Fluorescence Resonance Energy Transfer

1 The abbreviations used are: PI(3)P, phosphatidylinositol 3-phosphate; Ins(1,3)P 2 , inositol(1,3)diphosphate; FRET, fluorescence resonance energy transfer; GFP, green fluorescent protein; EGFP, enhanced GFP; YFP, yellow fluorescent protein; CFP, cyan fluorescent protein; TL, turret loops; DI, dimer interface loops.

Owing to the importance of explosive detection for the security of land and the environment, the exploration of new methodologies for sensing electron-deficient nitroaromatics explosives (NAEs) is urgently imperative. In this work, we firstly reported a colorimetric sensor for visual detection of 2,4,6-trinitrotoluene (TNT) based on Cysteamine capped-CdSe quantum dots (QDs) decorated graphene-chitosan xerogel (GSXS), which is shown to have high signal-to-background ratio. Meisenheimer complex formation, which is a well-known sensing mechanism, is characterized by steady state and time resolved spectroscopy supported by Density-Functional-Theory (DFT). Upon Green Fluorescent Protein (GFP) illumination, this stable Meisenheimer complex actively suppresses the attributed fluorescence of QD-GSXS and thus providing a novel path for chemical sensing applications. Under optimized conditions, the sensor displayed a wide linear range from 0.0 to 311.4 μ M with a limit of detection 9.7 μ M. T...

The impact of intra-ensemble Förster resonant energy transfer (FRET) on the optical properties of monodispersed quantum dot (QD) monolayers and a donor/acceptor FRET bilayer structure are presented. The QD structures are characterized by steady-state absorption and photoluminescence (PL) spectroscopy as well as time-resolved PL measurements. The optical properties of the monodispersed monolayers, such as peak emission wavelength and PL decays, are strongly influenced by FRET from smaller to larger QDs within the ensemble. Comparing several QD samples, the spectral overlap of the QD ensemble and the QD concentration were identified as parameters that allow for tuning of FRET in monodispersed QD structures. For the donor/acceptor QD bilayer structure an unexpected decrease of the FRET efficiency between donor and acceptor layers is observed with increasing donor QD concentration. The concentration-dependent donor lifetime and a constant donor-acceptor FRET rate can explain this decrea...

Evidence from multiple sources supports the hypothesis that Schwann cells in the peripheral nervous system transfer messenger RNA and ribosomes to the axons they ensheath. Several technical and methodological difficulties exist for investigators to unravel this process in myelinated axons-a complex twocell unit. We present an experimental design to demonstrate that newly synthesized RNA is transferred from Schwann cells to axons in association with Myosin Va. The use of quantitative confocal FRET microscopy to track newly-synthesized RNA and determine the molecular association with Myosin Va, is described in detail.

Fluorescence resonance energy transfer (FRET) is a widely utilized optical technique for measuring small distances of 1-10 nm in live cells. In recent years, its application has been greatly popularized by the discovery of green fluorescent protein (GFP) and many improved variants which make good donor-acceptor fluorophore pairs. GFP-based proteins are structurally stable, relatively inert, and can be reliably attached to points of interest. The combination of easy access to the GFP-based FRET technique and its obvious usefulness in many applications can lead to complacency. Potential problems such as light contaminants, e.g., bleed-through and cross-talk, and inconsistent donor and acceptor concentrations are easily overlooked and can lead to errors in FRET calculation and data interpretation. In this article, we outline possible pitfalls of GFP-based FRET and approaches that address these issues, including a "Spectra FRET" technique that can be easily applied to live cell studies.

The aim of this work was to study the energy transfer mechanisms from the ligand to the central lanthanide ion of tetracycline-europium (Tc-Eu) complex. The absorption spectra of a EuCl 3 .H 2 O solution was measured and absorption cross-section of Eu 3+ was estimated. The observed overlap predicts a resonant energy transfer from Tetracycline to Eu 3+ . The microscopic parameter of energy transfer was obtained using the overlap integral calculation considering a dipole-dipole energy transfer mechanism and results were compared considering an energy transfer by exchange.

