Förster Resonance Energy Transfer Studies Research Articles

Pulsed-Interleaved-Excitation Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy.

We report on pulsed-interleaved-excitation two-dimensional fluorescence lifetime correlation spectroscopy (PIE 2D FLCS) to study biomolecular structural dynamics with high sensitivity and high time resolution using Förster resonance energy transfer (FRET). PIE 2D FLCS is an extension of 2D FLCS, which is a unique single-molecule fluorescence method that uses fluorescence lifetime information to distinguish different fluorescence species in equilibrium and resolves their interconversion dynamics with a submicrosecond time resolution. Because 2D FLCS has used only a single-color excitation so far, it was difficult to distinguish a very low-FRET (or zero-FRET) species from only donor-labeled species. We overcome this difficulty by implementing the PIE scheme (i.e., alternate excitation of the donor and acceptor dyes using two temporally interleaved excitations with different colors) to 2D FLCS, realizing two-color excitation and two-color fluorescence detection in 2D FLCS. After proof-of-principle PIE 2D FLCS analysis on the photon data synthesized with Monte Carlo simulation, we apply PIE 2D FLCS to a DNA-hairpin sample and show that this method readily distinguishes four fluorescent species, i.e., high-FRET, low-FRET, and two single-dye-labeled species. In addition, we show that PIE 2D FLCS can also quantitatively evaluate the contributions of the donor-acceptor spectral crosstalk, which often appears as artifacts in FRET studies and degrades the information obtained.

In vivo quantitative FRET small animal imaging: Intensity versus lifetime-based FRET

Förster resonance energy transfer (FRET) microscopy is used in numerous biophysical and biomedical applications to monitor inter- and intramolecular interactions and conformational changes in the 2–10 nm range. FRET is currently being extended to in vivo optical imaging, its main application being in quantifying drug-target engagement or drug release in animal models of cancer using organic dye or nanoparticle-labeled probes. Herein, we compared FRET quantification using intensity-based FRET (sensitized emission FRET analysis with the three-cube approach using an IVIS imager) and macroscopic fluorescence lifetime (MFLI) FRET using a custom system using a time-gated-intensified charge-coupled device, for small animal optical in vivo imaging. The analytical expressions and experimental protocols required to quantify the product fDE of the FRET efficiency E and the fraction of donor molecules involved in FRET, fD, are described in detail for both methodologies. Dynamic in vivo FRET quantification of transferrin receptor-transferrin binding was acquired in live intact nude mice upon intravenous injection of a near-infrared-labeled transferrin FRET pair and benchmarked against in vitro FRET using hybridized oligonucleotides. Even though both in vivo imaging techniques provided similar dynamic trends for receptor-ligand engagement, we demonstrate that MFLI-FRET has significant advantages. Whereas the sensitized emission FRET approach using the IVIS imager required nine measurements (six of which are used for calibration) acquired from three mice, MFLI-FRET needed only one measurement collected from a single mouse, although a control mouse might be needed in a more general situation. Based on our study, MFLI therefore represents the method of choice for longitudinal preclinical FRET studies such as that of targeted drug delivery in intact, live mice.

FRETing about the details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer.

Förster resonance energy transfer (FRET) is a valuable method for monitoring protein conformation and biomolecular interactions. Intrinsically fluorescent amino acids that can be genetically encoded, such as acridonylalanine (Acd), are particularly useful for FRET studies. However, quantitative interpretation of FRET data to derive distance information requires careful use of controls and consideration of photophysical effects. Here we present two case studies illustrating how Acd can be used in FRET experiments to study small molecule induced conformational changes and multicomponent biomolecular complexes.

Förster resonance energy transfer studies of an intrinsically disordered peptide using a cyanophenylalanine derivative.

We report Förster Resonance Energy Transfer (FRET) studies of an intrinsically disordered peptide (IDP) using a phenylalanine derivative as the donor fluorophore. Due to its increased spectroscopic selectivity compared to phenylalanine, 2-cyanophenylalanine (2-PheCN) can be used as a site-specific probe of solvent environment and in FRET with tryptophan (Trp) as the acceptor for analysis of protein structure with an R0 of roughly 16 Å. Replacing phenylalanine with 2-PheCN in a 12 residue, intrinsically disordered olfactory peptide (OFP) where tryptophan occupies the N-terminus position provides two model IDPs: OFP Long, where 2-PheCN occupies the C-terminus, and OFP Short, in which 2-PheCN is two residues away from Trp. Measurement of the FRET efficiency within various solvent environments that either promote or inhibit secondary structures allows for examination of structural changes in the IDPs induced by the solvent environment. As expected, the energy transfer is highly efficient, approximately 0.99, between the nearly proximal fluorophores in OFP Short for all solvents examined. However, surprisingly the largest FRET efficiency for OFP Long is observed in solvent inhibiting secondary structures. Future FRET studies of both OFP Long and OFP Short will further investigate the solvent environment and temperature dependencies of the dynamics and structure of the disordered olfactory peptides.

