Beyond Förster resonance energy transfer in linear nanoscale systems

The line dipole approximation is used to investigate analytical corrections to the F?rster energy transfer rate, k, derived via the point dipole approximation. It is shown that that for molecules whose conjugation length, L, is much larger than the separation, R, between molecules the line dipole approximation predicts k ~ (RL)?2 ~ (RN)?2 (where N is the number of conjugated monomer units). This is in contrast to the point dipole approximation, which predicts k ~ L2R?? ~ N2R??.     

Theory of photon statistics in single-molecule Förster resonance energy transfer

We present the theory for the distribution of the number of donor and acceptor photons detected in a time bin and the corresponding energy-transfer efficiency distribution obtained from single-molecule Forster resonance energy-transfer measurements. Photon counts from both immobilized and freely diffusing molecules are considered. Our starting point is the joint distribution for the donor and acceptor photons for a system described by an arbitrary kinetic scheme. This is simplified by exploiting the time scale separation between fast fluorescent transitions and slow processes which include conformational dynamics, intersystem conversion to a dark state, and translational diffusion in and out of the laser spot. The fast fluorescent transitions result in a Poisson distribution of the number of photons which is then averaged over slow fluctuations of the local transfer efficiency and the total number of photons. The contribution of various processes to the distribution and the variance of the energy-transfer efficiency are analyzed.     

Spectral Förster resonance energy transfer detection of protein interactions in surface-supported bilayers

F?rster resonance energy transfer (FRET), a fluorescence detection technique, is often used for sensing molecular interactions in solution and in membranes. Here we show that (1) FRET spectra can be recorded in single bilayers, supported on a surface, and (2) the fluorescein/rhodamine dye pair is an adequate reporter of FRET when spectral detection is used. Thus, measurements pertaining to molecular interactions in membranes can be carried out in supported bilayers. Spectral FRET has advantages over imaging FRET, which monitors only signal amplitudes at certain wavelength. There are also advantages to performing spectral FRET measurements in supported bilayers as compared to free liposomes in suspension. However, the spectral properties of dyes can be altered in an unexpected manner in an ordered bilayer structure on a surface, such that fluorescence detection in surface-supported bilayers is not always trivial.     

Extending spectrum response of squaraine-sensitized solar cell by Förster resonance energy transfer

To extend the spectral response region of squaraine dye (SQ)-sensitized solar cell, eosin Y (EY) is encapsulated in the SQ-sensitized nanocrystalline thin film. EY is first adsorbed on nanocrystalline TiO₂ thin film (n-TiO₂), then a thin layer of EY contained ZnO (EY-ZnO) is electrodeposited, and SQ dye is finally sensitized to form two dye-sensitized nanocrystalline thin film with a structure of n-TiO₂/EY/EY-ZnO/SQ. There is a perfect spectral overlap between the emission of EY and the absorption of SQ; EY as an energy donor simultaneously transfers both electron and hole to the energy acceptor SQ according to the Förster resonance energy transfer (FRET) process. EY shifts the spectral response edge of SQ-sensitized solar cell toward blue from 550 to 450 nm through the FRET process in this new structure. Two dye-sensitized nanocrystalline thin film demonstrates a significant enhancement in light harvesting and photocurrent generation due to the FRET process. The thickness of the EY-ZnO thin layer and spectral overlap between emission of donor dye and absorption of acceptor dye are two important factors that affect the FRET process between EY and SQ in the structure of n-TiO₂/EY/EY-ZnO/SQ.     