Enhanced cyan fluorescent protein (ECFP) and its variant Cerulean are genetically encoded fluorophores widely used as donors in FRET-based cell imaging experiments. First, we have confirmed through denaturation experiments that the double-peak spectroscopic signature of these fluorescent proteins originates from the indole ring of the chromophore. Then, to explain the improvement in the fluorescence properties of Cerulean compared to those of ECFP, we have determined the high-resolution crystal structures of these two proteins at physiological pH and performed molecular dynamics simulations. In both proteins, the N-terminal half of the seventh strand exhibits two conformations. These conformations both have a complex set of van der Waals interactions with the chromophore and, as our simulations suggest, they interconvert on a nanosecond time scale. The Y145A and H148D mutations in Cerulean stabilize these interactions and allow the chromophore to be more planar, better packed, and less prone to collisional quenching, albeit only intermittently. As a consequence, the probability of nonradiative decay is significantly decreased. Our results highlight the considerable dynamical flexibility that exists in the vicinity of the tryptophan-based chromophore of these engineered fluorescent proteins and provide insights that should allow the design of mutants with enhanced optical properties.

Establishment and maintenance of cell structures and functions are highly dependent on the efficient regulation of intracellular transport in which proteins of the kinesin superfamily (KIFs) are very important. In this regard, how KIFs regulate the release of their cargo is a critical process that remains to be elucidated. To address this specific question, we have investigated the mechanism behind the regulation of the KIF17-Mint1 interaction. Here we report that the tail region of the molecular motor KIF17 is regulated by phosphorylation. Using direct visualization of protein-protein interaction by FRET and various in vitro and in vivo approaches we have demonstrated that CaMKII-dependent phosphorylation of KIF17 on Ser 1029 disrupts the KIF17-Mint1 association and results in the release of the transported cargo from its microtubule-based transport.

A quantitative real-time TaqMan PCR assay for detection of human adenoviruses (HAdV) was developed using broadly reactive consensus primers and a TaqMan probe targeting a conserved region of the hexon gene. The TaqMan assay correctly identified 56 representative adenovirus prototype strains and field isolates from all six adenovirus species (A to F). Based on infectious units, the TaqMan assay was able to detect as few as 0.4 and 0.004 infectious units of adenovirus serotype 2 (AdV2) and AdV41, respectively, with results obtained in less than 90 min. Using genomic equivalents, the broadly reactive TaqMan assay was able to detect 5 copies of AdV40 (which had zero mismatches with the PCR primers and probe), 8 copies of AdV41, and 350 copies of AdV3 (which had the most mismatches [seven] of any adenovirus serotype tested). For specific detection and identification of F species serotypes AdV40 and AdV41, a second real-time PCR assay was developed using fluorescence resonance energy tran...

Future developments in cellulosic materials are predicated by the need to understand the fundamental interactions that occur at cellulose fibre interfaces. These interfaces strongly influence the material properties of fibre networks and fibre reinforced composites. This study takes advantage of fluorescence resonance energy transfer (FRET) and fluorescence microscopy to image cellulose interfaces. Steady-state epi-fluorescence microscopy suggests that energy transfer from coumarin dyed fibres to fluorescein dyed fibres is occurring at the fibre-fibre interface. The FRET response for natural spruce fibre interfaces is distinctly different from that observed in synthetic viscose fibres. This approach constitutes a novel methodology for the characterization of soft material interfaces on the molecular scale, and represents a major opportunity for advancing the understanding of fibrous network structures.

The deficiency in the availability of petroleum products has given rise to the incorporation of electric vehicles (EVs) globally as a substitute for the conventional transportation system. Significant research has been pursued over last two decades in the development of efficient EV charging methods. A preliminary review of few methods developed for wireless charging revealed that ICPT is a promising and convenient method for the wireless charging of EVs. This paper includes the equivalent circuit analysis and characteristics of the ICPT system and focuses on the research progress in respect of the designs for the charging coil, leakage inductance compensation topologies, power level enhancement and misalignment toleration. The improvement in these factors has been essential for the implementation of EV charging. A brief discussion over design process and control of ICPT system has been added. Conclusions have been made on the basis of the information extracted from the literature a...

