Pulsed Interleaved Excitation (PIE) improves fluorescence cross-correlation spectroscopy (FCCS) and single pair Förster Resonance Energy Transfer (spFRET) measurements, by correlating each detected photon to the excitation source that generated it. It relies on the interleaving of two picosecond laser sources and time correlated single photon counting (TCSPC) detection. Here, we present an optical configuration based on a commercial supercontinuum laser, which generates multicoulour interleaved picosecond pulses with arbitrary spacing and wavelengths within the visible spectrum. This simple, yet robust configuration can be used as a versatile source for PIE experiments, as an alternative to an array of picosecond lasers and drivers.
©2013 Optical Society of America
Fluorescence spectroscopy is a powerful tool to investigate the structure and the dynamics of biological macromolecules. Thanks to the exquisite sensitivity of modern detection devices, useful information can be recovered from the fluorescence signal from single molecules [1,2]. Förster Resonance Energy Transfer (FRET) reports on the proximity between two complementary fluorophores through dipole-dipole interaction, and can be measured at a single molecule level . FRET has thus become a method of choice to investigate macromolecular structural dynamics. Fluorescence Correlation Spectroscopy (FCS) and Cross-Correlation Spectroscopy (FCCS) [4–7] inform on the diffusion properties of fluorescent molecules as well as their interaction. For all these ultrasensitive methods, it is important to maximize the information extracted from each photon, in terms of arrival time relative to the laser pulse (reporting on the excited state lifetime of the fluorophore), polarization (reporting on the rotation of the fluorophore), and energy (reporting on the spectrum of the fluorophore). When multiple laser sources are used, it is important to assign each photon to the laser source that generated it. It is therefore not suitable to illuminate the sample with the various laser sources simultaneously. This assignment can be achieved by using alternating laser excitation schemes, that can be performed at various time scales: millisecond (msALEX ), microsecond (µsALEX ), or nanosecond (nsALEX  or Pulsed Interleaved Excitation, PIE [11,12]). Milli or microsecond alternation schemes are achieved using Electro-Optic modulators or Acousto-Optic Tunable filters and CW lasers; at these relatively slow timescales, it is straightforward to assign the detected photons (from an emCCD camera or a Single Photon Avalanche Diode) to the excitation laser. Nanosecond alternation is performed by interleaving the pulses of two pulsed lasers. It is necessary to use Time Correlated Single Photon Counting (TCSPC) detection to assign each individual photon to the laser pulse that generates it. In particular, nsALEX/PIE has proven to be a useful tool to perform FCS and FCCS quantitatively by removing spectral crosstalk [11,12]. By using a lifetime filtering algorithm, unwanted contributions from detector afterpulsing or scattered light to the correlation function can be discarded [13,14]. Additionally, as demonstrated recently, it is also possible to combine multiparametric fluorescence detection (MFD) and PIE to recover, in a single measurement, all the calibration factors needed to perform an accurate spFRET measurement .
Performing nsALEX/PIE requires the use of two pulsed lasers, and of a picosecond laser controller to drive them and generate the delay between the pulses. Ideally, this delay needs to be adjustable, in order to optimize it and obtain a full decay for each dye excited by each laser. When it is required to use another spectrally distinct dye (that needs to be excited at another laser wavelength) it is necessary to purchase and install a new laser head. Often, many excitation lasers will be needed, such as in a user facility, for example, where many different samples with different fluorophores are analyzed. Supercontinuum sources make use of optical nonlinear effects in photonic crystal optical fibers to create light with a wide spectrum, which can span the visible and near-infrared, typically from around 400 to 2000 nm. Commercially available, they achieve high power densities (several mW/nm in the visible), and have variable repetition rates (up to 80MHz typically). Recently, their usefulness has initiated the replacement of conventional lasers for various types of advanced microscopies and spectroscopies techniques, including TCSPC fluorescence spectroscopy , stimulated emission depletion (STED) fluorescence microscopy [17,18], FLIM (Fluorescence Lifetime Imaging Microscopy)-FRET microscopy , coherent anti-Stokes Raman scattering (CARS) microscopy , and total internal reflection microscopy .
