Time-resolved detection of energy transfer: theory and application to immunoassays

Energy-transfer measurements based upon acceptor fluorophore emission are plagued with background fluorescence resulting from absorption of the excitation light by the acceptor fluorophore. The present work examines the use of a long-lifetime donor fluorophore and a short-lifetime acceptor fluorophore, combined with pulsed-laser excitation and electronic gating of detector signals, to separate the component of acceptor emission due to energy transfer from the component due to absorption of the excitation light. Theoretical equations describing the acceptor fluorescence and integrated acceptor fluorescence show that increasing the integration delay relative to the excitation pulse should greatly enhance detection of the energy-transfer component. The time-resolved detection of energy transfer was tested in a competitive immunoassay format in which antibodies to human immunoglobulin G (IgG) F(ab')2 fragments were covalently labeled with pyrenebutyrate (tau = 100 ns) and IgG Fab' fragments were covalently labeled with B-phycoerythrin (tau = 2.5 ns). Solutions containing these two conjugates exhibited energy transfer from the pyrenebutyrate to the B-phycoerythrin upon excitation with a nitrogen laser. Acceptor emission was measured with 0- and 20-ns integration delays and the ratios of the energy-transfer component to the laser-excited component were found to increase by 9- to 15-fold when the 20-ns delay was used in three series of immunoassays. Good agreement between the experimental data and theory was obtained following convolution of the theoretical fluorescence responses with the instrumental response of the fluorometer.     

A standard for calibration and shading correction of a fluorescence microscope

BACKGROUND: Numerous applications of fluorescence microscopy require quantitation of signal intensity in reproducible units. Two problems must be overcome to achieve this goal. First, due to various instrumental factors, the same sample imaged on two microscopes or even on the same microscope at different times may produce highly divergent readings. Second, because of shading, some areas within the same field may appear brighter than others despite the same amount of fluorophore. The first type of variability requires calibration using a sample of reproducible fluorescence yield; to correct for shading, a uniform fluorescent field is needed. METHODS: Standard slides were prepared by placing several microliters of 10%-50% w/v fluorescein or rhodamine between a coverglass and a slide. They were used to perform shading correction and normalization under a variety of imaging conditions. RESULTS: Concentrated fluorophores produced a uniform fluorescent field of moderate and reproducible brightness. By expressing the staining of a biological object in the units of standard slides, identical results were obtained irrespective of the imaging conditions or the microscope used. We compared shading correction based on concentrated fluorescein with two other standards. Concentrated fluorescein resulted in the best equalization of the field. CONCLUSIONS: Standardization of fluorescent images can be achieved by normalizing them to the image of a concentrated solution of a fluorophore. Due to its simplicity and efficiency, this method can be used in clinical analysis as well as in routine laboratory practice.     

Analysis of photoacoustic waveforms using the nonlinear least squares method.

Pulsed-laser photoacoustics is a technique which measures photoinduced enthalpic and volumetric changes on the nano- and microsecond timescales. Analysis of photoacoustic data generally requires deconvolution for a sum of exponentials, a procedure which has been developed extensively in the field of time-resolved fluorescence decay. Initial efforts to adapt an iterative nonlinear least squares computer program, utilizing the Marquardt algorithm, from the fluorescence field to photoacoustics indicated that significant modifications were needed. The major problem arises from the wide range of transient decay times which must be addressed by the photoacoustic technique. We describe an alternative approach to numerical convolution with exponential decays, developed to overcome the problems. Instead of using an approximation method (Simpson's rule) for evaluating the convolution integral, we construct a continuous instrumental response function by quadratic fitting of the discrete data and evaluate the convolution integral directly, without approximations. The success and limitations of this quadratic-fit convolution program are then demonstrated using simulated data. Finally, the program is applied to the analysis of experimental data to compare the resolution capabilities of two commercially available transducers. The advantages of a broadband, heavily damped transducer are shown for a standard organic photochemical system, the quenching of the triplet state of benzophenone by 2,5-dimethyl-2,4-hexadiene.     

