On the analyses of fluorescence depolarisation data in the presence of electronic energy migration. Part I: Theory and general description

A new and general procedure is described for a detailed analysis of time-resolved fluorescence depolarisation data in the presence of electronic energy migration. An isotropic ensemble of bifluorophoric molecules (D(1)-R-D(2)) has been studied to demonstrate its utility. Intramolecular donor-donor energy migration occurs between the two donor groups (D), which are covalently connected to a rigid linker group (R). These groups undergo restricted reorientational motions with respect to the R group. The analysis of depolarisation data basically involves the search for best-fit parameters which describe the local reorientational motions, the intermolecular D(1)-D(2) distance, as well as the mutual orientations of the donors. For this, the analysis is partly performed on the Fourier domain and the best-fit parameters are determined by using an approach based on a Genetic Algorithm. The energy migration process has been described by using Monte Carlo simulations and an extended F?rster theory (EFT). It is found that the EFT provides the least time-consuming computational method. Since one-photon and two-photon excited fluorescence experiments can be applied for energy migration studies, a general and unified theoretical formulation is given.     

Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 A domain

Fluorescence resonance energy transfer (FRET) between tryptophan (Trp) as donor and 2,3-diazabicyclo[2.2.2]oct-2-ene (Dbo) as acceptor was studied by steady-state and time-resolved fluorescence spectroscopy. The unique feature of this FRET pair is its exceptionally short F?rster radius (10 A), which allows one to recover distance distributions in very short structureless peptides. The technique was applied to Trp-(GlySer)n-Dbo-NH2 peptides with n = 0-10, for which the average probe/quencher distance ranged between 8.7 and 13.7 A experimentally (in propylene glycol, analysis according to wormlike chain model) and 8.6-10.2 A theoretically (for n = 0-6, GROMOS96 molecular dynamics simulations). The larger FRET efficiency in steady-state compared to time-resolved fluorescence experiments was attributed to a static quenching component, suggesting that a small but significant part (ca. 10%) of the conformations are already in van der Waals contact when excitation occurs.     

The determination of the Förster distance (R0) for phenanthrene and anthracene derivatives in poly(methyl methacrylate) films

Experiments that employ direct resonance energy transfer (DET) to obtain information about distances or domain sizes in polymer systems require independent information about the magnitude of the characteristic (F?rster) energy transfer distance R(0). Values of R(0) are relatively straightforward to obtain by the traditional spectral overlap method (R(0)(SO)) for dyes in fluid solution, but are much more difficult to obtain for dyes in rigid polymer films. Here one can obtain a value for R(0) as a fitting parameter (R(0)(FF)) for donor fluorescence decay experiments for samples containing a random distribution of donor and acceptor dyes in the polymer film. In previous experiments from our group, we needed values of R(0) for various phenanthrene (Phe, donor) and anthracene (An, acceptor) derivatives. In this paper, we describe experiments which determine R(0) values by both methods for a series of Phe-An donor-acceptor pairs in poly(methyl methacrylate) and polystyrene films. Both the location of substituents on the donor and acceptor as well as the choice of the medium had an effect on the measured R(0), which varied between 2.0 and 2.6 nm. We also ascertained that there is some unknown factor, also prevalent in the work of others, which results in the F?rster radius being larger when determined by the F?rster fit method than by the method of spectral overlap.     

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.     

A 10-A spectroscopic ruler applied to short polyprolines

Fluorescence resonance energy transfer (FRET) from the amino acid tryptophan (Trp) as donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as acceptor in peptides of the general structure Trp-(Pro)n-Dbo-NH2 (n = 1-6) was investigated by steady-state and time-resolved fluorescence, CD, and NMR spectroscopy as well as by molecular dynamics (MD) simulations (GROMOS96 force field). The Trp/Dbo FRET pair is characterized by a very short F?rster radius (R0 ca. 9 A), which allowed distance determinations in such short peptides. Water and propylene glycol were investigated as solvents. The peptides were designed to show an early nucleation of the poly(Pro)II (PPII) secondary helix structure for n > or = 2, which was confirmed by their CD spectra. The shortest peptide (n = 1) adopts preferentially the trans conformation about the Trp-Pro bond, as confirmed by NMR spectra. The FRET efficiencies ranged 2-72% and were found to depend sensitively on the peptide length, i.e., the number of intervening proline residues. The analysis of the FRET data at different levels of theory (assuming either a fixed distance or distance distributions according to a wormlike chain or Gaussian model) afforded donor-acceptor distances between ca. 8 A (n = 1) and ca. 16 A (n = 6) in water, which were found to be similar or slightly higher in propylene glycol. The distances afforded by the Trp/Dbo FRET pair were found to be reasonable in comparison to literature data, expectations from the PPII helix structure, and the results from MD simulations. The persistence lengths for the longer peptides were found to lie at 30-70 A in water and 220 +/- 40 A in propylene glycol, suggesting a more rigid PPII helical structure in propylene glycol. A detailed comparison with literature data on FRET in polyprolines demonstrates that the donor-acceptor distances extracted by FRET are correlated with the F?rster radii of the employed FRET pairs. This demonstrates the limitations of using FRET as a spectroscopic ruler for short polyprolines, which is presumably due to the breakdown of the point dipole approximation in F?rster theory, when the size of the chromophores becomes comparable or larger than the distances under investigation.     