Here we present a simple optical scheme, based on a commercial supercontinuum source, explaining how to perform nsALEX/PIE microscopies at any wavelength in the visible spectrum. In our experimental setup, the output beam of the supercontinuum source is divided in two paths, and each of them is spectrally filtered at the desired wavelength, using a simple bandpass filter. One beam path is much longer than the other, adjusted to the appropriate length (several meters), to generate the delay between the pulses. Recombination of the two beams leads to a pulsed interleaved excitation, with arbitrary wavelength (that depends on the filters), arbitrary delay (that depends on the path lengths), and perfect spatial overlap thanks to coupling into a single mode fiber. We present here the details of this realization, and demonstrate the use of this versatile setup for PIE / FCCS experiments.
2. Experimental setup
Our setup (Fig. 1 ) uses a SC450-4-20MhZ laser source (Fianium, Southampton, UK). It runs at 20MHz, and has a power density >2mW/nm over the 450-800nm range, with average pulse width of 100-150ps . The collimated, unpolarized output of the source is divided by a 50:50 beamsplitter cube BS1 (BS016, Thorlabs, NJ, USA), thus generating two beams (the “prompt” and the “delayed”). Each beam is spectrally filtered using an excitation bandpass filter at the wavelength of choice (typically 10nm bandpass, 532/10 (BP1) and 635/10 (BP2) in the present example). Virtually any combination of filters compatible with the double band dichroic mirror in the microscope (DM2) can be used here. The delayed beam is reflected by a set of 9 mirrors, adding a beam path length of up to 8m relative to the prompt beam. Four mirrors are mounted on optical rails (Thorlabs, NJ, USA) to reduce this distance and fine adjustement of the delay if needed. Since the output of the supercontinuum source fiber is not perfectly collimated, this set of mirrors causes a divergence and diffusion of the beam, that is re-collimated using a telescopic system of lenses (f = 1000mm (L1) and f = 500mm (L2)). The two beam paths can then recombined using a dichroic mirror (DM1) reflecting only the prompt beam. However, we prefer using a 50:50 beamsplitter cube (BS016, Thorlabs, NJ, USA) resulting in a 50% power loss, but consistent with any wavelength combination (including when the two beam paths are at the same wavelength, in order to obtain a 40Mhz monochromatic pulse train (see Discussion)). This power loss is not detrimental since beam attenuation is required for most confocal experiments. The two beams are then focused using a 10x objective, and coupled into a single-mode fiber (SMF) (P1-460A-FC, Thorlabs, NJ, USA), by which the beams become spatially overlapped and filtered. At the exit of the fiber, using this setup, a power of up to 1mW is obtained for each wavelength. This power is reduced typically to 10-100µW for each beam by using neutral density filters.
