Fluorescence detected linear dichroism spectroscopy: A selective and sensitive probe for fluorophores in flow-oriented systems

Advantages of a synchrotron light source for fluorescence-detected linear dichroism

Fluorescence-detected linear dichroism (FD-LD) enables one to collect linear dichroism spectra for oriented fluorophores in the presence of other absorbing species and light scattering. The experiment proceeds by scanning the excitation wavelength and using a filter to collect only emitted photons from the fluorophore. Thus, it has the potential to give data with enhanced selectivity and quality. By using a synchrotron radiation light source and fluorescence-detection, we show data for a range of fluorophores in different orienting environments. Film and flow-oriented FD-LD spectra were collected down to 170 nm. Even for flow-oriented liposomes, we have data collected down to 210 nm. For strongly scattering samples, for example, liposomes, FD-LD has the clear advantage that scattering is absent for the longer wavelength fluorescence photons. The collimated and smaller beam size of the synchrotron radiation also gives rise to sharper and more well-defined features in the spectra.

Linear Dichroism Measurements for the Study of Protein-DNA Interactions

Linear dichroism (LD) is a differential polarized light absorption spectroscopy used for studying filamentous molecules such as DNA and protein filaments. In this study, we review the applications of LD for the analysis of DNA-protein interactions. LD signals can be measured in a solution by aligning the sample using flow-induced shear force or a strong electric field. The signal generated is related to the local orientation of chromophores, such as DNA bases, relative to the filament axis. LD can thus assess the tilt and roll of DNA bases and distinguish intercalating from groove-binding ligands. The intensity of the LD signal depends upon the degree of macroscopic orientation. Therefore, DNA shortening and bending can be detected by a decrease in LD signal intensity. As examples of LD applications, we present a kinetic study of DNA digestion by restriction enzymes and structural analyses of homologous recombination intermediates, i.e., RecA and Rad51 recombinase complexes with single-stranded DNA. LD shows that the DNA bases in these complexes are preferentially oriented perpendicular to the filament axis only in the presence of activators, suggesting the importance of organized base orientation for the reaction. LD measurements detect DNA bending by the CRP transcription activator protein, as well as by the UvrB DNA repair protein. LD can thus provide information about the structures of protein-DNA complexes under various conditions and in real time.

Flow Linear Dichroism of Protein-Membrane Systems

Linear dichroism (LD) is the differential absorbance of light polarized parallel and perpendicular to an orientation direction. Any oriented sample will show a signal in its electronic as well as vibrational transitions. Model membrane small unilamellar vesicles or liposomes provide an oriented system when they are subject to shear flow in a Couette or other type of flow cell. Anything, including peptides and proteins, that is bound to the liposome also gives an LD signal whereas unbound analytes are invisible. Flow LD is the ideal technique for determining the orientation of different chromophores with respect to the membrane normal. To illustrate the power of the method, data for diphenyl hexatriene, fluorene, antimicrobial peptides (aurein 2.5 and gramicidin), are considered as well as another common chromophore, fluorene, often used to increase the hydrophobicity and hence membrane binding of peptides. How LD can be used both for geometry, structure analysis and probing kinetic processes is considered. Kinetic analysis usually involves identifying binding (appearance of an LD signal), insertion (sign change), often followed by loss of signal, if the inserted protein or peptide disrupts the membrane .

Spectroscopy of model-membrane liposome-protein systems: complementarity of linear dichroism, circular dichroism, fluorescence and SERS

A range of membrane models have been developed to study components of cellular systems. Lipid vesicles or liposomes are one such artificial membrane model which mimics many properties of the biological system: they are lipid bilayers composed of one or more lipids to which other molecules can associate. Liposomes are thus ideal to study the roles of cellular lipids and their interactions with other membrane components to understand a wide range of cellular processes including membrane disruption, membrane transport and catalytic activity. Although liposomes are much simpler than cellular membranes, they are still challenging to study and a variety of complementary techniques are needed. In this review article, we consider several currently used analytical methods for spectroscopic measurements of unilamellar liposomes and their interaction with proteins and peptides. Among the variety of spectroscopic techniques seeing increasing application, we have chosen to discuss: fluorescence based techniques such as FRET (fluorescence resonance energy transfer) and FRAP (fluorescence recovery after photobleaching), that are used to identify localisation and dynamics of molecules in the membrane; circular dichroism (CD) and linear dichroism (LD) for conformational and orientation changes of proteins on membrane binding; and SERS (Surface Enhanced Raman Spectroscopy) as a rapidly developing ultrasensitive technique for site-selective molecular characterisation. The review contains brief theoretical basics of the listed techniques and recent examples of their successful applications for membrane studies.

Fluorescence detected linear dichroism of small molecules oriented on polyethylene film

We have previously reported a novel method for measuring the spectral properties and orientation of fluorescent probes in solution, which we denoted fluorescence-detected linear dichroism (FDLD). In this work, we expand the scope of the technique by recording the FDLD spectra of the small organic fluorophores: anthracene, 4',6-diamidino-2-phenylindole (DAPI), 1,6-diphenylhexatriene (DPH), and 4-methylphenyl benzoate (MPB), oriented on stretched oxidised polyethylene film. Much like what was observed in solution, we found that the FDLD produced a large signal enhancement compared with absorbance LD, which lowers the sample requirement for measurement. We also found that FDLD has an increased sensitivity towards the immediate environment of the chromophore, revealing oligomeric structures on the film. We believe that FDLD has the potential to reveal important properties of molecules that are obscured or unattainable when using other methods.

Light scattering corrections to linear dichroism spectroscopy for liposomes in shear flow using calcein fluorescence and modified Rayleigh-Gans-Debye-Mie scattering

The interpretation of data from absorbance spectroscopy experiments of liposomes in flow systems is often complicated by the fact that there is currently no easy way to account for scattering artefacts. This has proved particularly problematic for linear dichroism (LD) spectroscopy, which may be used to determine binding modes of small molecules, peptides and proteins to liposomes if we can extract the absorbance signal from the combined absorbance/scattering experiment. Equations for a modified Rayleigh-Gans-Debye (RGD) approximation to the turbidity (scattering) LD spectrum are available in the literature though have not been implemented. This review summarises the literature and shows how it can be implemented. The implementation proceeds by first determining volume loss that occurs when a spherical liposome is subjected to flow. Calcein fluorescence can be used for this purpose since at high concentrations (> 60 mM) it has low intensity fluorescence with maxima at 525 and 563 nm whereas at low concentrations (<1 mM) the fluorescence intensity is enhanced and the band shifts to 536 nm. The scattering calculation process yields the average axis ratios of the distorted liposome ellipsoids and extent of orientation of the liposomes in flow. The scattering calculations require methods to estimate liposome integrity, volume loss, and orientation when subjected to shear stresses under flow.