Fӧrster resonance energy transfer analysis of amyloid state of proteins

The Förster resonance energy transfer (FRET) is a well-established and versatile spectroscopic technique extensively used for exploring a variety of biomolecular interactions and processes. The present review is intended to cover the main results of our FRET studies focused on amyloid fibrils, a particular type of disease-associated protein aggregates. Based on the examples of several fibril-forming proteins including insulin, lysozyme and amyloidogenic variants of N-terminal fragment of apolipoprotein A-I, it was demonstrated that: (i) the two- and three-step FRET with the classical amyloid marker Thioflavin T as an input donor has a high amyloid-sensing potential and can be used to refine the amyloid detection assays; (ii) the intermolecular time-resolved and single-molecule pulse interleaved excitation FRET can give quantitative information on the nucleation of amyloid fibrils; (iii) FRET between the membrane fluorescent probes and protein-associated intrinsic or extrinsic fluorophores is suitable for monitoring the membrane binding of fibrillar proteins, exploring their location relative to lipid-water interface and restructuring on a lipid matrix; (iv) the FRET-based distance estimation between fibril-bound donor and acceptor fluorophores can serve as one of the verification criteria upon structural modeling of amyloid fibrils.

Analysis of the conformational space and dynamics of RNA helicases by single-molecule FRET in solution and on surfaces.

RNA helicases are a diverse group of enzymes that catalyze the unwinding of RNA duplex regions in an ATP-dependent reaction. Both the helicase itself and its RNA substrate undergo conformational changes during the reaction, which are amenable to Förster resonance energy transfer (FRET) studies. Single-molecule FRET studies in solution by confocal microscopy and on surfaces by total internal reflection microscopy provide information on different conformers present, their fractional populations in equilibrium, and the rate constants of their inter-conversion. Collectively, the information gained can be integrated into a kinetic and thermodynamic framework that quantitatively describes the conformational dynamics of the helicase studied. FRET experiments also provide distance information to map and model the structures of individual conformational states. The integrated model provides a comprehensive description of the structure and dynamics of the helicase, which can be linked to its biological function. Single-molecule FRET studies have tremendous potential to define the relationship between structure, function and dynamics of RNA helicases and to understand the mechanistic basis for their broad range of biological functions. The focus of this chapter is on providing guidance in the design of single-molecule FRET experiments and on the interpretation of the data obtained. Selected examples illustrate important considerations when analyzing single-molecule experiments, as well as their limitations and possible pitfalls.

A Combined Acceptor Photobleaching and Donor Fluorescence Lifetime Imaging Microscopy Approach to Analyze Multi-Protein Interactions in Living Cells.

Protein–protein interaction studies often provide new insights, i.e., into the formation of protein complexes relevant for structural oligomerization, regulation of enzymatic activity or information transfer within signal transduction pathways. Mostly, biochemical approaches have been used to study such interactions, but their results are limited to observations from lysed cells. A powerful tool for the non-invasive investigation of protein–protein interactions in the context of living cells is the microscopic analysis of Förster Resonance Energy Transfer (FRET) among fluorescent proteins. Normally, FRET is used to monitor the interaction state of two proteins, but in addition, FRET studies have been used to investigate three or more interacting proteins at the same time. Here we describe a fluorescence microscopy-based method which applies a novel 2-step acceptor photobleaching protocol to discriminate between non-interacting, dimeric interacting and trimeric interacting states within a three-fluorophore setup. For this purpose, intensity- and fluorescence lifetime-related FRET effects were analyzed on representative fluorescent dimeric and trimeric FRET-constructs expressed in the cytosol of HEK293 cells. In particular, by combining FLIM- and intensity-based FRET data acquisition and interpretation, our method allows to distinguish trimeric from different types of dimeric (single-, double- or triple-dimeric) protein–protein interactions of three potential interaction partners in the physiological setting of living cells.