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.     

Vibrational energy transfer and anisotropy decay in liquid water: is the Förster model valid?

Ultrafast pump-probe anisotropy experiments have been performed on liquid H(2)O and D(2)O. In both cases, the anisotropy decay is extremely fast (on the order of 100 or 200 fs) and is presumed due to resonant vibrational energy transfer. The experiments have been interpreted in terms of the Fo?rster theory, wherein the rate constant for intermolecular hopping transport is proportional to the inverse sixth power of the distance between the vibrational chromophores. In particular, the anisotropy decay is assumed to be simply related to the survival probability as calculated with the Fo?rster theory. While the theory fits the data well, and is a reasonable model for these systems, there are several assumptions in the theory that might be suspect for water. Using our mixed quantum/classical model for vibrational spectroscopy and dynamics in liquid water, which agrees well with anisotropy decay experiments on the pure liquids as well as H(2)O/D(2)O mixtures, we critically analyze both the survival probability and anisotropy decay, in order to assess the applicability of the Fo?rster theory.     

Optimization of pairings and detection conditions for measurement of FRET between cyan and yellow fluorescent proteins.

Detection of F?rster resonance energy transfer (FRET) between cyan and yellow fluorescent proteins is a key method for quantifying dynamic processes inside living cells. To compare the different cyan and yellow fluorescent proteins, FRET efficiencies were measured for a set of the possible donor:acceptor pairs. FRET between monomeric Cerulean and Venus is more efficient than the ECFP:EYFP pair and has a 10% greater F?rster distance. We also compared several live cell microscopy methods for measuring FRET. The greatest contrast for changes in intramolecular FRET is obtained using a combination of ratiometric and spectral imaging. However, this method is not appropriate for establishing the presence of FRET without extra controls. Accurate FRET efficiencies are obtained by fluorescence lifetime imaging microscopy, but these measurements are difficult to collect and analyze. Acceptor photobleaching is a common and simple method for measuring FRET efficiencies. However, when applied to cyan to yellow fluorescent protein FRET, this method becomes prone to an artifact that leads to overestimation of FRET efficiency and false positive signals. FRET was also detected by measuring the acceptor fluorescence anisotropy. Although difficult to quantify, this method is exceptional for screening purposes, because it provides high contrast for discriminating FRET.     

Transfer of electronic excitation energy between randomly mixed dye molecules in the channels of zeolite L

Host-guest materials containing strongly fluorescent donor and acceptor molecules have been prepared. Fine-tuning of the donor to acceptor distance in this material allows beautiful visible and quantitative observation of electronic excitation energy transfer phenomena. Oxonine and pyronine have been used as guest molecules and zeolite L as host. The dyes have been inserted by ion exchange. Stationary state and time-resolved experiments have been carried out with zeolite crystals of 300 and 700 nm size in the dye concentration range of 10(-4) mol/L up to 0.042 mol/L. The fluorescence decay of the donor and the pumping of the acceptor via energy transfer, which can be well observed, became faster with increasing loading. The behavior of the system follows requirements expected for F?rster energy transfer material.     

A schematic model for energy and charge transfer in the chlorophyll complex

A theory for simultaneous charge and energy transfer in the carotenoid-chlorophyll-a complex is presented here and discussed. The observed charge transfer process in these chloroplast complexes is reasonably explained in terms of this theory. In addition, the process leads to a mechanism to drive an electron in a lower to a higher-energy state, thus providing a mechanism for the ejection of the electron to a nearby molecule (chlorophyll) or into the environment. The observed lifetimes of the electronically excited states are in accord/agreement with the investigations of Sundstr?m et al. and are in the range of pico-seconds and less. The change in electronic charge distribution in internuclear space as the system undergoes an electronic transition to a higher-energy state could, under appropriate physical conditions, lead to oscillating dipoles capable of transmitting energy from the carotenoid-chlorophylls chromophore to the reaction center by sending an electromagnetic wave (a photon) which provides a novel new mechanism for energy production. In the simplest version of the F?rster?CDexter theory, the excitation energy of a donor is transferred to an acceptor and then de-excited to the ground state by fluorescence with no electron being transferred. In the process proposed herein, charge and energy both are transferred from donor to acceptor which can further de-excite by fluorescence. The charge transfer time scale involving an actual transfer of electron is in the pico-second range.     