A strand exchange FRET assay for DNA

A new displacement hybridisation method is reported using a single strand DNA probe, labelled with an acceptor fluorophore (oregon green 488). Detection of double stranded sample target is shown, with discrimination between the probe, duplexed during the assay, and free single stranded probe DNA achieved through the FRET from a donor grove fluorophore (Hoechst 33258). A model for the kinetics of the displacement assay is presented and the course of the assay predicted according to probe/target ratios and sequence. The modelled predictions are consistent with the experimental data showing single base pair mismatch discrimination. The pattern of response according to the mismatch/perfect complement ratio in a mixed sample is also considered with an allele-discrimination ratio lying between the homozygous gene and total mismatch case, according to ratio. The assay is shown to be tolerant of different probe concentrations and ratios and through the dual wavelength recorded signals from donor and FRET acceptor, internal baseline correction is achieved with excellent noise reduction through ratiometric measurement.     

A method for analysis of lipid vesicle domain structure from confocal image data

Quantitative characterization of the lateral structure of curved membranes based on fluorescence microscopy requires knowledge of the fluorophore distribution on the surface. We present an image analysis approach for extraction of the fluorophore distribution on a spherical lipid vesicle from confocal imaging stacks. The technique involves projection of volumetric image data onto a triangulated surface mesh representation of the membrane, correction of photoselection effects and global motion of the vesicle during image acquisition and segmentation of the surface into domains using histograms. The analysis allows for investigation of the morphology and size distribution of domains on the surface.     

A model-free method for mass spectrometer response correction

A new method for correction of mass spectrometer output signals is described. Response-time distortion is reduced independently of any model of mass spectrometer behavior. The delay of the system is found first from the cross-correlation function of a step change and its response. A two-sided time-domain digital correction filter (deconvolution filter) is generated next from the same step response data using a regression procedure. Other data are corrected using the filter and delay. The mean squared error between a step response and a step is reduced considerably more after the use of a deconvolution filter than after the application of a second-order model correction. O2 consumption and CO2 production values calculated from data corrupted by a simulated dynamic process return to near the uncorrupted values after correction. Although a clean step response or the ensemble average of several responses contaminated with noise is needed for the generation of the filter, random noise of magnitude less than or equal to 0.5% added to the response to be corrected does not impair the correction severely.     

Real-time background suppression during frequency domain lifetime measurements

We describe real time background suppression of autofluorescence from biological samples during frequency domain or phase modulation measurements of intensity decays. For these measurements the samples were excited with a train of light pulses with widths below 1 ps. The detector was gated off for a short time period of 10 to 40 ns during and shortly after the excitation pulse. The reference signal needed for the frequency domain measurement was provided by a long-lifetime reference fluorophore which continues to emit following the off-gating pulse. Both the sample and the reference were measured under identical optical and electronic conditions avoiding the need for correction of the photomultiplier tube signal for the gating sequence. We demonstrate frequency domain background suppression using a mixture of short- and long-lifetime probes and for a long-lifetime probe in human plasma with significant autofluorescence.     

Setup and characterization of a multiphoton FLIM instrument for protein-protein interaction measurements in living cells.

BACKGROUND: Fluorescence lifetime microscopy (FLIM) is currently one of the best techniques to perform accurate measurements of interactions in living cells. It is independent of the fluorophore concentration, thus avoiding several common artifacts found in F?rster Resonance Energy Transfer (FRET) imaging. However, for FLIM to achieve high performance, a rigorous instrumental setup and characterization is needed. METHODS: We use known fluorophores to perform characterization experiments in our instrumental setup. This allows us to verify the accuracy of the fluorescence lifetime determination, and test the linearity of the instrument by fluorescence quenching. RESULTS: We develop and validate here a protocol for rigorous characterization of time-domain FLIM instruments. Following this protocol, we show that our system provides accurate and reproducible measurements. We also used HeLa cells expressing proteins fused to Green Fluorescent Proteins variants (CFP and YFP) to confirm its ability to detect interactions in living cells by FRET. CONCLUSIONS: We report a well-designed protocol in which precise and reproducible lifetime measurements can be performed. It is usable for all confocal-based FLIM instruments and is a useful tool for anyone who wants to perform quantitative lifetime measurements, especially when studying interactions in living cells using FRET.     