Differential flexibility leading to crucial microelastic properties of asymmetric lipid vesicles for cellular transfection: A combined spectroscopic and atomic force microscopy studies

The role of microscopic elasticity of nano-carriers in cellular uptake is an important aspect in biomedical research. Herein we have used AFM nano-indentation force spectroscopy and Förster resonance energy transfer (FRET) measurements to probe microelastic properties of three novel cationic liposomes based on di-alkyl dihydroxy ethyl ammonium chloride based lipids having asymmetry in their hydrophobic chains (Lip1818, Lip1814 and Lip1810). AFM data reveals that symmetry in hydrophobic chains of a cationic lipid (Lip1818) imparts higher rigidity to the resulting liposomes than those based on asymmetric lipids (Lip1814 and Lip1810). The stiffness of the cationic liposomes is found to decrease with increasing asymmetry in the hydrophobic lipid chains in the order of Lip1818 > Lip1814 > lip1810. FRET measurements between Coumarin 500 (Donor) and Merocyanine 540 (Acceptor) have revealed that full width at half-maxima (hw) of the probability distribution (P(r)) of donor-acceptor distance (r), increases in an order Lip1818 < Lip1814 < Lip1810 with increasing asymmetry of the hydrophobic lipid chains. This increase in width (hw) of the donor-acceptor distance distributions is reflective of increasing flexibility of the liposomes with increasing asymmetry of their constituent lipids. Thus, the results from AFM and FRET studies are complementary to each other and indicates that an increase in asymmetry of the hydrophobic lipid chains increases elasticity and or flexibility of the corresponding liposomes. Cell biology experiments confirm that liposomal flexibility or rigidity directly influences their cellular transfection efficiency, where Lip1814 is found to be superior than the other two liposomes manifesting that a critical balance between flexibility and rigidity of the cationic liposomes is key to efficient cellular uptake. Taken together, our studies reveal how asymmetry in the molecular architecture of the hydrophobic lipid chains influences the microelastic properties of the liposomes, and hence, their cellular uptake efficiency.

Photoswitching FRET Studies of Doxorubicin-Chromatin Interactions

The molecular basis for the action of anti-cancer drugs is of interest for further drug development as well as for better understanding of adverse side effects. Doxorubicin is a DNA intercalating anti-cancer drug thought to work by inhibition of topoisomerase II leading to double-strand breaks and subsequent cancer cell death. It is also proposed to display a novel mechanism of action which results in eviction of some core histones from chromatin and leads to deregulation of the cancer cell transcriptome. Uncommon amongst anti-cancer drugs, many anthracyclines such as doxorubicin have absorption spectra in the visible range which allows Förster Resonance Energy Transfer (FRET) studies of their interactions with chromatin. Since Fluorescence Lifetime Imaging Microscopy (FLIM) FRET studies do not require an acceptor to be fluorescent to measure energy transfer, previous works concentrated on doxorubicin-chromatin interactions within intact tumors by imaging the fluorescence lifetimes of EGFP labeled histone H1 or H2B. Our previously developed photoswitching FRET (psFRET) method mimics the advantage of FLIM by also not requiring a fluorescent acceptor. This property allows us to monitor energy transfer between doxorubicin and the core histone proteins tagged with the photoswitchable fluorescent protein, Dronpa. By tagging the N or C termini of the core histones, the Dronpa protein can be placed at multiple different positions on the periphery of a nucleosome and thus allow a survey of FRET efficiencies from numerous points. Here, we present psFRET studies in our efforts to better define binding sites for doxorubicin as well as its potential for histone eviction from chromatin.

Crowder induced structural modulation of a multi-domain protein during its early stages of aggregation: A FRET-based and protein solvation study.

Protein aggregation has been known for long to be the prime cause for several neurological disorders in human beings. While protein aggregation is itself a complex process, understanding the same in the context of a crowded cellular medium remains a challenge. In this work, using Förster resonance energy transfer (FRET) and solvation dynamics, we have tried to gain important insights into the structural rearrangements, during the early stages of aggregation of the multidomain protein bovine serum albumin (BSA) in presence of a range of synthetic macromolecular crowding agents. FRET studies show that there is an initial compaction in the domain size (domain I) at the early time points of incubation followed by an increase in the distance between the donor-acceptor pair. Analyses of the solvent correlation traces of BADAN (labeled at free Cys-34 in domain I of BSA) reveal that the same domain becomes rigid during the initial phase of the aggregation process subsequent to which there was a gradual increase in flexibility, the latter we propose being a necessary step that allows facile addition of more protein units.

