Measurement of two-photon excitation spectra of fluorescent proteins with nonlinear Fourier-transform spectroscopy

Improving Spectral, Spatial, and Mechanistic Resolution Using Fourier Transform Nonlinear Optics: A Tutorial Review

Fourier transform nonlinear optics (FT-NLO) is a powerful experimental physical chemistry tool that provides insightful spectroscopic and imaging data. FT-NLO has revealed key steps in both intramolecular and intermolecular energy flow. Using phase-stabilized pulse sequences, FT-NLO is employed to resolve coherence dynamics in molecules and nanoparticle colloids. Recent advances in time-domain NLO interferometry using collinear beam geometries makes determination of molecular and material linear and nonlinear excitation spectra, homogeneous line width, and nonlinear excitation pathways straightforward. When combined with optical microscopy, rapid acquisition of hyperspectral images with the information content of FT-NLO spectroscopy is possible. With FT-NLO microscopy, molecules and nanoparticles colocated within the optical diffraction limit can be distinguished based on their excitation spectra. The suitability of certain nonlinear signals for statistical localization present exciting prospects for using FT-NLO to visualize energy flow on chemically relevant length scales. In this tutorial review, descriptions of FT-NLO experimental implementations are provided along with theoretical formalisms for obtaining spectral information from time-domain data. Select case studies that illustrate the use of FT-NLO are presented. Finally, strategies for extending super-resolution imaging capabilities based on polarization-selective spectroscopy are offered.

Achieving sub-diffraction spatial resolution using combined Fourier transform spectroscopy and nonlinear optical microscopy

Fourier transform nonlinear optical microscopy is used to perform nonlinear spectroscopy of single gold nanorods in an imaging platform, which enables sub-diffraction spatial resolution. The nonlinear optical signal is detected as a function of the time delay between two phase-locked pulses, forming an interferogram that can be used to retrieve the resonant response of the nanoparticles. Detection of the nonlinear signal through a microscopy platform enables wide-field hyperspectral imaging of the longitudinal plasmon resonances in individual gold nanorods. Super-resolution capabilities are demonstrated by distinguishing multiple nanorods that are co-located within the optical diffraction limit and are spatially separated by only tens of nanometers. The positions and resonance energies obtained through Fourier transform nonlinear optical microscopy agree with the relative positions and aspect ratios deduced from electron microscopy.

Identifying subpopulations in multicellular systems by quantitative chemical imaging using label-free hyperspectral CARS microscopy

Quantitative hyperspectral coherent Raman scattering microscopy merges imaging with spectroscopy and utilises quantitative data analysis algorithms to extract physically meaningful chemical components, spectrally and spatially-resolved, with sub-cellular resolution. This label-free non-invasive method has the potential to significantly advance our understanding of the complexity of living multicellular systems. Here, we have applied an in-house developed hyperspectral coherent anti-Stokes Raman scattering (CARS) microscope, combined with a quantitative data analysis pipeline, to imaging living mouse liver organoids as well as fixed mouse brain tissue sections xenografted with glioblastoma cells. We show that the method is capable of discriminating different cellular sub-populations, on the basis of their chemical content which is obtained from an unsupervised analysis, i.e. without prior knowledge. Specifically, in the organoids, we identify sub-populations of cells at different phases in the cell cycle, while in the brain tissue, we distinguish normal tissue from cancer cells, and, notably, tumours derived from transplanted cancer stem cells versus non-stem glioblastoma cells. The ability of the method to identify different sub-populations was validated by correlative fluorescence microscopy using fluorescent protein markers. These examples expand the application portfolio of quantitative chemical imaging by hyperspectral CARS microscopy to multicellular systems of significant biomedical relevance, pointing the way to new opportunities in non-invasive disease diagnostics.

What is the Optimal Size of the Quantum Region in Embedding Calculations of Two-Photon Absorption Spectra of Fluorescent Proteins?

We systematically investigate an impact of the size and content of a quantum (QM) region, treated at the density functional theory level, in embedding calculations on one- (OPA) and two-photon absorption (TPA) spectra of the following fluorescent proteins (FPs) models: Aequorea victoria green FP (avGFP) with neutral (avGFP-n) and anionic (avGFP-a) chromophore as well as Citrine FP. We find that amino acid (a.a.) residues as well as water molecules hydrogen-bonded (h-bonded) to the chromophore usually boost both OPA and TPA processes intensity. The presence of hydrophobic a.a. residues in the quantum region also non-negligibly affects both absorption spectra but decreases absorption intensity. We conclude that to reach a quantitative description of OPA and TPA spectra in multiscale modeling of FPs, the quantum region should consist of a chromophore and most of a.a. residues and water molecules in a radius of 0.30–0.35 nm (ca. 200–230 atoms) when the remaining part of the system is approximated by the electrostatic point-charges. The optimal size of the QM region can be reduced to 80–100 atoms by utilizing a more advanced polarizable embedding model. We also find components of the QM region that are specific to a FP under study. We propose that the F165 a.a. residue is important in tuning the TPA spectrum of avGFP-n but not other investigated FPs. In the case of Citrine, Y203 and M69 a.a. residues must definitely be part of the QM subsystem. Furthermore, we find that long-range electrostatic interactions between the QM region and the rest of the protein cannot be neglected even for the most extensive QM regions (ca. 350 atoms).