The output of the fiber is collimated using a 10x microscope objective lens (04OAS010; CVI Melles Griot, Albuquerque, NM, USA), and coupled into an inverted microscope (Axio observer D1, Carl Zeiss, Germany). The light is reflected by a dichroic mirror (DM2) that matches the excitation/emission wavelengths (FF545/650-Di01, Semrock, Rochester, NY, USA) and coupled into a Plan Apochromat 100x, NA1.4 objective (Carl Zeiss, Germany). Emitted photons are then collected by the objective and focused by the tube lens (TL) on a pinhole of desired width (typically 75µm for FCS and 150µm for spFRET). The detection part of our setup is a classical MFD/nsALEX configuration [10,22]. The photon stream is collimated (L3), and divided using a beamsplitter cube (BS2). In each created channel, the photons are spectrally separated using dichroic mirrors (DM3, here BS 649, Semrock, Rochester, NY, USA) and filtered using high quality emission bandpass filters (here ET BP 585/65 (BP3) and ET BP 700/75 (BP4), Chroma, Bellows Falls, VT, USA). Single photons are detected using Single Photon Avalanche Diodes. We use two MPD-1CTC (MPD, Bolzano, Italy) for the lowest wavelength channels (hereafter named the green channels) and two SPCM AQR-14 (Perkin Elmer, Fremont, CA, USA) for the highest wavelength channels (hereafter named the red channels). This choice is driven by the fact that MPD detectors have a better time resolution (which is important especially for spFRET experiments based on donor lifetime measurements), but have a lower quantum efficiency above 550nm than SPCM AQR detectors. Having two identical detection channels for each spectral range reduces the distortion of the autocorrelation functions by eliminating the effect of detector afterpulsing . The output of the detectors is coupled into a TCSPC counting board (SPC-150, Becker&Hickl, Berlin, Germany), through a HRT41 router (B&H), using appropriate pulse inverters and attenuators. The sync signal that triggers the TCSPC board is provided by picking a small fraction of the light from the prompt path (reflected by a coverslip), and focusing it on an avalanche diode (APM-400, B&H). We note that when polarized emission and detection are needed (for MFD experiments for example), BS1 and BS2 can be replaced with polarizing beamsplitters (PBS ; PBS201, Thorlabs, NJ, USA). Control of the polarization can be performed on each of the prompt and delayed paths using ½ and ¼ waveplates.
Detection of the emitted photons after prompted and delayed excitation
The detected fluorescence decays for the green and the red channels for a mixture of tetramethylrhodamine (TMR) and Atto655 fluorophores are presented on Fig. 2 (only one curve is represented / channel for clarity, using a linear or a logarithmic scale (inset)). The photons generated by the prompt beam (at 532nm, exciting mainly the TMR) appear in the 0-25 ns time window, while those generated by the delayed beam (at 635nm, exciting mainly Atto655) are detected in the 25-50ns window. The 25 ns delay between the pulses allows for a complete decay of the fluorescence intensities (Fig. 2, insets). As expected, excited state lifetimes τ of TMR and Atto655 were measured to be respectively 2.5 ns  and 1.8 ns (as provided by the manufacturer). Obtaining these complete decays justifies the use of a supercontinuum source running at 20MHz. Indeed, a source running at 40 MHz or higher would result in incomplete decays, and thus crosstalk between the prompt and delayed channels, while a source running at 10 MHz or lower would decrease the photon yield per molecule. Supercontinuum sources equipped with a pulse picker are also available, allowing an adjustment of the pulse frequency as needed. We note that if a fluorophore has a longer lifetime, it is possible to adjust the size of the prompt and delayed observation windows by changing the delay between the two laser pulses, simply by changing the length of the delay line.
The photons in the delayed decay appear only in the red channel, as expected. However, in the prompt decay, a significant fraction of photons appear in the red channel. The measured average decay time for these photons is 2.1 ns, indicating that they arise from two sources of cross-talk: the leakage of TMR emission (τ = 2.5 ns) in the red channel, due to its emission spectrum properties, and the emission of Atto655 (τ = 1.8 ns) directly excited by the prompt beam (at 532nm), due to its excitation spectrum properties (see below).
Alignment of the emission detectors and the excitation lasers
It is possible to take advantage of these cross talk effects to verify the correct alignment of the detection channels and the correct overlap of the two excitation beams, by using FCS and FCCS. In an FCS experiment, the amplitude of the correlation function depends on the number of molecules in the observation volume . In an FCCS experiment, the signal from two observation volumes is cross-correlated. The amplitude of the cross-correlation function relative to the correlation function for one of the volumes depends on the fraction of molecules detected in both channels relative to those detected in this specific volume [25,26]. Thus, if only one type of molecules that is able to emit photons in both channels is present, the amplitude of the cross correlation will reflect the overlap between the observation volumes.