Förster energy transfer in chlorosomes of green photosynthetic bacteria

Energy transfer properties of whole cells and chlorosome antenna complexes isolated from the green sulfur bacteria Chlorobium limicola (containing bacteriochlorophyll c), Chlorobium vibrioforme (containing bacteriochlorophyll d) and Pelodictyon phaeoclathratiforme (containing bacteriochlorophyll e) were measured. The spectral overlap of the major chlorosome pigment (bacteriochlorophyll c, d or, e) with the bacteriochlorophyll a B795 chlorosome baseplate pigment is greatest for bacteriochlorophyll c and smallest for bacteriochlorophyll e. The absorbance and fluorescence spectra of isolated chlorosomes were measured, fitted to gaussian curves and the overlap factors with B795 calculated. Energy transfer times from the bacteriochlorophyll c, d or e to B795 were measured in whole cells and the results interpreted in terms of the F?rster theory of energy transfer.     

Probing the dynamic nature of DNA multilayer films using förster resonance energy transfer

DNA films are of interest for use in a number of areas, including sensing, diagnostics, and as drug/gene delivery carriers. The specific base pairing of DNA materials can be used to manipulate their architecture and degradability. The programmable nature of these materials leads to complex and unexpected structures that can be formed from solution assembly. Herein, we investigate the structure of DNA multilayer films using F?rster resonance energy transfer (FRET). The DNA films are assembled on silica particles by depositing alternating layers of homopolymeric diblocks (polyA(15)G(15) and polyT(15)C(15)) with fluorophore (polyA(15)G(15)-TAMRA) and quencher (polyT(15)C(15)-BHQ2) layers incorporated at predesigned locations throughout the films. Our results show that DNA films are dynamic structures that undergo rearrangement. This occurs when the multilayer films are perturbed during new layer formation through hybridization but can also take place spontaneously when left over time. These films are anticipated to be useful in drug delivery applications and sensing applications.     

Förster energy transfer from nonexponentially decaying donors

Necessary modifications to the expression for the F?rster energy transfer rate are discussed when fluorescence decay of the donor in the absence of acceptor is nonexponential. Discrete and continuous models of the nonexponentiality are taken into account. No general solution of the problem is found. It is, however, suggested that in many of the biochemical problems the most appropriate modification of the transfer rate can be that which is based on the assumption of the same constant value of the radiative decay rate for all donor molecules. The effect of the assumed form of the F?rster energy transfer rate on the recovered values of the distance distribution and dynamics parameters of some exemplary bichromophoric systems is examined.     

Förster resonance energy transfer in nanoclusters of InP@ZnS colloidal quantum dots with dodecylamine ligand shells

Förster resonance energy transfer between InP@ZnS hydrophobic colloidal quantum dots of two different sizes has been studied in the closely packed nanoclusters formed spontaneously in an organic solvent upon the addition of a precipitating solvent. The quantum dots had a core@shell structure and were stabilized by dodecylamine ligands.     

Ratiometric pH sensor based on mesoporous silica nanoparticles and Förster resonance energy transfer

Incorporation of a dual-FRET dye pair into mesoporous silica nanoparticles yields sensitive and sensing-range tunable nanosensors with good reversibility that can be used for ratiometric pH measurements under a single-wavelength excitation.     

Fluorescence resonance energy transfer (FRET) for DNA biosensors: FRET pairs and Förster distances for various dye-DNA conjugates

Fluorescence resonance energy transfer (FRET) between the extrinsic dye labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethyl Rhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ), and Iowa Black RQ (IabRQ) has been studied. The F?rster distances for these FRET-pairs in single- and double-stranded DNA conjugates have been determined. In particular, it should be noted that the quantum yield of the donors Cy3 and TAMRA varies between single- and double-stranded DNA. While this alters the F?rster distance for a donor-acceptor pair, this also allows for detection of thermal denaturation events with a single non-intercalating fluorophore. The utility of FRET in the development of nucleic acid biosensor technology is illustrated by using TAMRA and IabRQ as a FRET pair in selectivity experiments. The differential quenching of TAMRA fluorescence by IabRQ in solution has been used to discriminate between 0 and 3 base pair mismatches at 60 degrees C for a 19 base sequence. At room temperature, the quenching of TAMRA fluorescence was not an effective indicator of the degree of base pair mismatch. There appears to be a threshold of duplex stability at room temperature which occurs beyond two base pair mismatches and reverses the observed trend in TAMRA fluorescence prior to that degree of mismatch. When this experimental system is transferred to a glass surface through covalent coupling and organosilane chemistry, the observed trend in TAMRA fluorescence at room temperature is similar to that obtained in bulk solution, but without a threshold of duplex stability. In addition to quenching of fluorescence by FRET, it is believed that several other quenching mechanisms are occurring at the surface.     