Optimizing FRET-FLIM Labeling Conditions to Detect Nuclear Protein Interactions at Native Expression Levels in Living Arabidopsis Roots.

Protein complex formation has been extensively studied using Förster resonance energy transfer (FRET) measured by Fluorescence Lifetime Imaging Microscopy (FLIM). However, implementing this technology to detect protein interactions in living multicellular organism at single-cell resolution and under native condition is still difficult to achieve. Here we describe the optimization of the labeling conditions to detect FRET-FLIM in living plants. This study exemplifies optimization procedure involving the identification of the optimal position for the labels either at the N or C terminal region and the selection of the bright and suitable, fluorescent proteins as donor and acceptor labels for the FRET study. With an effective optimization strategy, we were able to detect the interaction between the stem cell regulators SHORT-ROOT and SCARECROW at endogenous expression levels in the root pole of living Arabidopsis embryos and developing lateral roots by FRET-FLIM. Using this approach we show that the spatial profile of interaction between two transcription factors can be highly modulated in reoccurring and structurally resembling organs, thus providing new information on the dynamic redistribution of nuclear protein complex configurations in different developmental stages. In principle, our optimization procedure for transcription factor complexes is applicable to any biological system.

Different Conformational Subensembles of the Intrinsically Disordered Protein α-Synuclein in Cells.

The intrinsically disordered protein α-synuclein (αS) is thought to play an important role in cellular membrane processes. Although in vitro experiments indicate that this initially disordered protein obtains structure upon membrane binding, NMR and EPR studies in cells could not single out any conformational subensemble. Here we microinjected small amounts of αS, labeled with a Förster resonance energy transfer (FRET) pair, into SH-SY5Y cells to investigate conformational changes upon membrane binding. Our FRET studies show a clear conformational difference between αS in the cytosol and when bound to small vesicles. The identification of these different conformational subensembles inside cells resolves the apparent contradiction between in vitro and in vivo experiments and shows that at least two different conformational subensembles of αS exist in cells. The existence of conformational subensembles supports the idea that αS can obtain different functions which can possibly be dynamically addressed with changing intracellular physicochemical conditions.

Ensemble and single-molecule FRET studies of protein synthesis.

Protein synthesis is a complex, multi-step process that involves large conformational changes of the ribosome and protein factors of translation. Over the last decade, Förster resonance energy transfer (FRET) has become instrumental for studying structural rearrangements of the translational apparatus. Here, we discuss the design of ensemble and single-molecule (sm) FRET assays of translation. We describe a number of experimental strategies that can be used to introduce fluorophores into the ribosome, tRNA, mRNA and protein factors of translation. Alternative approaches to tethering of translation components to the microscope slide in smFRET experiments are also reviewed. Finally, we discuss possible challenges in the interpretation of FRET data and ways to address these challenges.

Conformational Changes Spanning Angstroms to Nanometers via a Combined Protein-Induced Fluorescence Enhancement-Förster Resonance Energy Transfer Method.

Förster resonance energy transfer (FRET)-based single-molecule techniques have revolutionized our understanding of conformational dynamics in biomolecular systems. Recently, a new single-molecule technique based on protein-induced fluorescence enhancement (PIFE) has aided studies in which minimal (<3 nm) displacements occur. Concerns have been raised regarding whether donor fluorophore intensity (and correspondingly fluorescence quantum yield Φf) fluctuations, intrinsic to PIFE methods, may adversely affect FRET studies when retrieving the donor-acceptor dye distance. Here, we initially show through revisions of Förster's original equation that distances may be calculated in FRET experiments regardless of protein-induced intensity (and Φf) fluctuations occurring in the donor fluorophore. We additionally demonstrate by an analysis of the recorded emission intensity and competing decay pathways that PIFE and FRET methods may be conveniently combined, providing parallel complementary information in a single experiment. Single-molecule studies conducted with Cy3- and ATTO647N-labeled RNA structures and the HCV-NS5B polymerase protein undergoing binding dynamics along the RNA backbone provide a case study to validate the results. The analysis behind the proposed method enables for PIFE and FRET changes to be disentangled when both FRET and PIFE fluctuate over time following protein arrival and, for example, sliding. A new method, intensity-FRET, is thus proposed to monitor conformational changes spanning from angstroms to nanometers.

