Temperature-dependent conformations of a membrane supported zinc porphyrin tweezer by 2D fluorescence spectroscopy

Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA

DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.

Light Emission from Vibronic Polaritons in Coupled Metalloporphyrin-Multimode Cavity Systems

In this study, we explore how one can use cavity polariton formation and a non-Condon vibronic coupling mechanism to form a type of hybrid light-matter state we denote as Herzberg-Teller (HT) vibronic polaritons. We use simple models to define the basic characteristics of these hybrid light-matter excitations including their dispersive energies. Experimentally, we find evidence of HT polaritons in the light emission spectra from copper(II) tetraphenylporphyrin (CuTPP) molecules strongly coupled to both single and multimode Fabry-Perot resonator structures. For specific resonator designs, we find evidence of significant enhancement of light emission from a short-lived sing-doublet state of CuTPP, which couples to a higher energy singlet state via a non-Condon vibronic mechanism. The results of a two-state model support the conclusion that this enhancement and the temperature-dependent dispersion of the light emission peak energy stem from radiative relaxation into cavity photon states dressed by collective vibrations of the molecules participating in polariton formation. These results show how researchers can leverage the complex interplay of electronic and nuclear degrees of freedom in light absorbing molecules to form a vaster array of coherent light-matter states and potentially transform platforms in optoelectronic and photocatalytic technologies.

Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy

DNA replication and the related processes of genome expression require binding, assembly, and function of protein complexes at and near single-stranded (ss)-double-stranded (ds) DNA junctions. These central protein-DNA interactions are likely influenced by thermally induced conformational fluctuations of the DNA scaffold across an unknown distribution of functionally relevant states to provide regulatory proteins access to properly conformed DNA binding sites. Thus, characterizing the nature of conformational fluctuations and the associated structural disorder at ss-dsDNA junctions is critical for understanding the molecular mechanisms of these central biological processes. Here, we describe spectroscopic studies of model ss-dsDNA fork constructs that contain dimers of "internally labeled" cyanine (iCy3) chromophore probes that have been rigidly inserted within the sugar-phosphate backbones of the DNA strands. Our combined analyses of absorbance, circular dichroism, and two-dimensional fluorescence spectroscopy permit us to characterize the local conformational parameters and conformational distributions. We find that the DNA sugar-phosphate backbones undergo abrupt successive changes in their local conformations-initially from a right-handed and ordered DNA state to a disordered splayed-open structure and then to a disordered left-handed conformation-as the dimer probes are moved across the ss-dsDNA junction. Our results suggest that the sugar-phosphate backbones at and near ss-dsDNA junctions adopt specific position-dependent local conformations and exhibit varying extents of conformational disorder that deviate widely from the Watson-Crick structure. We suggest that some of these conformations can function as secondary-structure motifs for interaction with protein complexes that bind to and assemble at these sites.

Multidimensional electronic spectroscopy in high-definition-Combining spectral, temporal, and spatial resolutions

Over the past two decades, coherent multidimensional spectroscopies have been implemented across the terahertz, infrared, visible, and ultraviolet regions of the electromagnetic spectrum. A combination of coherent excitation of several resonances with few-cycle pulses, and spectral decongestion along multiple spectral dimensions, has enabled new insights into wide ranging molecular scale phenomena, such as energy and charge delocalization in natural and artificial light-harvesting systems, hydrogen bonding dynamics in monolayers, and strong light-matter couplings in Fabry-Pérot cavities. However, measurements on ensembles have implied signal averaging over relevant details, such as morphological and energetic inhomogeneity, which are not rephased by the Fourier transform. Recent extension of these spectroscopies to provide diffraction-limited spatial resolution, while maintaining temporal and spectral information, has been exciting and has paved a way to address several challenging questions by going beyond ensemble averaging. The aim of this Perspective is to discuss the technological developments that have eventually enabled spatially resolved multidimensional electronic spectroscopies and highlight some of the very recent findings already made possible by introducing spatial resolution in a powerful spectroscopic tool.