Characterization of one- and two-photon excitation fluorescence resonance energy transfer microscopy

Advances in molecular biology provide various methods to define the structure and function of the individual proteins that form the component parts of subcellular structures. The ability to see the dynamic behavior of a specific protein inside the living cell became possible through the application of advanced fluorescence resonance energy transfer (FRET) microscope techniques. The fluorophore molecule used for FRET imaging has a characteristic absorption and emission spectrum that should be considered for characterizing the FRET signal. In this article we describe the system development for the image acquisition for one- and two-photon excitation FRET microscopy. We also describe the precision FRET (PFRET) data analysis algorithm that we developed to remove spectral bleed-through and variation in the fluorophore expression level (or concentration) for the donor and acceptor molecules. The acquired images have been processed using a PFRET algorithm to calculate the energy transfer efficiency and the distance between donor and acceptor molecules. We implemented the software correction to study the organization of the apical endosome in epithelial polarized MDCK cells and dimerization of the CAATT/enhancer binding protein alpha (C/EBPalpha). For these proteins, the results revealed that the extent of correction affects the conventionally calculated energy transfer efficiency (E) and the distance (r) between donor and acceptor molecules by 38 and 9%, respectively.     

Analysis of Fluorescence Decay by the Nonlinear Least Squares Method

Fluorescence decay deconvolution analysis to fit a multiexponential function by the nonlinear least squares method requires numerical calculation of a convolution integral. A linear approximation of the successive data of the instrument response function is proposed for the computation of the convolution integral. Deconvolution analysis of simulated fluorescence data were carried out to show that the linear approximation method is generally better when one of the lifetimes is comparable to the time interval between data.     

Anisotropy-based sensing with reference fluorophores

We describe a new approach to fluorescence sensing based on measurements of steady-state anisotropies in the presence of reference fluorophores with known anisotropies. The basic concept is that the anisotropy of a mixture reflects a weighted average of the anisotropies of the emitting species. By use of reference fluorophores the starting anisotropy can be near zero, or near 0.9 for oriented films which contain the reference fluorophore. Changing intensities of the analyte result in changes in anisotropy. A wide dynamic range of anisotropies is available because of the freedom to select high or low starting values. Anisotropy-based sensing was demonstrated for pH using 6-carboxyfluorescein and for protein affinity or immunoassay using an oriented film with high anisotropy and a protein labeled with a metal-ligand complex. The latter measurements were performed with a simple light-emitting diode excitation source without an excitation polarizer. The sensitive range of the assay can be adjusted by changing the intensity of the reference fluorophore. Anisotropy-based sensing can have numerous applications in clinical and analytical chemistry.     

A batch correction method for liquid chromatography–mass spectrometry data that does not depend on quality control samples

The need for reproducible and comparable results is of increasing importance in non-targeted metabolomic studies, especially when differences between experimental groups are small. Liquid chromatography–mass spectrometry spectra are often acquired batch-wise so that necessary calibrations and cleaning of the instrument can take place. However this may introduce further sources of variation, such as differences in the conditions under which the acquisition of individual batches is performed. Quality control (QC) samples are frequently employed as a means of both judging and correcting this variation. Here we show that the use of QC samples can lead to problems. The non-linearity of the response can result in substantial differences between the recorded intensities of the QCs and experimental samples, making the required adjustment difficult to predict. Furthermore, changes in the response profile between one QC interspersion and the next cannot be accounted for and QC based correction can actually exacerbate the problems by introducing artificial differences. “Background correction” methods utilise all experimental samples to estimate the variation over time rather than relying on the QC samples alone. We compare non-QC correction methods with standard QC correction and demonstrate their success in reducing differences between replicate samples and their potential to highlight differences between experimental groups previously hidden by instrumental variation.     

DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method

Molecular beacon is a DNA probe containing a sequence complementary to the target that is flanked by self-complementary termini, and carries a fluorophore and a quencher at the ends. We used the fluorescein and dabcyl as fluorophore and quencher respectively, and studied with DFT calculations at the GGA/DNP level, and taking into account DFT dispersion corrections by the Grimme and Tkatchenko-Scheffler (TS) schemes, the distance, where the most favorable energetic interaction between the fluorophore and quencher in conjugated form occurs. This distance occurs at a separation distance of 29.451?? between the centers of Dabcyl and fluorescein employing the TS DFT dispersion correction scheme, indicating FRET efficiency around 94.28?%. The calculated emission spectra of the conjugated pair in water indicated that the emission and absorption spectrum overlap completely and thus no fluorescence can be observed due to the fluorescence resonance energy transfer (FRET) effect. The DFT results confirmed the experimentally observing fluorescence quenching of the fluorescein-dabcyl conjugated system by FRET.     