Membrane proteins exhibit different affinities for different lipid species, and protein-lipid selectivity regulates the membrane composition in close proximity to the protein, playing an important role in the formation of nanoscale membrane heterogeneities. The sensitivity of Förster resonance energy transfer (FRET) for distances of 10 Å up to 100 Å is particularly useful to retrieve information on the relative distribution of proteins and lipids in the range over which protein-lipid selectivity is expected to influence membrane composition. Several FRET-based methods applied to the quantification of protein-lipid selectivity are described herein, and different formalisms applied to the analysis of FRET data for particular geometries of donor-acceptor distribution are critically assessed.

Fluorescence spectroscopy and circular dichroism (CD) spectroscopy were used to investigate the interaction of coumarin-3-carboxylic acid with human serum albumin (HSA) and bovine serum albumin (BSA) under physiological conditions in a buffer solution of pH 7.4. Quenching constants were determined using the Lineweaver-Burk equation to provide a measure of the binding affinity of coumarin-3-carboxylic acid to HSA/BSA. Binding studies concerning

Resonant ͑nonphonon-assisted͒ Nd 3+ → Yb 3+ energy transfer has been observed in Nd 3+ and Yb 3+ codoped Sr 0.6 Ba 0.4 ͑NbO 3 ͒ 2 crystals. The Nd 3+ → Yb 3+ energy transfer in this system has been compared to those taking place in other Nd 3+ -Yb 3+ codoped hosts, for which, in most of cases, the transfer is only possible by assistance of phonons. The resonant nature is explained as a result of both the very broad optical bands of Nd 3+ and Yb 3+ ions in Sr 0.6 Ba 0.4 ͑NbO 3 ͒ 2 and the short energy gap ͑636 cm −1 ͒ between the 4 F 3/2 ͑Nd 3+ ͒ and 2 F 5/2 ͑Yb 3+ ͒ excited states. Spectroscopic data revealed that the energy transfer occurs via a nonradiative process and is dominated by an electric dipole-dipole interaction. The most relevant spectroscopic properties of the Nd 3+ → Yb 3+ energy transfer have been systematically investigated as a function of Yb 3+ ion concentration. The energy transfer efficiency increases linearly with the Yb 3+ ion concentration so that about a 50% is attained for a 10 at. % of ion acceptor concentration.

There is an urgent need to develop technology for continuous in vivo glucose monitoring in subjects with diabetes mellitus. Problems with existing devices based on electrochemistry have encouraged alternative approaches to glucose sensing in recent years, and those based on fluorescence intensity and lifetime have special advantages, including sensitivity and the potential for non-invasive measurement when nearinfrared light is used. Several receptors have been employed to detect glucose in fluorescence sensors, and these include the lectin concanavalin A (Con A), enzymes such as glucose oxidase, glucose dehydrogenase and hexokinase/glucokinase, bacterial glucose-binding protein, and boronic acid derivatives (which bind the diols of sugars). Techniques include measuring changes in fluorescence resonance energy transfer (FRET) between a fluorescent donor and an acceptor either within a protein which undergoes glucose-induced changes in conformation or because of competitive displacement; measurement of glucose-induced changes in intrinsic fluorescence of enzymes (e.g. due to tryptophan residues in hexokinase) or extrinsic fluorophores (e.g. using environmentally sensitive fluorophores to signal protein conformation). Noninvasive glucose monitoring can be accomplished by measurement of cell autofluorescence due to NAD(P)H, and fluorescent markers of mitochondrial metabolism can signal changes in extracellular glucose concentration. Here we review the principles of operation, context and current status of the various approaches to fluorescence-based glucose sensing.