Coherent 2D electronic spectroscopy with complete characterization of excitation pulses during all scanning steps

Coherent two-dimensional (2D) electronic spectroscopy has become a standard tool in ultrafast science. Thus it is relevant to consider the accuracy of data considering both experimental imperfections and theoretical assumptions about idealized conditions. It is already known that chirped excitation pulses can affect 2D line shapes. In the present work, we demonstrate performance-efficient, automated characterization of the full electric field of each individual multipulse sequence employed during a 2D scanning procedure. Using Fourier-transform spectral interferometry, we analyze how the temporal intensity and phase profile varies from scanning step to scanning step and extract relevant pulse-sequence parameters. This takes into account both random and systematic variations during the scan that may be caused, for example, by femtosecond pulse-shaping artifacts. Using the characterized fields, we simulate and compare 2D spectra obtained with idealized and real shapes obtained from an LCD-based pulse shaper. Exemplarily, we consider fluorescence of a molecular dimer and multiphoton photoemission of a plasmonic nanoslit. The deviations from pulse-shaper artifacts in our specific case do not distort strongly the population-based multidimensional data. The characterization procedure is applicable to other pulses-shaping technologies or excitation geometries, including also pump-probe geometry with multipulse excitation and coherent detection, and allows for accurate consideration of realistic optical excitation fields at all inter-pulse time-delays.

Phosphorescent palladium-tetrabenzoporphyrin indicators for immunosensing of small molecules with a novel optical device

Small-molecule detection is important for many applications including clinical diagnostics, drug discovery, environmental screening, and food technology. Current techniques suffer from various limitations including cost, complex sample processing, massive instrumentation, and need for expertise. To overcome these limitations, a new optical immunosensing assay for the detection of small molecules was developed and assessed with the targets estrone (E1) and estradiol (E2). For this purpose, phosphorescent indicators were designed based on the tetrabenzoporphyrin skeleton directly linked to E1 or E2, or attached through a linker, with phosphorescence lifetimes in the range of ~100-~300 μs. The assay is an indicator displacement assay (IDA). The best performances of our optical immunosensor were obtained with the indicators E1-L-Por and E2-L-Por. As they bound to specific polyclonal antibodies, their phosphorescence (τ ~200 μs) was quenched. When an endogenous competitor was added, the indicator was displaced, and the phosphorescence was immediately recovered. These effects were measured with a new optical device, described here, and able to detect picograms of luminescent molecules emitting in the NIR range, simply by measuring phosphorescence decay. This radical switch-off/switch on process demonstrates that E1-L-Por and E2-L-Por are good candidates for in vivo and in vitro immunosensing of E1 and E2. Importantly, the present immunosensing assay can be easily adapted to other small molecules such as other hormones and drugs.

Monitoring the evolution of intersite and interexciton coherence in electronic excitation transfer via wave-packet interferometry

We detail an experimental strategy for tracking the generation and time-development of electronic coherence within the singly excited manifold of an energy-transfer dimer. The technique requires that the two monomers have nonparallel electronic transition-dipole moments and that these possess fixed orientations in space. It makes use of two-dimensional wave-packet interferometry (WPI or whoopee) measurements in which the A, B, C, and D pulses have respective polarizations e, e, e, and e'. In the case of energy-transfer coupling that is weak or strong compared to electronic-nuclear interactions, it is convenient to follow the evolution of intersite or interexciton coherence, respectively. Under weak coupling, e could be perpendicular to the acceptor chromophore's transition dipole moment and the unit vector e' would be perpendicular to the donor's transition dipole. Under strong coupling, e could be perpendicular to the ground-to-excited transition dipole to the lower exciton level and e' would be perpendicular to the ground-to-excited transition dipole to the upper exciton level. If the required spatial orientation can be realized for an entire ensemble, experiments of the kind proposed could be performed by either conventional four-wave-mixing or fluorescence-detected WPI methods. Alternatively, fluorescence-detected whoopee experiments of this kind could be carried out on a single energy-transfer dimer of fixed orientation. We exhibit detailed theoretical expressions for the desired WPI signal, explain the physical origin of electronic coherence detection, and show calculated observed-coherence signals for model dimers with one, two, or three internal vibrational modes per monomer and both weak and strong energy-transfer coupling.

Simulating Fluorescence-Detected Two-Dimensional Electronic Spectroscopy of Multichromophoric Systems

We present a theory for modeling fluorescence-detected two-dimensional electronic spectroscopy of multichromophoric systems. The theory is tested by comparison of the predicted spectra of the light-harvesting complex LH2 with experimental data. A qualitative explanation of the strong cross-peaks as compared to conventional two-dimensional electronic spectra is given. The strong cross-peaks are attributed to the clean ground-state signal that is revealed when the annihilation of exciton pairs created on the same LH2 complex cancels oppositely signed signals from the doubly excited state. This annihilation process occurs much faster than the nonradiative relaxation. Furthermore, the line shape difference is attributed to slow dynamics, exciton delocalization within the bands, and intraband exciton-exciton annihilation. This is in line with existing theories presented for model systems. We further propose the use of time-resolved fluorescence-detected two-dimensional spectroscopy to study state-resolved exciton-exciton annihilation.