Reaction Fields in the Environment of Fluorescent Probes: Polarity Profiles in Membranes

Fluorescent probes in biological systems are sensitive to environmental polarity by virtue of their response to the reaction field created by polarization of the dielectric medium. Classically, fluorophore solvatochromism is analyzed in terms of the Lippert equation and later variants, all of which rely upon the original reaction field of Onsager. A recent survey of the solvent dependence of EPR spin-label probes, which are responsive solely to the reaction field in the ground state without the complication of excited states, shows that the reaction field of Block and Walker performs best in describing the polarity dependence. In this model, the step-function transition to the bulk dielectric medium used by Onsager is replaced by a graded transition. Analysis of the Stokes shifts for representative fluorescent membrane probes, such as PRODAN, DANSYL, and anthroyl fatty acid, reveals that, of several different reaction fields (including that of Onsager), the Block-Walker model best describes the dependence on solvent dielectric constant and refractive index for the different probes simultaneously. This is after full allowance is made for all contributions involving polarizability of the fluorophore, a point that is frequently neglected or treated incorrectly in studies using biological fluorescent probes. By using the full range of polar and apolar solvents, it is then possible to establish a common reference for the polarity dependence of different fluorophores and to relate this also to the polarity dependence of biologically relevant spin-label EPR probes. An important application is calibration of the transmembrane polarity profile recorded by fluorescent probes in terms of the high-resolution profile obtained from site-specifically spin-labeled lipid chains.     

NIST/ISAC standardization study: Variability in assignment of intensity values to fluorescence standard beads and in cross calibration of standard beads to hard dyed beads

Results from a standardization study cosponsored by the International Society for Advancement of Cytometry (ISAC) and the US National Institute of Standards and Technology (NIST) are reported. The study evaluated the variability of assigning intensity values to fluorophore standard beads by bead manufacturers and the variability of cross calibrating the standard beads to stained polymer beads (hard-dyed beads) using different flow cytometers. Hard dyed beads are generally not spectrally matched to the fluorophores used to stain cells, and spectral response varies among flow cytometers. Thus if hard dyed beads are used as fluorescence calibrators, one expects calibration for specific fluorophores (e.g., FITC or PE) to vary among different instruments. Using standard beads surface-stained with specific fluorophores (FITC, PE, APC, and Pacific Blue?), the study compared the measured intensity of fluorophore standard beads to that of hard dyed beads through cross calibration on 133 different flow cytometers. Using robust CV as a measure of variability, the variation of cross calibrated values was typically 20% or more for a particular hard dyed bead in a specific detection channel. The variation across different instrument models was often greater than the variation within a particular instrument model. As a separate part of the study, NIST and four bead manufacturers used a NIST supplied protocol and calibrated fluorophore solution standards to assign intensity values to the fluorophore beads. Values assigned to the reference beads by different groups varied by orders of magnitude in most cases, reflecting differences in instrumentation used to perform the calibration. The study concluded that the use of any spectrally unmatched hard dyed bead as a general fluorescence calibrator must be verified and characterized for every particular instrument model. Close interaction between bead manufacturers and NIST is recommended to have reliable and uniformly assigned fluorescence standard beads. ? 2012 International Society for Advancement of Cytometry.     

Subtraction of background fluorescence in multiharmonic frequency-domain fluorimetry.

Background fluorescence is a major concern in time-resolved microfluorimetry studies of biological samples. A general method for subtraction of an arbitrary background signal in measurements of lifetime and anisotropy decay by multiharmonic Fourier transform spectroscopy is presented. Multifrequency phase and modulation values are measured in parallel by transformation of digitized time-domain waveforms into the frequency domain. For subtraction of background, time-domain waveforms are acquired for emission and reference photomultipliers for sample (e.g., cell containing fluorophore) and blank (e.g., unlabeled cell). Time-domain waveforms obtained in a series of measurements (e.g., sample and blank for parallel and perpendicular orientations of an emission polarizer) are time-justified by least-squares fitting of reference channel waveforms or by phase comparison of the first Fourier harmonics of the reference channel. Background is then subtracted directly in the time domain, and the subtracted waveform is Fourier transformed to the frequency domain for analysis of lifetime or anisotropy decay. This approach yielded excellent background correction over a wide range of background intensities and decay profiles. The method was tested in cuvette fluorimetry with fluorescein and acridine orange and in fluorescence microscopy with living MDCK cells loaded with the pH indicator BCECF. Sample lifetimes and rotational parameters could be recovered accurately with greater than 50% of the signal arising from background. These results establish a direct and practical approach to subtraction of background in complex biological and chemical samples studied by frequency-domain fluorimetry.     