In this work, we characterized streptavidin-conjugated quantum dots (QDs) manufactured by Quantum Dot Corporation. We present data on: (1) two-photon excitation; (2) fluorescence lifetimes; (3) ensemble and single QD emission anisotropy; (4) QDs as donors for Förster resonance energy transfer (FRET); and (5) spectral conversion of QDs exposed to high-intensity illumination. We also demonstrate the utility of QDs for (1) imaging the binding and uptake of biotinylated transferrin on living cells, and (2) resolving by fluorescence lifetime imaging microscopy (FLIM) signals originating from QDs from those of spatially and spectrally overlapping visible fluorescent proteins (VFPs). Microsc. Res. Tech. 65:169–179, 2004. © 2005 Wiley-Liss, Inc.

Establishment and maintenance of cell structures and functions are highly dependent on the efficient regulation of intracellular transport in which proteins of the kinesin superfamily (KIFs) are very important. In this regard, how KIFs regulate the release of their cargo is a critical process that remains to be elucidated. To address this specific question, we have investigated the mechanism behind the regulation of the KIF17-Mint1 interaction. Here we report that the tail region of the molecular motor KIF17 is regulated by phosphorylation. Using direct visualization of protein-protein interaction by FRET and various in vitro and in vivo approaches we have demonstrated that CaMKII-dependent phosphorylation of KIF17 on Ser 1029 disrupts the KIF17-Mint1 association and results in the release of the transported cargo from its microtubule-based transport.

Photophysical studies on binding interactions of a negatively charged anti-tumor photosensitizer, Merocyanine 540 (MC 540), with serum proteins, bovine serum albumin (BSA) and human serum albumin (HSA), have been performed using absorption and steady-state as well as time-resolved fluorescence techniques. Formation of ground state complex has been confirmed from the detailed studies of absorption spectra of MC 540 in presence of SAs producing isosbestic points. Binding between the proteins and MC 540, which perturbs the existing equilibrium between the fluorescent monomer and its non-fluorescent dimer, induces a remarkable enhancement in fluorescence anisotropy and intensity of MC 540 along with a red shift of its maximum. The binding stoichiometry of MC 540 and SAs are more than 1.0 which depicts that two types of complexes, i.e., 1:1 and 2:1 are formed with addition of varied concentration of protein. Both the steady-state and time-resolved fluorescence results show that in 2:1 complex one of the MC 540 molecules is exposed towards aqueous environment with a greater extent when bound with HSA compared to BSA due to the structural flexibility of that protein. Thermodynamic analyses using van't Hoff plot indicate that the binding between MC 540 and individual SA is an entropy-driven phenomenon. The probable hydrophobic binding site has been located by denaturation of proteins, micropolarity measurement and Förster resonance energy transfer and that is further supported by molecular docking studies. Changes in circular dichroism spectra of BSA in presence of MC 540 depict secondary structural changes of the protein. The induced-CD shows that BSA due to its rigid structure generates chirality in MC 540 much more efficiently compared to HSA.

We report the picosecond timescale fluorescence dynamics of a dye-labeled DNA oligonucleotide or "aptamer" designed to bind specifically to Immunoglobulin E. Comparison of the photophysics of Texas Red (TR), fluorescein and 5'-carboxytetramethylrhodamine (TAMRA)-labeled aptamers reveals surprising differences with significant implications for measurements of oligonucleotide structure and dynamics. The fluorescence decay of the TR-aptamer is a simple single exponential with a weak temperature dependence. The fluorescence decay of the fluorescein-aptamer (fl-aptamer) is pH dependent and displays a complex temperature dependence with significant changes on melting of the aptamer tertiary structure. Despite its similarities to TR, TAMRA is strongly quenched when conjugated to the aptamer and displays complex fluorescence kinetics best described by a distributed rate model. Using the maximum entropy method, we have discovered two highly temperature-dependent fluorescence lifetimes for the TAMRA-aptamer. One of these lifetimes is similar to that of free TAMRA and displays the same temperature dependence. The other lifetime is quenched and displays a temperature dependence characteristic of a charge transfer reaction. These data set TR apart as an attractive alternative to TAMRA and fluorescein for studies such as fluorescence polarization and fluorescence resonance energy transfer, where environmental sensitivity of the probe is not desired.

