Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy andmicroscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in thesemembranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3–4 Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using themasmembrane reporters.

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy andmicroscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in thesemembranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3–4 Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using themasmembrane reporters.

Evaluation of portable Raman spectroscopy and handheld X-ray fluorescence analysis (hXRF) for the direct analysis of glyptics

In archaeometry, the advantages of a combined use of Raman spectroscopy and X-ray fluorescence spectroscopy are extensively discussed for applications such as the analysis of paintings, manuscripts, pottery, etc. Here, we demonstrate for the first time the advantage of using both techniques for analysing glyptics. These engraved gemstones or glass materials were originally used as stamps, to identify the owner, for instance on letters, but also on wine vessels. For this research, a set of 64 glyptics (42 Roman glass specimens and 22 modern ones), belonging to the collection of the museum ‘Quinta das Cruzes’ in Funchal (Madeira, Portugal), was analysed with portable Raman spectroscopy and handheld X-ray fluorescence (hXRF). These techniques were also used to confirm the gemological identification of these precious objects and can give extra information about the glass composition. Raman spectroscopy identifies the molecular composition as well as on the crystalline phases present. On the other hand, hXRF results show that the antique Roman glass samples are characterised with low Pb and Sn levels and that the modern specimens can be discriminated in two groups: lead-based and non-lead-based ones.

Uncover the mantle: rediscovering Gregório Lopes palette and technique with a study on the painting “Mater Misericordiae”

Grego´rio Lopes (c. 1490–1550) was one of the most prominent painters of the renaissance and Mannerism in Portugal. The painting “Mater Misericordiae” made for the Sesimbra Holy House of Mercy, circa 1535–1538, is one of the most significant works of the artist, and his only painting on this theme, being also one of the most significant Portuguese paintings of sixteenth century. The recent restoration provided the possibility to study materially the painting for the first time, with a multianalytical methodology incorporating portable energy-dispersive X-ray fluorescence spectroscopy, scanning electron microscopy–energy-dispersive spectroscopy, micro-X-ray diffraction, micro-Raman spectroscopy and high-performance liquid chromatography coupled to diode array and mass spectrometry detectors. The analytical study was complemented by infrared reflectography, allowing the study of the underdrawing technique and also by dendrochronology to confirm the date of the wooden panels (1535–1538). The results of this study were compared with previous ones on the painter’s workshop, and significant differences and similitudes were found in the materials and techniques used

Fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids in model membranes is connected not to lipid mobility but to probe location

Nitrobenzoxadiazole (NBD)-labeled lipids are popular fluorescent membrane probes. However, the understanding of important aspects of the photophysics of NBD remains incomplete, including the observed shift in the emission spectrum of NBD-lipids to longer wavelengths following excitation at the red edge of the absorption spectrum (red-edge excitation shift or REES). REES of NBD-lipids in membrane environments has been previously interpreted as reflecting restricted mobility of solvent surrounding the fluorophore. However, this requires a large change in the dipole moment (Dm) of NBD upon excitation. Previous calculations of the value of Dm of NBD in the literature have been carried out using outdated semi-empirical methods, leading to conflicting values. Using up-to-date density functional theory methods, we recalculated the value of Dm and verified that it is rather small (B2 D). Fluorescence measurements confirmed that the value of REES is B16 nm for 1,2-dioleoyl-sn-glycero-3- phospho-L-serine-N-(NBD) (NBD-PS) in dioleoylphosphatidylcholine vesicles. However, the observed shift is independent of both the temperature and the presence of cholesterol and is therefore insensitive to the mobility and hydration of the membrane. Moreover, red-edge excitation leads to an increased contribution of the decay component with a shorter lifetime, whereas time-resolved emission spectra of NBD-PS displayed an atypical blue shift following excitation. This excludes restrictions to solvent relaxation as the cause of the measured REES and TRES of NBD, pointing instead to the heterogeneous transverse location of probes as the origin of these effects. The latter hypothesis was confirmed by molecular dynamics simulations, from which the calculated heterogeneity of the hydration and location of NBD correlated with the measured fluorescence lifetimes/REES. Globally, our combination of theoretical and experiment-based techniques has led to a considerably improved understanding of the photophysics of NBD and a reinterpretation of its REES in particular.

RNA-FISH Technique: Probe Cocktails vs Single Probes

RNA-Fluorescence In Situ Hybridization (RNA-FISH) enables to analyze and visualize the microorganisms of interest within microbial communities in their natural environments by fluorescent labelling of specific RNA sequences. Poor accessibility or low content of the RNA target region can cause false positives/negatives due to low fluorescence of the cells. To reduce the chances of this occurring, probe cocktails – i.e. mixture of several probes that hybridize to different regions of the target RNA- has been proposed as an alternative to single probes use for increasing the Fluorescence Intensities (FI). However, is this really a good solution? The key finding of this work was that the use of probe cocktails is not always a good solution for maximizing the FI as at high concentrations the single probe EUK516-6 FAM yielded higher FI than the probe cocktails.