The observation volume results from the combination of the excitation volume defined by the excitation beam and the emission volume defined by the emission optics (pinhole + lenses + avalanche photodiodes). First, in order to verify the overlap of the emissions volumes, we use a solution of a fluorophore emitting photons in all detections channels (such as TMR), upon excitation by the prompt laser. In our setup, around 10 to 15% of the signal emitted by TMR in the green detection channels is detected in the red detection channels, due to TMR emission spectral properties. Figure 3(a) presents a correlation analysis of the fluorescence signal from a 1nM TMR solution, upon excitation by the prompt beam (the delayed beam is blocked). We observe equivalent correlation amplitudes (within error) for the autocorrelation curves for the photons detected in the green channels (G(0) green = 0.217 ± 0.005), the red channels (G(0) red = 0.212 ± 0.004), and the cross-correlation curve for the photons detected in both channels (G(0)cross = 0.215 ± 0.004). A similar, perfect overlap is also observed when cross correlating the two green channels together, or the two red channels (not shown). This shows that the TMR molecules emitting in all the channels are the same, and thus indicates a perfect overlap of the four emission volumes, upon excitation by a single beam. This type of control can be easily performed on any single color confocal microscope that can acquire FCS data.
Second, in order to verify the overlap of the excitation volumes by FCS, we need to make use of the ability offered by PIE to separate the photons generated by the two excitation beams. We use a solution of Atto655, excited by the prompt beam (at 532 nm) at about 10% of the level of excitation generated by the delayed beam (at 635 nm) (due to its excitation spectrum properties). By decreasing the power of the delayed beam by a factor of 10 compared to the prompt beam, a similar signal level is thus expected for the two beams, in the red detection channels. This is indeed the case, and enabled the calculation of the autocorrelation curves for the photons generated by the prompt beam based on their arrival time (Fig. 3(b), green, G(0)prompt = 0.126 ± 0.003), for those generated by the delayed beam (Fig. 3(b), red, G(0)delayed = 0.103 ± 0.003), and the cross-correlation between these photons streams (Fig. 3(b), black, G(0)cross = 0.118 ± 0.003). These data indicate a 22% difference in the autocorrelation amplitudes of the signals generated by the prompt (green) and the delayed (red) pulses. This indicates that the effective observation volume generated by the delayed (red) beams is 22% larger than the one generated by the prompt (green) beam, which is expected for diffraction limited volumes at 635nm vs. 532nm respectively. As expected theoretically , in such a case, for a single species emitting in both channels, the cross correlation curves lies between the two autocorrelation curves (Fig. 3(b)). Altogether, these data indicate that the two excitation volumes present an excellent overlap, and that the size of the observation volumes in our configuration is governed by the wavelength of the excitation light, and not the configuration of the emission module (equipped with a 75µm pinole).
Elimination of cross-talk effects in FCCS experiments
The crosstalk originating from the leakage of the emission of the green dye and the direct excitation of the red dye by the green laser is a well-known source of artifact in FCCS experiments , which can be minimized by choosing fluorophores whose spectral overlap is minimal. Using PIE, however, it is possible to eliminate this source of artifact by discarding these irrelevant photons based on their arrival time relative to the laser pulses, without loss in the signal to noise ratio of the correlation function . This is demonstrated in Fig. 4 . We used a mixture of two DNA fragments (labeled with Cy3 and Atto655), whose sequences are not complementary, and thus are not expected to hybridize. The correlation functions of all photons detected in the green and the red channels is presented in Fig. 4(a). A significant fraction of cross-correlation (ACC = 14% of ACC, green (black curve vs. green curve)) is observed, due to spectral crosstalk. However, when the photons detected in the green channels only after prompt excitation are correlated with the photons detected in the red channels only after delayed excitation, the amplitude of the cross-correlation function drops to zero, demonstrating an efficient suppression of the crosstalk (Fig. 4(b)). On the contrary, when using a mixture of two DNA fragments (labeled with Cy3 and Atto655), for which the sequences are complementary and that have been hybridized, a significant cross correlation amplitude is observed (ACC = 57%, Fig. 4(c)), that only slightly decreases after photon selection based on their arrival time (ACC = 46%, Fig. 4(d))
3. Discussion and conclusion
We have presented here a simple optical configuration to perform nsALEX/PIE experiments at any wavelength combination within the visible spectrum, using a commercial supercontinuum source. Using this configuration, it becomes possible to benefit from the advantages offered by these alternating laser excitation technologies, such as: removing the cross-talk effects that complicate the interpretation of FCCS experiments, thus permitting the measurement of weaker interactions [11,12] ; removing spectral crosstalk in multicoulour fluorescence imaging ; separating in spFRET experiments the complexes that have a low FRET efficiency from those where the acceptor is inactive or absent [10,11].