Advancements in single molecule detection (SMD) continue to unfold powerful ways to study the behavior of individual and complex molecular systems in real time. SMD enables the characterization of complex molecular interactions and reveals basic physical phenomena underlying chemical and biological processes. We present here a systematic study of the quenching efficiency of Förster-type energy-transfer (FRET) for multiple fluorophores immobilized on a single antibody. We simultaneously monitor the fluorescence intensity, fluorescence lifetime, and the number of available photons before photobleaching as a function of the number of identical emitters bound to a single IgG antibody. The detailed studies of FRET between individual fluorophores reveal complex through-space interactions. In general, even for two or three fluorophores immobilized on a single protein, homo-FRET interactions lead to an overall non-linear intensity increase and shortening of fluorescence lifetime. Over-labeling of protein in solution (ensemble) results in the loss of fluorescence signal due to the self-quenching of fluorophores making it useless for assays applications. However, in the single molecule regime, over-labeling may bring significant benefits in regards to the number of available photons and the overall survival time. Our investigation reveals possibilities to significantly increase the observation time for a single macromolecule allowing studies of macromolecular interactions that are not obscured by ensemble averaging. Extending the observation time will be crucial for developing immunoassays based on single-antibody.

Amyloidogenesis is a characteristic feature of the 40 or so known protein deposition diseases, and accumulating evidence strongly suggests that self-association of misfolded proteins into either fibrils, protofibrils, or soluble oligomeric species is cytotoxic. The most likely mechanism for toxicity is through perturbation of membrane structure, leading to increased membrane permeability and eventual cell death. There have been a rather limited number of investigations of the interactions of amyloidogenic polypeptides and their aggregated states with membranes; these are briefly reviewed here. Amyloidogenic proteins discussed include A-beta from Alzheimer's disease, the prion protein, α-synuclein from Parkinson's disease, transthyretin (FAP, SSA amyloidosis), immunoglobulin light chains (primary (AL) amyloidosis), serum amyloid A (secondary (AA) amyloidosis), amylin or IAPP (Type 2 diabetes) and apolipoproteins. This review highlights the significant role played by fluorescence techniques in unraveling the nature of amyloid fibrils and their interactions and effects on membranes. Fluorescence spectroscopy is a valuable and versatile method for studying the complex mechanisms of protein aggregation, amyloid fibril formation and the interactions of amyloidogenic proteins with membranes. Commonly used fluorescent techniques include intrinsic and extrinsic fluorophores, fluorescent probes incorporated in the membrane, steady-state and lifetime measurements of fluorescence emission, fluorescence correlation spectroscopy, fluorescence anisotropy and polarization, fluorescence resonance energy transfer (FRET), fluorescence quenching, and fluorescence microscopy.

Förster (or fluorescence) resonance energy transfer (FRET) is a process involving the radiation-less transfer of energy from a "donor" fluorophore to an "acceptor" fluorophore. FRET technology enables the quantitative analysis of molecular dynamics in biophysics and in molecular biology, such as the monitoring of protein-protein interactions, protein-DNA interactions, and protein conformational changes. FRET-based biosensors have been utilized to monitor cellular dynamics not only in heterogeneous cellular populations, but also at the single-cell level in real time. Lately, applications of FRET-based biosensors range from basic biological to biomedical disciplines. Despite the diverse applications of FRET, FRET-based sensors still face many challenges. There is an increasing need for higher fluorescence resolution and improved specificity of FRET biosensors. Additionally, as more FRET-based technologies extend to medical diagnostics, the affordability of FRET reagents becomes a significant concern. Here, we will review current advances and limitations of FRET-based biosensor technology and discuss future FRET applications.