The effect of Brownian motion of fluorescent probes on measuring nanoscale distances by Förster resonance energy transfer

F?rster resonance energy transfer (FRET) is a powerful optical technique to determine intra-molecular distances. However, the dye rotational motion and the linker flexibility complicate the relationship between the measured energy transfer efficiency and the distance between the anchoring points of the dyes. In this study, we present a simple model that describes the linker and dye dynamics as diffusion on a sphere. Single-pair energy transfer was treated in the weak excitation limit, photon statistics and scaffold flexibility were ignored, and different time-averaging regimes were considered. Despite the approximations, our model provides new insights for experimental designs and results interpretation in single-molecule FRET. Monte Carlo simulations produced distributions of the inter-dye distance, the dipole orientation factor, κ(2), and the transfer efficiency, E, which were in perfect agreement with independently derived theoretical functions. Contrary to common perceptions, our data show that longer linkers will actually restrict the motion of dye dipoles and hence worsen the isotropic 2∕3 approximation of κ(2). It is also found that the thermal motions of the dye-linker system cause fast and large efficiency fluctuations, as shown by the simulated FRET time-trajectories binned on a microsecond time scale. A fundamental resolution limit of single-molecule FRET measurements emerges around 1-10 μs, which should be considered for the interpretation of data recorded on such fast time scales.     

Estimating the size of laterally phase separated cholesterol domains in model membranes with Förster resonance energy transfer: a simulation study

In this work, we use two vertically-coupled square two-dimensional lattices to simulate membrane bilayers containing a uniform size distribution of cholesterol immiscible domains of a predetermined size distribution. We substitute cholesterols and phospholipids with their fluorescent analogs and calculate the efficiency of energy transfer as a function of acceptor concentration for four membrane configurations. The simulated efficiency of energy transfer as a function of acceptor concentration data is then fit with an analytical FRET model to estimate the domain size, in the same manner in which experimental FRET data is analyzed. The fitted model parameters (domain size and donor partition coefficient) are compared to the simulation inputs to test the applicability of the FRET model to estimating the size of laterally phase separated cholesterol domains. We show that the FRET model yields good size estimates for domains that range between 1 and 25 nm. We also find that the assumed fluorophore configuration in the FRET model leads to a constant under-prediction of these values. Finally, we demonstrate that when two parameters are open to the fit, the FRET model adequately predicts the donor partition coefficient in addition to the domain size.     

Interaction of an antituberculosis drug with nano-sized cationic micelle: Förster resonance energy transfer from dansyl to rifampicin in the microenvironment

In this contribution, we report studies on the interaction of an antituberculosis drug rifampicin (RF) in a macromolecular assembly of CTAB with an extrinsic fluorescent probe, dansyl chloride (DC). The absorption spectrum of the drug RF has been employed to study Förster resonance energy transfer (FRET) from DC, bound to the CTAB micelle using picosecond resolved fluorescence spectroscopy. We have applied a kinetic model developed by Tachiya to understand the kinetics of energy transfer and the distribution of acceptor (RF) molecules around the donor (DC) molecules in the micellar surface with increasing quencher concentration. The mean number of RF molecules associated with the micelle increases from 0.24 at 20 μm RF concentration to 1.5 at 190 μm RF concentration and consequently the quenching rate constant (k_q) due to the acceptor (RF) molecules increases from 0.23 to 0.75 ns^?1 at 20 and 190 μm RF concentration, respectively. However, the mean number of the quencher molecule and the quenching rate constant does not change significantly beyond a certain RF concentration (150 μm ), which is consistent with the results obtained from time resolved FRET analysis. Moreover, we have explored the diffusion controlled FRET between DC and RF, using microfluidics setup, which reveals that the reaction pathway follows one‐step process.     

Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I

Enzymatic reactions typically involve complex dynamics during substrate binding, conformational rearrangement, chemistry, and product release. The noncovalent steps provide kinetic checkpoints that contribute to the overall specificity of enzymatic reactions. DNA polymerases perform DNA replication with outstanding fidelity by actively rejecting noncognate nucleotide substrates early in the reaction pathway. Substrates are delivered to the active site by a flexible fingers subdomain of the enzyme, as it converts from an open to a closed conformation. The conformational dynamics of the fingers subdomain might also play a role in nucleotide selection, although the precise role is currently unknown. Using single-molecule F?rster resonance energy transfer, we observed individual Escherichia coli DNA polymerase I (Klenow fragment) molecules performing substrate selection. We discovered that the fingers subdomain actually samples through three distinct conformations--open, closed, and a previously unrecognized intermediate conformation. We measured the overall dissociation rate of the polymerase-DNA complex and the distribution among the various conformational states in the absence and presence of nucleotide substrates, which were either correct or incorrect. Correct substrates promote rapid progression of the polymerase to the catalytically competent closed conformation, whereas incorrect nucleotides block the enzyme in the intermediate conformation and induce rapid dissociation from DNA. Remarkably, incorrect nucleotide substrates also promote partitioning of DNA to the spatially separated 3'-5' exonuclease domain, providing an additional mechanism to prevent misincorporation at the polymerase active site. These results reveal the existence of an early innate fidelity checkpoint, rejecting incorrect nucleotide substrates before the enzyme encloses the nascent base pair.     

Small-molecule ligands strongly affect the Förster resonance energy transfer between a quantum dot and a fluorescent protein

We report herein the study of F?rster resonance energy transfer (FRET) between a CdSe/ZnS core/shell quantum dot (QD) capped with three different small-molecule ligands, 3-mercaptopropionic acid (MPA), glutathione (GSH), and dihydrolipoic acid (DHLA), and a hexa-histidine (His(6))-tagged fluorescent protein, mCherry (FP). The F?rster radius (R(0)) and the corresponding donor-acceptor distances (r) for each of the QD-FP FRET systems were evaluated by using the F?rster dipole-dipole interaction formula. Interestingly, both the FRET efficiency (E) and r were found to be strongly dependent on the capping small-molecule ligands on the QD surface, where E ≈ 85% was obtained at a FP:QD copy number of 2:1 for the MPA capped QD, while that for the DHLA capped QD was <25% under the same conditions. A molecular model was proposed to explain the possible reasons behind these observations. The dissociation constants (K(d)s) and kinetics of the self-assembled QD-FP systems were also evaluated. Results show that the QD-FP self-assembly process is fast (completes in minutes at low nM concentrations), strong (with K(d) ≈ 1 nM) and positively cooperative (with the Hill coefficient n > 1), suggesting that the QD-His(6)-tagged biomolecule self-assembly is a facile, effective approach for making compact QD-bioconjugates which may have a wide range of sensing and biomedical applications.     