In the setup presented here, four detection channels are used, but in principle only two channels are needed to perform PIE / FCCS experiments. However, using four channels offers several advantages. First, it allows a direct hardware-based correction for the spurious effects due to detector afterpulsing. Indeed, cross correlating the signals from two spectrally equivalent detectors removes the large autocorrelation signal observed at short time scales (typically <1µs) in the autocorrelation curves arising from detector afterpulsing . Second, by using a polarizing beamsplitter in the detection module (BS2, Fig. 1) and polarization optics in the excitation module to polarize the excitation beam, it becomes possible to use this setup to perform multiparameter fluorescence detection (MFD [22,28], ), and MFP combined with PIE . These techniques enable accurate determination of FRET efficiencies on single diffusing molecules, and thereby a possible quantification of the structural dynamics of these biomolecules on a nanosecond to millisecond timescale. We would also like to point out that we have successfully modified the setup presented here in order to be able to perform single color excitation MFD experiments at twice the frequency of the supercontinuum source (i.e. 40MHz). This has been achieved by placing the 532/10 bandpass filter directly at the output of the supercontinuum source, and by adjusting the delayed path length so that the two pulses are interleaved with a delay of exactly 25ns. This configuration results in increasing the photon yield per molecule, or decreasing the photobleaching .
The optical setup presented here can also be used to perform Fluorescence Lifetime Correlation Spectroscopy (FLCS) [13,14], a method consisting in using the excited state lifetime information to separate the autocorrelation function of individual components of a mixture of fluorophores. This method also removes some parasitic contributions such as scattered light from the correlation curves (that typically lowers the amplitude of the correlation at low fluorophores concentrations). It allows as well efficient removal of detector afterpulsing when only one detector per channel is used . Moreover the setup can be used to perform filtered FCS (fFCS) experiments, a technique that uses MFD data sets to create species-specific filters based on lifetime, spectral, and polarization information, and measure binding processes and fast conformational dynamics within diffusing molecules . Finally, our setup can be modified to measure the rotational diffusion of macromolecules, by using the polarization-sensitive PIE-FCS method presented in . It simply requires to generate two pulses streams (at the same wavelength), with orthogonal linear polarizations, instead of using two identical synchronized pulsed lasers with orthogonal polarizations, as previously described .
In conclusion, we show that it is possible to perform PIE-FCS and related techniques, using a supercontinuum laser source, for a cost equivalent to two pulsed picosecond sources and their drivers. However, the supercontinuum source configuration offers a much higher level of versatility, since changing the excitation wavelengths simply requires switching between interference filters, rather than require to purchase and install additional lasers and driver modules.
This work by supported by the GIS « IBiSA: Infrastructures en Biologie Sante et Agronomie », a “Chercheur d’avenir” grant to E.M. from the Région Languedoc-Roussillon, and a doctoral grant from the Ministère de la Recherche to L.O. We thank Louis-Simon Rameau for his help in the initial phase of this project, and Ted Laurence (LLNL) and Antoine Le Gall (CBS) for their help with the FCS algorithm.
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