The deficiency in the availability of petroleum products has given rise to the incorporation of electric vehicles (EVs) globally as a substitute for the conventional transportation system. Significant research has been pursued over last two decades in the development of efficient EV charging methods. A preliminary review of few methods developed for wireless charging revealed that ICPT is a promising and convenient method for the wireless charging of EVs. This paper includes the equivalent circuit analysis and characteristics of the ICPT system and focuses on the research progress in respect of the designs for the charging coil, leakage inductance compensation topologies, power level enhancement and misalignment toleration. The improvement in these factors has been essential for the implementation of EV charging. A brief discussion over design process and control of ICPT system has been added. Conclusions have been made on the basis of the information extracted from the literature and some future recommendations are provided.

The human pregnane X nuclear receptor (PXR) is a xenobioticregulated receptor that is activated by a range of diverse chemicals, including antibiotics, antifungals, glucocorticoids, and herbal extracts. PXR has been characterized as an important receptor in the metabolism of xenobiotics due to induction of cytochrome P450 isozymes and activation by a large number of prescribed medications. Developing methodologies that can efficiently detect PXR ligands will be clinically beneficial to avoid potential drug-drug interactions. To facilitate the identification of PXR ligands, a time-resolved fluorescence resonance energy transfer (TR-FRET) assay was miniaturized to a 1,536-well microtiter plate format to employ quantitative highthroughput screening (qHTS). The optimized 1,536-well TR-FRET assay showed Z'-factors of ≥0.5. Seven-to 15-point concentration-response curves (CRCs) were generated for 8,280 compounds using both terbium and fluorescein emission data, resulting in the generation of 241,664 data points. The qHTS method allowed us to retrospectively examine single concentration screening datasets to assess the sensitivity and selectivity of the PXR assay at different compound screening concentrations. Furthermore, nonspecific assay artifacts such as concentration-based quenching of the terbium signal and compound fluorescence were identified through the examination of CRCs for specific emission channels. The CRC information was also used to define chemotypes associated with PXR ligands. This study demonstrates the feasibility of profiling thousands of compounds against PXR using the TR-FRET assay in a high-throughput format.

The homotypic fusion of endoplasmic reticulum (ER) membranes is mediated by atlastin (ATL), which consists of an N-terminal cytosolic domain containing a GTPase module and a three-helix bundle followed by two transmembrane (TM) segments and a Cterminal tail (CT). Fusion depends on a GTP hydrolysis-induced conformational change in the cytosolic domain. Here, we show that the CT and TM segments also are required for efficient fusion and provide insight into their mechanistic roles. The essential feature of the CT is a conserved amphipathic helix. A synthetic peptide corresponding to the helix, but not to unrelated amphipathic helices, can act in trans to restore the fusion activity of tailless ATL. The CT promotes vesicle fusion by interacting directly with and perturbing the lipid bilayer without causing significant lysis. The TM segments do not serve as mere membrane anchors for the cytosolic domain but rather mediate the formation of ATL oligomers. Point mutations in either the C-terminal helix or the TMs impair ATL's ability to generate and maintain ER morphology in vivo. Our results suggest that protein-lipid and protein-protein interactions within the membrane cooperate with the conformational change of the cytosolic domain to achieve homotypic ER membrane fusion. membrane perturbation | content mixing | organelle shaping | organelle remodeling | hereditary spastic paraplegia

The bioluminescence resonance energy transfer (BRET) method is based on resonance energy transfer between a light-emitting enzyme and a fluorescent acceptor. Since its first description in 1999, several versions of BRET have been described using different substrates and energy donor/acceptor couples. Today, BRET is considered as one of the most versatile techniques for studying the dynamics of protein-protein interactions in living cells. Various studies have applied BRET-based assays to screen new receptor ligands and inhibitors of disease-related-proteases. Inhibitors of protein-protein interactions are likely to become a new major class of therapeutic drugs, and BRET technology is expected to play an important role in the identification of such compounds. This review describes the original BRET-based methodology, more recent variants, and potential applications to drug screening.