Assessment of Functionals for TDDFT Calculations of One- and Two-Photon Absorption Properties of Neutral and Anionic Fluorescent Proteins Chromophores

Performance of DFT functionals with different percentages of exact Hartree-Fock exchange energy (EX) is assessed for recovery of the CC2 reference one- (OPA) and two-photon absorption (TPA) spectra of fluorescent proteins chromophores in vacuo. The investigated DFT functionals, together with their EX contributions are BLYP (0%), B3LYP (20%), B1LYP (25%), BHandHLYP (50%), and CAM-B3LYP (19% at short range and 65% at long range). Our test set consists of anionic and neutral chromophores as naturally occurring in the fluorescent proteins. For the first time, we compare TDDFT and CC2 methods for higher excited states than the S₁ state, exhibiting relatively large TPA intensity. Our TDDFT results for neutral chromophores reveal an increase in excitation energies as well as TPA and OPA intensities errors, compared to CC2-derived results, as the DFT functional contains less exact exchange. The long-range-corrected CAM-B3LYP functional performs the best, closely followed by BHandHLYP, while BLYP usually significantly underestimates all investigated spectral properties, hence being the worst in reproducing the reference CC2 results. The hybrid B3LYP and B1LYP functionals can be roughly placed in between. We propose that TDDFT may underestimate the TPA intensities for neutral chromophores of fluorescent proteins due to underestimated oscillator strengths between some excited states. In the case of anionic chromophores, we find that B3LYP and B1LYP functionals overcome others in terms of reproducing CC2 excitation energies. On the other hand, however, TPA intensity is usually significantly underestimated, and in this respect, CAM-B3LYP functional seems to be again superior. In contrast to the case of neutral chromophores, it seems that a large magnitude of excited-state dipole moments or changes in dipole moments upon excitation may be the driving force behind high TPA transition moments.

Two-photon probes for in vivo multicolor microscopy of the structure and signals of brain cells

Imaging the brain of living laboratory animals at a microscopic scale can be achieved by two-photon microscopy thanks to the high penetrability and low phototoxicity of the excitation wavelengths used. However, knowledge of the two-photon spectral properties of the myriad fluorescent probes is generally scarce and, for many, non-existent. In addition, the use of different measurement units in published reports further hinders the design of a comprehensive imaging experiment. In this review, we compile and homogenize the two-photon spectral properties of 280 fluorescent probes. We provide practical data, including the wavelengths for optimal two-photon excitation, the peak values of two-photon action cross section or molecular brightness, and the emission ranges. Beyond the spectroscopic description of these fluorophores, we discuss their binding to biological targets. This specificity allows in vivo imaging of cells, their processes, and even organelles and other subcellular structures in the brain. In addition to probes that monitor endogenous cell metabolism, studies of healthy and diseased brain benefit from the specific binding of certain probes to pathology-specific features, ranging from amyloid-β plaques to the autofluorescence of certain antibiotics. A special focus is placed on functional in vivo imaging using two-photon probes that sense specific ions or membrane potential, and that may be combined with optogenetic actuators. Being closely linked to their use, we examine the different routes of intravital delivery of these fluorescent probes according to the target. Finally, we discuss different approaches, strategies, and prerequisites for two-photon multicolor experiments in the brains of living laboratory animals.

Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors

Small molecule biosensors based on Förster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.

Multimodal Nonlinear Microscopy by Shaping a Fiber Supercontinuum From 900 to 1160 nm

Nonlinear microscopy has become widely used in biophotonic imaging. Pulse shaping provides control over nonlinear optical processes of ultrafast pulses for selective imaging and contrast enhancement. In this study, nonlinear microscopy, including two-photon fluorescence, second harmonic generation, and third harmonic generation, was performed using pulses shaped from a fiber supercontinuum (SC) spanning from 900 to 1160 nm. The SC generated by coupling pulses from a Yb:KYW pulsed laser into a photonic crystal fiber was spectrally filtered and compressed using a spatial light modulator. The shaped pulses were used for nonlinear optical imaging of cellular and tissue samples. Amplitude and phase shaping the fiber SC offers selective and efficient nonlinear optical imaging over a broad bandwidth with a single-beam and an easily tunable setup.