Hybrid nanocomposites of a fluorescent block copolymer and quantum dots: An efficient way for energy transfer

Förster resonance energy transfer (FRET) phenomenon has great potential in several applications, whose efficiency is dependent on the energy transfer between a suitable pair of fluorophores. In this work, a new block copolymer, PS-b-PS(co-pyren-1-yl), with fluorescent properties, was synthetized and used as donor component in the fluorophores pair copolymer/cadmium telluride quantum dots (CdTe QDs). Thus, water-soluble CdTe QDs, previously transferred into organic phase, by replacing the stabilizer ligands, thioglycolic acid by 1-dodecanethiol (1-DDT), were used to prepare a new hybrid nanocomposite. FRET studies between the fluorescent copolymer and CdTe-DDT QDs revealed that this fluorophores pair can experience FRET with an efficiency of 48%, being an efficient antenna system for light harvesting applications.

Accurate Determination of the RNA Three-Way Junctions Via Single-Molecule High-Precision Fret Measurements

In nature RNA helices are often linked via various junctions and bulges that determine overall 3D structure which are used as building blocks and functional components in nanotechnology applications. Hence visualization of RNA conformations is crucial for understanding their biological functions. Förster-Resonance-Energy-Transfer (FRET) restrained high-precision structural modeling can be used to determine the structure of these junctions. Multi-parameter fluorescence detection (MFD) of single molecules and ensemble Time-Correlated Single Photon Counting (eTCSPC) measurements were applied to perform FRET study on systematic series of 6 RNA three- way-junctions (3WJs) derived from the hairpin ribozyme. Bulge and sequence variations were considered as dominant factors influencing junction, two of which have bulge (two and five unpaired nucleotides) in the junction region. We have generated a database of overall 252 different RNA 3WJs labeled with Alexa488 and Cy5 fluorescent dyes. The analysis toolkit included probability distribution analysis (PDA) for FRET distance determination and FRET position and screening (FPS) toolkit for structural model generation. We detected only one predominant conformer for RNAs 3WJ. Furthermore we report that bulges in the junction determine orientation and rotation of helices, inducing coaxial stacking. We provide a geometrical description of the junction geometry and our results show that small changes in the sequence make dramatic changes in RNA 3WJ tertiary structures which are expected to have significant impact on the functionality. As the accuracy of FRET restrained modeling depends on the correct description of the dye behavior, we characterized the position dependent fluorescent properties of the coupled dyes and statistically analyzed the systematic deviations of the calculated FRET distances from the model generated distances. This allowed us to identify the problematic labeling positions. Thus we could improve the accuracy of the FRET method by careful selection of labeling sites.

Probe-location dependent resonance energy transfer at lipid/water interfaces: comparison between the gel- and fluid-phase of lipid bilayer.

Despite significant interest in understanding the role of the local dielectric environment and lipid-bilayer fluidity/rigidity in resonance energy transfer between chromophores at lipid/water interfaces, a comprehensive approach to quantify such environmental dependence on energy transfer is missing - primarily because of the scarcity of suitable probes. Here we present the results on multi-chromophoric Förster resonance energy transfer (FRET) from a series of 4-aminophthalimide-based molecules (4AP-Cn; n = 2-10, 12) of different lipophilicity (donors), which reside at different depths across the lipid/water interfaces, to rhodamine-6G (Rh6G; acceptor) molecules that stay in a water-rich region near the lipid headgroups. We apply steady-state and time-resolved fluorescence spectroscopy, and find that multi-chromophoric FRET from the series of 4AP-Cn donors to the Rh6G acceptor occurs in a peculiar stepwise fashion at the lipid/water interface of a gel-phase (Lβ') DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) bilayer at room temperature. However, the same donor-acceptor pairs show only subtle but continuous donor-depth-dependent FRET at the lipid/water interface of a fluid-phase (Lα) DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayer. These features were found to correlate with the lipid-phase dependent local environmental polarity sensed by 4AP-Cn donors at the interfaces. Molecular dynamics (MD) simulations, combined with experimental results, show that relative depth (and angle) variation of the 4AP-Cn donors and Rh6G acceptor directly controls the FRET efficiencies through fine tuning of the emission and absorption spectra of the donors and acceptor, respectively. The results indicate that the 4AP-Cn probes are well-suited as donors for FRET studies, which allow the FRET parameters at lipid/water interfaces of gel- and fluid-phases of lipid-bilayers to be quantified and compared simultaneously.