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3)₂ that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)-single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)₂-DNA construct can be systematically varied with temperature below the ds-ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3)₂ dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)₂ dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)₂-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.

Fluorescence-Detected Two-Quantum and One-Quantum-Two-Quantum 2D Electronic Spectroscopy

We demonstrate two-quantum (2Q) coherent two-dimensional (2D) electronic spectroscopy using a shot-to-shot-modulated pulse shaper and fluorescence detection. Broadband collinear excitation is realized with the supercontinuum output of an argon-filled hollow-core fiber, enabling us to excite multiple transitions simultaneously in the visible range. The 2Q contribution is extracted via a three-pulse sequence with 16-fold phase cycling and simulated employing cresyl violet as a model system. Furthermore, we report the first experimental realization of one-quantum-two-quantum (1Q-2Q) 2D spectroscopy, offering less congested spectra as compared with the 2Q implementation. We avoid scattering artifacts and nonresonant solvent contributions by using fluorescence as the observable. This allows us to extract quantitative information about doubly excited states that agree with literature expectations. The high sensitivity and background-free nature of fluorescence detection allow for a general applicability of this method to many other systems.

Simple Quantum Dynamics with Thermalization

In this paper, we introduce two simple quantum dynamics methods. One is based on the popular surface-hopping method, and the other is based on rescaling of the propagation on the bath ground-state potential surface. The first method is special, as it avoids specific feedback from the simulated quantum system to the bath and can be applied for precalculated classical trajectories. It is based on the equipartition theorem to determine if hops between different potential energy surfaces are allowed. By comparing with the formally exact Hierarchical Equations Of Motion approach for four model systems we find that the method generally approximates the quantum dynamics toward thermal equilibrium very well. The second method is based on rescaling of the nonadiabatic coupling and also neglect the effect of the state of the quantum system on the bath. By the nature of the approximations, they cannot reproduce the effect of bath relaxation following excitation. However, the methods are both computationally more tractable than the conventional fewest switches surface hopping, and we foresee that the methods will be powerful for simulations of quantum dynamics in systems with complex bath dynamics, where the system-bath coupling is not too strong compared to the thermal energy.

Fifty years of DNA "breathing": Reflections on old and new approaches

The coding sequences for genes, and much other regulatory information involved in genome expression, are located 'inside' the DNA duplex. Thus the "macromolecular machines" that read-out this information from the base sequence of the DNA must somehow access the DNA "interior." Double-stranded (ds) DNA is a highly structured and cooperatively stabilized system at physiological temperatures, but is also only marginally stable and undergoes a cooperative "melting phase transition" at temperatures not far above physiological. Furthermore, due to its length and heterogeneous sequence, with AT-rich segments being less stable than GC-rich segments, the DNA genome 'melts' in a multistate fashion. Therefore the DNA genome must also manifest thermally driven structural ("breathing") fluctuations at physiological temperatures that should reflect the heterogeneity of the dsDNA stability near the melting temperature. Thus many of the breathing fluctuations of dsDNA are likely also to be sequence dependent, and could well contain information that should be "readable" and useable by regulatory proteins and protein complexes in site-specific binding reactions involving dsDNA "opening." Our laboratory has been involved in studying the breathing fluctuations of duplex DNA for about 50 years. In this "Reflections" article we present a relatively chronological overview of these studies, starting with the use of simple chemical probes (such as hydrogen exchange, formaldehyde, and simple DNA "melting" proteins) to examine the local stability of the dsDNA structure, and culminating in sophisticated spectroscopic approaches that can be used to monitor the breathing-dependent interactions of regulatory complexes with their duplex DNA targets in "real time."

Time resolved structural dynamics of butadiyne-linked porphyrin dimers

In this work, the timescales and mechanisms associated with the structural dynamics of butadiyne-linked porphyrin dimers are investigated through time resolved narrowband pump/broadband probe transient absorption spectroscopy. Our results confirm previous findings that the broadening is partly due to a distribution of structures with different (dihedral) angular conformations. Comparison of measurements with excitations on the red and blue sides of the Q-band unravel the ground and excited state conformational re-equilibration timescales. Further comparison to a planarized dimer, through the addition of a ligand, provides conclusive evidence for the twisting motion performed by the porphyrin dimer in solution.