Förster energy transfer in cholesteric mixtures: a new type of phototunable fluorescent material

A new approach to the creation of cholesteric glass‐forming materials with photovariable fluorescent properties is suggested. This approach is based on Förster type energy transfer from a photochemically active donor to a highly fluorescent acceptor. For this purpose, a cholesteric mixture containing two fluorescent dopants based on anthracene (Dianthr) and stilbene (DCM) was prepared and studied. The absorbance peak of DCM molecules overlaps the emission peak of Dianthr. The possibility of using energy transfer in cholesteric mixtures containing a photoactive energy donor capable of photobleaching is demonstrated. It is shown that UV irradiation of planarly oriented films of the mixture leads to photodimerization of the Dianthr dopant. This photoreaction results in a significant decrease in the emission intensity of the DCM dopant. In all cases the emitted light is strongly circularly polarized, and the degree of polarization does not change during photoreaction. Such types of photo‐patternable glass‐forming cholesteric materials combining fluorescent properties, the possibility of energy transfer between two fluorescent dyes and a photoactivity of one fluorescent component, provide new opportunities for optical data recording and storage.     

Intramolecular directional förster resonance energy transfer at the single-molecule level in a dendritic system

We report on the directional F?rster resonance energy transfer (FRET) process taking place in single molecules of a first (T1P4) and a second (T2P8) generation of a perylenemonoimide (P)-terrylenediimide (T)-based dendrimer in which the chromophores are separated by rigid polyphenylene arms. At low excitation powers, single-molecule detection and spectroscopy of T1P4 and T2P8 dendrimers point to a highly efficient directional FRET from P donors to the central T acceptor, optical excitation at 488 nm resulting in exclusively acceptor emission in the beginning of the detected fluorescence intensity. Donor emission is seen only upon the bleaching of the acceptor. High-resolution time-resolved single-molecule fluorescence data measured with a microchannel plate photomultiplier reveal, for T2P8, a broad range of FRET rates as a result of a broad range of distances and orientations experienced by the donor-acceptor dendrimers when immobilized in a polymer matrix. Single-molecule data from T2P8 on 488 nm excitation are indicative for the presence, after terrylenediimide bleaching, of a P-P excited dimer characterized by a broad emission spectrum peaking around 600 nm and by fluctuating fluorescence decay times. At high excitation powers, single T1P4 and T2P8 molecules display simultaneous emission from both donor and acceptor chromophores. The effect, called "exciton blockade", occurs due to the presence of multiple excitations in a single molecule.     

Does Förster theory predict the rate of electronic energy transfer for a model dyad at low temperature?

The use of the F?rster model to predict the dynamics of resonant electronic energy transfer (RET) in a model donor-acceptor dyad (a terphenyl-bridged perylene diimide (PDI)-terrylene diimide (TDI) dyad molecule) embedded at low temperature in a PMMA matrix is tested against experiment. The relevant ingredients involved in the F?rster rate for RET, namely electronic coupling, spectral overlap, and screening effects, are accounted for in a quantitative manner. Electronic couplings are obtained from time-dependent density functional theory calculations, and the effect of the PMMA environment is included both on the transition densities and on their interaction through the IEFPCM model. We find that the presence of the terphenyl bridge induces a slight delocalization of the PDI and TDI transition densities over the bridge originating in a 56% increase in the coupling and in the breakdown of the dipole-dipole approximation. The spectral overlap is determined on the basis of a detailed simulation of the homogeneously broadened donor emission and acceptor absorption line shapes determined by fitting the single molecule spectra measured at 1.2 K. The corresponding distribution of spectral overlap throughout the ensemble is then estimated by assuming an uncorrelated inhomogeneous line broadening for the donor and acceptor. Combining the calculated electronic couplings and spectral overlaps sampled from Monte Carlo realizations of the energetic disorder, we obtain a mean RET time (approximately 8 ps) and a distribution in reasonable agreement with experiment.     

Intramolecular Förster energy transfer in a dendritic system at the single molecule level

The photophysics of a dendrimer containing four donor chromophores and one acceptor chromophore are studied at the single-molecule level. Upon excitation of the donors exclusive acceptor emission is observed due to efficient F?rster energy transfer. For 70% of the molecules donor emission is observed after bleaching of the acceptor, leading to a reduction of the F?rster energy transfer efficiency. Furthermore, we demonstrate that in this molecular system the donor chromophores do not bleach by a triplet-sensitized photooxidation.