Solution-Based Single-Molecule FRET Studies of K+ Channel Gating in a Lipid Bilayer

Ion channels are dynamic multimeric proteins that often undergo multiple unsynchronized structural movements as they switch between their open and closed states. Such structural changes are difficult to measure within the context of a native lipid bilayer and have often been monitored via macroscopic changes in Förster resonance energy transfer (FRET) between probes attached to different parts of the protein. However, the resolution of this approach is limited by ensemble averaging of structurally heterogeneous subpopulations. These problems can be overcome by measurement of FRET in single molecules, but this presents many challenges, in particular the ability to control labeling of subunits within a multimeric protein with acceptor and donor fluorophores, as well as the requirement to image large numbers of individual molecules in a membrane environment. To address these challenges, we randomly labeled tetrameric KirBac1.1 potassium channels, reconstituted them into lipid nanodiscs, and performed single-molecule FRET confocal microscopy with alternating-laser excitation as the channels diffused in solution. These solution-based single-molecule FRET measurements of a multimeric ion channel in a lipid bilayer have allowed us to probe the structural changes that occur upon channel activation and inhibition. Our results provide direct evidence of the twist-to-shrink movement of the helix bundle crossing during channel gating and demonstrate how this method might be applied to real-time structural studies of ion channel gating.

Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα

Total internal reflection fluorescence-based single-molecule Förster resonance energy transfer (FRET) measurements were previously carried out on the ankyrin repeat domain (ARD) of IκBα, the temporally regulated inhibitor of canonical NFκB signaling. Under native conditions, most of the IκBα molecules showed stable, high FRET signals consistent with distances between the fluorophores estimated from the crystal structures of the NFκB(RelA/p50)-IκBα complex. Similar high FRET efficiencies were found when the IκBα molecules were either free or in complex with NFκB(RelA/p50), and were interpreted as being consistent with the crystallographically observed ARD structure. An exception to this was observed when the donor and acceptor fluorophores were attached in AR3 (residue 166) and AR6 (residue 262). Surprisingly, the FRET efficiency was lower for the bound IκBα molecules (0.67) than for the free IκBα molecules (0.74), apparently indicating that binding of NFκB(RelA/p50) stretches the ARD of IκBα. Here, we conducted confocal-based single-molecule FRET studies to investigate this phenomenon in greater detail. The results not only recapitulated the apparent stretching of the ARD but also showed that the effect was more pronounced when the N-terminal domains (NTDs) of both RelA and p50 were present, even though the interface between NFκB(RelA/p50) and IκBα encompasses only the dimerization domains. We also performed mass spectrometry-detected amide hydrogen/deuterium exchange (HDXMS) experiments on IκBα as well as IκBα bound to dimerization-domain-only constructs or full-length NFκB(RelA/p50). Although we expected the stretched IκBα to have regions with increased exchange, instead the HDXMS experiments showed decreases in exchange in AR3 and AR6 that were more pronounced when the NFκB NTDs were present. Simulations of the interaction recapitulated the increased distance between residues 166 and 262, and also provide a plausible mechanism for a twisting of the IκBα ARD induced by interactions of the IκBα proline-glutamate-serine-threonine-rich sequence with positively charged residues in the RelA NTD.

A practical method for monitoring FRET-based biosensors in living animals using two-photon microscopy.

The commercial availability of multiphoton microscope systems has nurtured the growth of intravital microscopy as a powerful technique for evaluating cell biology in the relevant context of living animals. In parallel, new fluorescent protein (FP) biosensors have become available that enable studies of the function of a wide range of proteins in living cells. Biosensor probes that exploit Förster resonance energy transfer (FRET) are among the most sensitive indicators of an array of cellular processes. However, differences between one-photon and two-photon excitation (2PE) microscopy are such that measuring FRET by 2PE in the intravital setting remains challenging. Here, we describe an approach that simplifies the use of FRET-based biosensors in intravital 2PE microscopy. Based on a systematic comparison of many different FPs, we identified the monomeric (m) FPs mTurquoise and mVenus as particularly well suited for intravital 2PE FRET studies, enabling the ratiometric measurements from linked FRET probes using a pair of experimental images collected simultaneously. The behavior of the FPs is validated by fluorescence lifetime and sensitized emission measurements of a set of FRET standards. The approach is demonstrated using a modified version of the AKAR protein kinase A biosensor, first in cells in culture, and then in hepatocytes in the liver of living mice. The approach is compatible with the most common 2PE microscope configurations and should be applicable to a variety of different FRET probes.