A wide variety of methods used in the study of signal transduction in eukaryotes rely on the ability to precipitate proteins from whole cell extracts. Immunoprecipitation and related methods of affinity purification are routinely used to assess binding partner interactions and enzyme activity in addition to the size of a protein, rates of protein synthesis and turnover, and protein abundance, thus making it a mainstay of a wide variety of protocols. This chapter will provide starting-point methods for immunoprecipitation of proteins under denaturing and nondenaturing conditions and the detection of protein-protein interactions by co-precipitation. The Notes section gives recommendations on how to troubleshoot potential problems that can arise while doing these methodologies.

Förster resonance energy transfer (FRET) in association with the recent advancements in optical techniques provides a way to understand the detailed mechanisms in different biological systems at the molecular level. Improvements in wide-field, confocal and two-photon microscopy facilitate the measurements of two-dimensional spatial distribution in steady-state as well as dynamic bimolecular interactions. In the recent decade, FRET became an exceptional fluorescence-based technique due to its potential advantages for studying the biological processes in living cells and more for spatial resolution at nanometer scale. In particular, FRET investigations have shown that biomolecules adopt different conformational structures to perform their functions. In this review, the basic principles and applications of FRET in chemistry, biology, and physics are discussed. Along with, the recent improvements in fluorophore design and labeling and FRET measurement methods are briefly mentioned.

Förster (or fluorescence) resonance energy transfer amongst semiconductor quantum dots (QDs) is reviewed, with particular interest in biosensing applications. The unique optical properties of QDs provide certain advantages and also specific challenges with regards to sensor design, compared to other FRET systems. The brightness and photostability of QDs make them attractive for highly sensitive sensing and long-term, repetitive imaging applications, respectively, but the overlapping donor and acceptor excitation signals that arise when QDs serve as both the donor and acceptor lead to high background signals from direct excitation of the acceptor. The fundamentals of FRET within a nominally homogeneous QD population as well as energy transfer between two distinct colors of QDs are discussed. Examples of successful sensors are highlighted, as is cascading FRET, which can be used for solar harvesting.

Absorption and fluorescence spectroscopy are the heart of life science laboratory techniques. These two spectroscopic tools are sensitive, are easy to use, and can provide a wide range of information. The goal of this chapter is to familiarize the reader with some basic principles and applications of absorption and steady-state fluorescence spectroscopy. Selected applications are illustrated with examples.

Membrane microdomains and their involvement in cellular processes are part of the current paradigm of biomembranes. However, a better characterization of domains, namely lipid rafts, is needed. In this review, it is shown how the use of time-resolved fluorescence, with the adequate parameters and probes, helps elucidating the type, number, fraction, composition and size of lipid phases and domains in multicomponent model systems. The determination of phase diagrams for lipid mixtures containing sphingolipids and/or cholesterol is exemplified. The use of fluorescence quenching and Förster resonance energy transfer (FRET) are also illustrated. Strategies for studying protein-induced domains are presented. The advantages of using single point microscopic decays and fluorescence lifetime imaging microscopy (FLIM) in systems with three-phase coexistence are explained. Finally, the introduction of FLIM allows studies in live cell membranes, and the nature of the microdomains observed is readily elucidated due to the information retrieved from fluorescence lifetimes.

The yeast protein Fis1p has been shown to participate in mitochondrial fission mediated by the dynaminrelated protein Dnm1p. In mammalian cells, the dynamin-like protein DLP1/Drp1 functions as a mitochondrial fission protein, but the mechanisms by which DLP1/Drp1 and the mitochondrial membrane interact during the fission process are undefined. In this study, we have tested the role of a mammalian homologue of Fis1p, hFis1, and provided new and mechanistic information about the control of mitochondrial fission in mammalian cells. Through differential tagging and deletion experiments, we demonstrate that the intact C-terminal structure of hFis1 is essential for mitochondrial localization, whereas the N-terminal region of hFis1 is necessary for mitochondrial fission. Remarkably, an increased level of cellular hFis1 strongly promotes mitochondrial fission, resulting in an accumulation of fragmented mitochondria. Conversely, cell microinjection of hFis1 antibodies or treatment with hFis1 antisense oligonucleotides induces an elongated and collapsed mitochondrial morphology. Further, fluorescence resonance energy transfer and coimmunoprecipitation studies demonstrate that hFis1 interacts with DLP1. These results suggest that hFis1 participates in mitochondrial fission through an interaction that recruits DLP1 from the cytosol. We propose that hFis1 is a limiting factor in mitochondrial fission and that the number of hFis1 molecules on the mitochondrial surface determines fission frequency.