Role of intralaminar thalamic nuclei in strengthening inhibition induced by stimulation of the caudate nucleus

The influence of preliminary subthreshold activation of thalamic intralaminary nuclei on achievement of instrumental reflex and on inhibitory effects, caused by stimulation of the caudate nucleus head, were studied in chronic experiments on 5 dogs with a model of instrumental defensive conditioned reflexes, providing for maintainance of a given posture. It was shown that the preceding high-frequency electrostimulation of intralaminary nuclei activates motor components of the instrumental response (shortened latency, EMG and mechanogram of the response, increased amplitude of instrumental response) and significantly lowers threshold strength of the current, necessary for obtaining "caudate pause". The greatest increase in inhibitory influences, caused by stimulation of the caudate nucleus head, was observed when thalamic stimulation preceded stimulations, localized in the dorsolateral segment of the caudate nucleus head. The obtained data are discussed in aspect of Buchwald et al. hypothesis on the existence of "caudate loop".     

Array biosensor based on enzyme kinetics monitoring by fluorescence spectroscopy: application for neurotoxins detection

The aim of the present work is to develop an evanescence wave array biosensor exploiting the “kinetic” approach of enzymatic reaction and further detection of the reaction products via pH sensitive fluorophore reporter. To demonstrate the feasibility of this approach, we have developed a biosensor array with the potential for direct detection of organophosphates using as a biorecognition element, an enzyme organophosphorus hydrolase (OPH), conjugated with a pH-sensitive fluorophore, carboxynaphthofluorescein (CNF). The presence of reference spots allows the discrimination of the enzymatic and non-enzymatic based pH changes; bovine serum albumin (BSA) was used as a non-enzymatic scaffold protein for CNF attachment at the reference spots. An array biosensor unit developed at the Naval Research Laboratories (NRL) was adopted as the detection platform and appropriately modified for enzyme-based measurements. A planar multi-mode waveguide was covered with an optically transparent TiO₂ layer to increase the surface area available for immobilization.

The biosensor enabled the detection of 2.5 μM paraoxon, and 10 μM DFP and parathion, respectively. Very short response time of 30 s can be achieved with a total analysis time of less than 2 min. When operated at room temperature and stored at 4 °C, the waveguide retained reasonable activity for greater than 45 days.     

A simplified approach to quasi-linear viscoelastic modeling

The fitting of quasi-linear viscoelastic (QLV) constitutive models to material data often involves somewhat cumbersome numerical convolution. A new approach to treating quasi-linearity in 1-D is described and applied to characterize the behavior of reconstituted collagen. This approach is based on a new principle for including nonlinearity and requires considerably less computation than other comparable models for both model calibration and response prediction, especially for smoothly applied stretching. Additionally, the approach allows relaxation to adapt with the strain history. The modeling approach is demonstrated through tests on pure reconstituted collagen. Sequences of "ramp-and-hold" stretching tests were applied to rectangular collagen specimens. The relaxation force data from the "hold" was used to calibrate a new "adaptive QLV model" and several models from literature, and the force data from the "ramp" was used to check the accuracy of model predictions. Additionally, the ability of the models to predict the force response on a reloading of the specimen was assessed. The "adaptive QLV model" based on this new approach predicts collagen behavior comparably to or better than existing models, with much less computation.     

Application of multivariate curve resolution alternating least squares method for determination of caffeic acid in the presence of catechin interference

In the current article, preparation and application of a graphene oxide nanosheets-based sensor for electrochemical determination of caffeic acid (CA) in the presence of catechin is described. This measurement was performed using the differential pulse voltammetry (DPV) technique and chemometric methods such as multivariate curve resolution–alternating least squares (MCR–ALS). The modified sensor was characterized by various techniques such as Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, ultraviolet–visible, X-ray diffraction (XRD), and scanning electron microscopy (SEM). Operating conditions and influencing variables (involving several chemical and instrumental variables) were optimized with central composite rotatable design and response surface methodology. The second-order electrochemical data were generated by changing the pulse height in DPV, and after potential shift correction MCR–ALS was applied. Under the optimized conditions, the dynamic range for CA was from 0.5 to 100.0 μM and the detection limit was found to be 1.1 × 10^–9 M. The results revealed that the modified electrode shows an improvement in anodic oxidation activity of CA due to a marked enhancement in the current response compared with the bare carbon paste electrode. The modified electrode demonstrated good sensitivity, selectivity, and stability. The proposed method was successfully applied in determination of caffeic acid in the presence of unexpected electroactive interferences with a very high degree of overlapping such as catechin in real samples.