Describing two-photon absorptivity of fluorescent proteins with a new vibronic coupling mechanism

Fluorescent proteins (FPs) are widely used in two-photon microscopy as genetically encoded probes. Understanding the physical basics of their two-photon absorption (2PA) properties is therefore crucial for creation of two-photon brighter mutants. On the other hand, it can give us better insight into molecular interactions of the FP chromophore with a complex protein environment. It is known that, compared to the one-photon absorption spectrum, where the pure electronic transition is the strongest, the 2PA spectrum of a number of FPs is dominated by a vibronic transition. The physical mechanism of such intensity redistribution is not understood. Here, we present a new physical model that explains this effect through the "Herzberg-Teller"-type vibronic coupling of the difference between the permanent dipole moments in the ground and excited states (Δμ) to the bond-length-alternating coordinate. This model also enables us to quantitatively describe a large variability of the 2PA peak intensity in a series of red FPs with the same chromophore through the interference between the "Herzberg-Teller" and Franck-Condon terms.

Two-photon excited fluorescence enhancement with broadband versus tunable femtosecond laser pulse excitation

The inverse relationship between two-photon excited fluorescence (TPEF) and laser pulse duration suggests that two-photon microscopy (TPM) performance may be improved by decreasing pulse duration. However, for ultrashort pulses of sub-10 femtosecond (fs) in duration, its spectrum contains the effective gain bandwidth of Ti:Sapphire and its central wavelength is no longer tunable. An experimental study was performed to explore this apparent tradeoff between untuned sub-10 fs transform-limited pulse (TLP) and tunable 140 fs pulse for TPEF. Enhancement factors of 1.6, 6.7, and 5.2 are measured for Indo-1, FITC, and TRITC excited by sub-10 fs TLP compared with 140 fs pulse tuned to the two-photon excitation (TPE) maxima at 730 nm, 800 nm, and 840 nm, respectively. Both degenerate (v(1) = v(2)) and nondegenerate (v(1) ≠ v(2)) mixing of sub-10 fs TLP spectral components result in its broad second-harmonic (SH) power spectrum and high spectral density, which can effectively compensate for the lack of central wavelength tuning and lead to large overlap with dye TPE spectra for TPEF enhancements. These pulse properties were also exploited for demonstrating its potential applications in multicolor imaging with TPM.

Pulse-shaping multiphoton FRET microscopy

Fluorescence Resonance Energy Transfer (FRET) microscopy is a commonly-used technique to study problems in biophysics that range from uncovering cellular signaling pathways to detecting conformational changes in single biomolecules. Unfortunately, excitation and emission spectral overlap between the fluorophores create challenges in quantitative FRET studies. It has been shown previously that quantitative FRET stoichiometry can be performed by selective excitation of donor and acceptor fluorophores. Extending this approach to two-photon FRET applications is difficult when conventional femtosecond laser sources are used due to their limited bandwidth and slow tuning response time. Extremely broadband titanium:sapphire lasers enable the simultaneous excitation of both donor and acceptor for two-photon FRET, but do so without selectivity. Here we present a novel two-photon FRET microscopy technique that employs pulse-shaping to perform selective excitation of fluorophores in live cells and detect FRET between them. Pulse-shaping via multiphoton intrapulse interference can tailor the excitation pulses to achieve selective excitation. This technique overcomes the limitation of conventional femtosecond lasers to allow rapid switching between selective excitation of the donor and acceptor fluorophores. We apply the method to live cells expressing the fluorescent proteins mCerulean and mCherry, demonstrating selective excitation of fluorophores via pulse-shaping and the detection of two-photon FRET. This work paves the way for two-photon FRET stoichiometry.

Temporal control of local plasmon distribution on Au nanocrosses by ultra-broadband femtosecond laser pulses and its application for selective two-photon excitation of multiple fluorophores

We theoretically demonstrate spatiotemporal control of local plasmon distribution on Au nanocrosses, which have different aspect ratios, by chirped ultra-broadband femtosecond laser pulses. We also demonstrate selective excitation of fluorescence proteins using this spatiotemporal local plasmon control technique for applications to two-photon excited fluorescence microscopy.

Two-photon absorption properties of fluorescent proteins

Two-photon excitation of fluorescent proteins is an attractive approach for imaging living systems. Today researchers are eager to know which proteins are the brightest and what the best excitation wavelengths are. Here we review the two-photon absorption properties of a wide variety of fluorescent proteins, including new far-red variants, to produce a comprehensive guide to choosing the right fluorescent protein and excitation wavelength for two-photon applications.

Measurement of two-photon excitation spectrum used to photoconvert a fluorescent protein (Kaede) by nonlinear Fourier-transform spectroscopy

We demonstrate the measurement of two-photon excitation (TPE) spectra, used not only for fluorescence but also for photoconversion in green-to-red photoconvertible Kaede, using nonlinear Fourier-transform spectroscopy. It was found that in unphotoconverted Kaede, the TPE spectrum for photoconversion is much different to that for green-fluorescence. This is similar to the difference between the one-photon excitation of photoconversion in the neutral form and that of green-fluorescence in the ionized form.