics lab than in a biology lab. In this overview, we aim to help neuroscientists overcome these obstacles and thus feel more comfortable with the FLIM-FRET method. Our goal is to aid researchers in the neuroscience community to achieve a better understanding of the fundamentals of FLIM-FRET and encourage them to fully leverage its powerful ability as a research tool. Published 2020. U.S. Government.

The Importance of Mechanical Forces for in vitro Endothelial Cell Biology

Blood and lymphatic vessels are lined by endothelial cells which constantly interact with their luminal and abluminal extracellular environments. These interactions confer physical forces on the endothelium, such as shear stress, stretch and stiffness, to mediate biological responses. These physical forces are often altered during disease, driving abnormal endothelial cell behavior and pathology. Therefore, it is critical that we understand the mechanisms by which endothelial cells respond to physical forces. Traditionally, endothelial cells in culture are grown in the absence of flow on stiff substrates such as plastic or glass. These cells are not subjected to the physical forces that endothelial cells endure in vivo, thus the results of these experiments often do not mimic those observed in the body. The field of vascular biology now realize that an intricate analysis of endothelial signaling mechanisms requires complex in vitro systems to mimic in vivo conditions. Here, we will review what is known about the mechanical forces that guide endothelial cell behavior and then discuss the advancements in endothelial cell culture models designed to better mimic the in vivo vascular microenvironment. A wider application of these technologies will provide more biologically relevant information from cultured cells which will be reproducible to conditions found in the body.

Illuminating the kinome: Visualizing real-time kinase activity in biological systems using genetically encoded fluorescent protein-based biosensors

Genetically encoded fluorescent protein-based kinase biosensors are a central tool for illumination of the kinome. The adaptability and versatility of biosensors have allowed for spatiotemporal observation of real-time kinase activity in living cells and organisms. In this review, we highlight various types of kinase biosensors, along with their burgeoning applications in complex biological systems. Specifically, we focus on kinase activity reporters used in neuronal systems and whole animal settings. Genetically encoded kinase biosensors are key for elucidation of the spatiotemporal regulation of protein kinases, with broader applications beyond the Petri dish.

Imaging of fluorescence anisotropy during photoswitching provides a simple readout for protein self-association

Monitoring of protein oligomerization has benefited greatly from Förster Resonance Energy Transfer (FRET) measurements. Although donors and acceptors are typically fluorescent molecules with different spectra, homo-FRET can occur between fluorescent molecules of the same type if the emission spectrum overlaps with the absorption spectrum. Here, we describe homo-FRET measurements by monitoring anisotropy changes in photoswitchable fluorescent proteins while photoswitching to the off state. These offer the capability to estimate anisotropy in the same specimen during homo-FRET as well as non-FRET conditions. We demonstrate photoswitching anisotropy FRET (psAFRET) with a number of test chimeras and example oligomeric complexes inside living cells. We also present an equation derived from FRET and anisotropy equations which converts anisotropy changes into a factor we call delta r FRET (drFRET). This is analogous to an energy transfer efficiency and allows experiments performed on a given homo-FRET pair to be more easily compared across different optical configurations.

Performing homo-FRET measurements in cells using a fluorescence microscope is challenging, especially when using high numerical aperture objective lenses. Here the authors present a method for improved homo-FRET measurements based on anisotropy changes in photoswitchable fluorescent proteins.

FRET Microscopy in Yeast

Förster resonance energy transfer (FRET) microscopy is a powerful fluorescence microscopy method to study the nanoscale organization of multiprotein assemblies in vivo. Moreover, many biochemical and biophysical processes can be followed by employing sophisticated FRET biosensors directly in living cells. Here, we summarize existing FRET experiments and biosensors applied in yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, two important models of fundamental biomedical research and efficient platforms for analyses of bioactive molecules. We aim to provide a practical guide on suitable FRET techniques, fluorescent proteins, and experimental setups available for successful FRET experiments in yeasts.

Circularly Permuted Fluorescent Protein-Based Indicators: History, Principles, and Classification

Genetically encoded biosensors based on fluorescent proteins (FPs) are a reliable tool for studying the various biological processes in living systems. The circular permutation of single FPs led to the development of an extensive class of biosensors that allow the monitoring of many intracellular events. In circularly permuted FPs (cpFPs), the original N- and C-termini are fused using a peptide linker, while new termini are formed near the chromophore. Such a structure imparts greater mobility to the FP than that of the native variant, allowing greater lability of the spectral characteristics. One of the common principles of creating genetically encoded biosensors is based on the integration of a cpFP into a flexible region of a sensory domain or between two interacting domains, which are selected according to certain characteristics. Conformational rearrangements of the sensory domain associated with ligand interaction or changes in the cellular parameter are transferred to the cpFP, changing the chromophore environment. In this review, we highlight the basic principles of such sensors, the history of their creation, and a complete classification of the available biosensors.

The extracellular matrix and Ca(2+)signaling mechanisms

The extracellular matrix (ECM) consists of proteins, glycosaminoglycans and glycoproteins, that support the dynamic interactions between cells, including intercellular communication, cell attachment, cell differentiation, cell growth and migration. As such, the ECM represents an essential and very sensitive system within the tissue microenvironment that is involved in processes such as tissue regeneration and carcinogenesis. The aim of the present review is to evaluate its diversity through Ca(2+) signaling and its role in muscle cell function. Here, we discuss some methodological approaches dissecting Ca(2+) handling mechanisms in myogenic and non-myogenic cells, e.g. the importance of Ca(2+) and calpains in muscle dystrophy. We also consider the reconstruction of skeletal muscle by colonization of decellularized ECM with muscle-derived cells isolated from skeletal muscle. Therefore, it is necessary to establish new methodological procedures based on Ca(2+) signaling in skeletal muscle cells and their effect on ECM homeostasis, allowing the monitoring of skeletal muscle reconstruction and organ repair.