Fluorescence properties of systems with multiple Förster transfer pairs

A mathematical model has been developed to compute the spectroscopic properties of fluorescence systems with multiple F?rster transfer pairs in a homogeneous 3-dimensional matrix. This model is based on F?rster energy transfer theory and needs only a limited number of parameters which depend only on the properties of the individual dyes and their pair-wise interactions. Yet, the model allows the accurate prediction on the fluorescence properties of systems comprising mutual F?rster transfer between three dyes. The model is compared to an experimental system composed of reverse micelles and water soluble dyes. Although the experimental system might include additional effects that may influence the fluorescence properties (e.g. adsorption to the micelle walls, aggregation of the dyes) the agreement between the mathematical model and the experimental system is reasonably good.     

Fluorescence lifetime based distance measurement illustrates conformation changes of PYL10-CL2 upon ABA binding in solution state

The fluorescence lifetime based FRET distance measurements using sitespecific incorporated unnatural amino acid HC and Alexa488 as FRET pair revealed the different conformations of PYL10-CL2 upon ABA binding.     

Excitation energy transfer between closely spaced multichromophoric systems: effects of band mixing and intraband relaxation

We theoretically analyze the excitation energy transfer between two closely spaced linear molecular J-aggregates, whose excited states are Frenkel excitons. The aggregate with the higher (lower) exciton band edge energy is considered as the donor (acceptor). The celebrated theory of F?rster resonance energy transfer (FRET), which relates the transfer rate to the overlap integral of optical spectra, fails in this situation. We point out that, in addition to the well-known fact that the point-dipole approximation breaks down (enabling energy transfer between optically forbidden states), also the perturbative treatment of the electronic interactions between donor and acceptor system, which underlies the F?rster approach, in general loses its validity due to overlap of the exciton bands. We therefore propose a nonperturbative method, in which donor and acceptor bands are mixed and the energy transfer is described in terms of a phonon-assisted energy relaxation process between the two new (renormalized) bands. The validity of the conventional perturbative approach is investigated by comparing to the nonperturbative one; in general, this validity improves for lower temperature and larger distances (weaker interactions) between the aggregates. We also demonstrate that the interference between intraband relaxation and energy transfer renders the proper definition of the transfer rate and its evaluation from experiment a complicated issue that involves the initial excitation condition. Our results suggest that the best way of determining this transfer rate between two J-aggregates is to measure the fluorescence kinetics of the acceptor J-band after resonant excitation of the donor J-band.     

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.     

Intramolecular energy hopping and energy trapping in polyphenylene dendrimers with multiple peryleneimide donor chromophores and a terryleneimide acceptor trap chromophore

Intramolecular F?rster-type excitation energy transfer (FRET) processes in a series of first-generation polyphenylene dendrimers substituted with spatially well-separated peryleneimide chromophores and a terryleneimide energy-trapping chromophore at the rim were investigated by steady-state and time-resolved fluorescence spectroscopy. Energy-hopping processes among the peryleneimide chromophores are revealed by anisotropy decay times of 50--80 ps consistent with a FRET rate constant of k(hopp) = 4.6 ns(-1). If a terryleneimide chromophore is present at the rim of the dendrimer together with three peryleneimide chromophores, more than 95% of the energy harvested by the peryleneimide chromophores is transferred and trapped in the terryleneimide. The two decay times (tau(1) = 52 ps and tau(2) = 175 ps) found for the peryleneimide emission band are recovered as rise times at the terryleneimide emission band proving that the energy trapping of peryleneimide excitation energy by the terryleneimide acceptor occurs via two different, efficient pathways. Molecular- modeling-based structures tentatively indicate that the rotation of the terryleneimide acceptor group can lead to a much smaller distance to a single donor chromophore, which could explain the occurrence of two energy-trapping rate constants. All energy-transfer processes are quantitatively describable with F?rster energy transfer theory, and the influence of the dipole orientation factor in the F?rster equation is discussed.     

Resonance Energy Transfer in a Genetically Engineered Polypeptide Results in Unanticipated Fluorescence Intensity

The fluorescence intensity of a C-terminal acceptor chromophore, N-(7-dimethylamino-4-methyl coumarin (DACM), increased proportionally with 280 nm irradiation of an increasing number of donor tryptophan residues located on a β-sheet forming polypeptide. The fluorescence intensity of the acceptor chromophore increased even as the length of the β-sheet edge approached 256 Å, well beyond the Förster radius for the tryptophan–acceptor chromophore pair. The folding of the peptides under investigation was verified by circular dichroism (CD) and deep UV resonance Raman experiments. Control experiments showed that the enhancement of DACM fluorescence occurred concomitantly with peptide folding. In other control experiments, the DACM fluorescence intensity of the solutions of tryptophan and DACM did not show any enhancement of DACM fluorescence with increasing tryptophan concentrations. Formation of fibrillar aggregates of the substrate peptides prepared for the fluorescence studies was undetectable by thioflavin T (ThT) fluorescence.