G raphene has unique mechanical, electronic, and optical properties, which researchers have used to develop novel electronic materials including transparent conductors and ultrafast transistors. Recently, the understanding of various chemical properties of graphene has facilitated its application in high-performance devices that generate and store energy. Graphene is now expanding its territory beyond electronic and chemical applications toward biomedical areas such as precise biosensing through graphene-quenched fluorescence, graphene-enhanced cell differentiation and growth, and graphene-assisted laser desorption/ionization for mass spectrometry. In this Account, we review recent efforts to apply graphene and graphene oxides (GO) to biomedical research and a few different approaches to prepare graphene materials designed for biomedical applications.

Kinases are important drug discovery targets for a wide variety of therapeutic indications; consequently, the measurement of kinase activity remains a common high-throughput screening (HTS) application. Recently, enzyme-coupled luciferase-kinase (LK) format assays have been introduced. This format measures luminescence resulting from metabolism of adenosine triphosphate (ATP) via a luciferin/luciferase-coupled reaction. In the research presented here, 1536-well format time-resolved fluorescence resonance energy transfer (TR-FRET) and LK assays were created to identify novel Rho-associated kinase II (ROCK-II) inhibitors. HTS campaigns for both assays were conducted in this miniaturized format. It was found that both assays were able to consistently reproduce the expected pharmacology of inhibitors known to be specific to ROCK-II (fasudil IC50: 283 ± 27 nM and 336 ± 54 nM for TR-FRET and LK assays, respectively; Y-27632 IC50: 133 ± 7.8 nM and 150 ± 22 nM for TR-FRET and LK assays, respectively). In addition, both assays proved robust for HTS efforts, demonstrating excellent plate Z′ values during the HTS campaign (0.84 ± 0.03; 0.72 ± 0.05 for LK and TR-FRET campaigns, respectively). Both formats identified scaffolds of known and novel ROCK-II inhibitors with similar sensitivity. A comparison of the performance of these 2 assay formats in an HTS campaign was enabled by the existence of a subset of 25,000 compounds found in both our institutional and the Molecular Library Screening Center Network screening files. Analysis of the HTS campaign results based on this subset of common compounds showed that both formats had comparable total hit rates, hit distributions, amount of hit clusters, and format-specific artifact. It can be concluded that both assay formats are suitable for the discovery of ROCK-II inhibitors, and the choice of assay format depends on reagents and/or screening technology available. (Journal of Biomolecular Screening 2008:17-28)

Agrobacterium is the only cellular organism on Earth that is naturally capable of transferring genetic material between the kingdoms of life, from prokaryotes to eukaryotes. Studies have uncovered a wealth of information on the process of Agrobacterium-mediated genetic transformation and on the bacterial and host cell factors involved in the infection. Agrobacterium has been shown to genetically transform, under laboratory conditions a large number of plant species and numerous non-plant organisms, indicating the truly basic nature of the transformation process. It is therefore not surprising that Agrobacterium and the genetic transformation itself have also become the focus of numerous ethical and legal debates.

Single-molecule fluorescence resonance energy transfer (smFRET) is one of the most general and adaptable single-molecule techniques. Despite the explosive growth in the application of smFRET to answer biological questions in the last decade, the technique has been practiced mostly by biophysicists. We provide a practical guide to using smFRET, focusing on the study of immobilized molecules that allow measurements of single-molecule reaction trajectories from 1 ms to many minutes. We discuss issues a biologist must consider to conduct successful smFRET experiments, including experimental design, sample preparation, single-molecule detection and data analysis. We also describe how a smFRET-capable instrument can be built at a reasonable cost with off-the-shelf components and operated reliably using well-established protocols and freely available software.