Laurence Salomé

Probing DNA conformational changes with high temporal resolution by tethered particle motion.

The tethered particle motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA molecule and detecting changes of its amplitude of movement. We discuss in this context the time resolution of TPM, which strongly depends on the particle-DNA complex relaxation time, i.e. the characteristic time it takes to explore its configuration space by diffusion. By comparing theory, simulations and experiments, we propose a calibration of TPM at the dynamical level: we analyze how the relaxation time grows with both DNA contour length (from 401 to 2080 base pairs) and particle radius (from 20 to 150 nm). Notably we demonstrate that, for a particle of radius 20 nm or less, the hydrodynamic friction induced by the particle and the surface does not significantly slow down the DNA. This enables us to determine the optimal time resolution of TPM in distinct experimental contexts which can be as short as 20 ms.

Dependence of DNA persistence length on ionic strength of solutions with monovalent and divalent salts: a joint theory-experiment study

Using high-throughput tethered particle motion single-molecule experiments, the double-stranded DNA persistence length, Lp, is measured in solutions with Na+ and Mg2+ ions of various ionic strengths, I. Several theoretical equations for Lp(I) are fitted to the experimental data, but no decisive theory is found which fits all the Lp values for the two ion valencies. Properly extracted from the particle trajectory using simulations, Lp varies from 30 to 55 nm, and is comparable to previous experimental results. For the Na+-only case, Lp is an increasing concave function of I–1, well fitted by Manning’s electrostatic stretching approach, but not by classical Odjik–Skolnick–Fixman theories with or without counterion condensation. With added Mg2+ ions, Lp shows a marked decrease at low I, interpreted as an ion–ion correlation effect, with an almost linear law in I–1, fitted by a proposed variational approach.

Membrane functional organisation and dynamic of μ-opioid receptors

The activation and signalling activity of the membrane μ-opioid receptor (MOP-R) involve interactions among the receptor, G-proteins, effectors and many other membrane or cytosolic proteins. Decades of investigation have led to identification of the main biochemical processes, but the mechanisms governing the successive protein–protein interactions have yet to be established. We will need to unravel the dynamic membrane organisation of this complex and multifaceted molecular machinery if we are to understand these mechanisms. Here, we review and discuss advances in our understanding of the signalling mechanism of MOP-R resulting from biochemical or biophysical studies of the organisation of this receptor in the plasma membrane.

Heterologous regulation of Mu-opioid (MOP) receptor mobility in the membrane of SH-SY5Y cells.

Background: MOP receptor function is presumably linked to a specific dynamic organization in the membrane. Results: Inhibition of MOP receptor signaling by NPFF2 and α2 receptors is accompanied by diffusion changes, with a particular behavior for heterodimers. Conclusion: MOP receptor function, diffusion, and confinement are subject to specific heterologous regulation by other GPCRs. Significance: Specific GPCR regulation is associated with particular dynamic organization in the membrane. The dynamic organization of G protein-coupled receptors in the plasma membrane is suspected of playing a role in their function. The regulation of the diffusion mode of the mu-opioid (MOP) receptor was previously shown to be agonist-specific. Here we investigate the regulation of MOP receptor diffusion by heterologous activation of other G protein-coupled receptors and characterize the dynamic properties of the MOP receptor within the heterodimer MOP/neuropeptide FF (NPFF2) receptor. The data show that the dynamics and signaling of the MOP receptor in SH-SY5Y cells are modified by the activation of α2-adrenergic and NPFF2 receptors, but not by the activation of receptors not described to interact with the opioid receptor. By combining, for the first time, fluorescence recovery after photobleaching at variable radius experiments with bimolecular fluorescence complementation, we show that the MOP/NPFF2 heterodimer adopts a specific diffusion behavior that corresponds to a mix of the dynamic properties of both MOP and NPFF2 receptors. Altogether, the data suggest that heterologous regulation is accompanied by a specific organization of receptors in the membrane.

A model for the molecular organisation of the IS911 transpososome

Tight regulation of transposition activity is essential to limit damage transposons may cause by generating potentially lethal DNA rearrangements. Assembly of a bona fide protein-DNA complex, the transpososome, within which transposition is catalysed, is a crucial checkpoint in this regulation. In the case of IS911, a member of the large IS3 bacterial insertion sequence family, the transpososome (synaptic complex A; SCA) is composed of the right and left inverted repeated DNA sequences (IRR and IRL) bridged by the transposase, OrfAB (the IS911-encoded enzyme that catalyses transposition). To characterise further this important protein-DNA complex in vitro, we used different tagged and/or truncated transposase forms and analysed their interaction with IS911 ends using gel electrophoresis. Our results allow us to propose a model in which SCA is assembled with a dimeric form of the transposase. Furthermore, we present atomic force microscopy results showing that the terminal inverted repeat sequences are probably assembled in a parallel configuration within the SCA. These results represent the first step in the structural description of the IS911 transpososome, and are discussed in comparison with the very few other transpososome examples described in the literature.

Probing a label-free local bend in DNA by single molecule tethered particle motion

Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of proteins. Developing a method to measure DNA bend angles that does not perturb the conformation of the DNA itself or the DNA-protein complex is a challenging task. Here, we propose a joint theory-experiment high-throughput approach to rigorously measure such bend angles using the Tethered Particle Motion (TPM) technique. By carefully modeling the TPM geometry, we propose a simple formula based on a kinked Worm-Like Chain model to extract the bend angle from TPM measurements. Using constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven 6A-tracts, we find that the sequence CA6CGG induces a bend angle of 19° ± 4°. Our method is successfully compared to more theoretically complex or experimentally invasive ones such as cyclization, NMR, FRET or AFM. We further apply our procedure to TPM measurements from the literature and demonstrate that the angles of bends induced by proteins, such as Integration Host Factor (IHF) can be reliably evaluated as well.

Transfer of hydrophobic ZnO nanocrystals to water: an investigation of the transfer mechanism and luminescent properties

We investigated the “interdigitated double layer” strategy, with the objective to transfer to water hydrophobic photoluminescent ZnO nanocrystals (Ncs) stabilized by a hydrophobic ligand (octylamine). This strategy relies on the formation of a double layer around the Ncs by interdigitation of an added surfactant within the alkyl chains of the pristine ligand. Various surfactants were evaluated and, surprisingly, transfer could only be achieved with a limited choice of molecular structures. Among them, the family of glycolic acid ethoxylate ethers surfactant yielded transfers up to 60%. The molecular organization of the organic coating in water was characterized using dynamic light scattering, photoluminescence and NMR (including DOSY and NOESY). Our results suggest that the success of this transfer strategy depends on a subtle interplay of interactions between the added surfactant, the ligand and the surface of the Ncs. The ZnO Ncs exhibit a strong luminescence in water.

Oligomeric and polymeric surfactants for the transfer of luminescent ZnO nanocrystals to water

The water dispersion of luminescent nanocrystals (NCs) synthesized in organic solvent by encapsulation in a surfactant bilayer is a promising strategy for preserving the optical properties of NCs. The phase transfer of highly monodispersed ZnO NCs using the monomer, dimer, trimer and polymer of a series of alkyl ammonium surfactants is compared. Transfer yields over 60% could be obtained with the oligomers and the polymer. In contrast, we observed no measurable transfer using the single chain surfactant. NMR spectroscopy, including DOSY and NOESY, demonstrated that increasing the oligomerization number ameliorates the stability within the coating bilayer. The NCs exhibit a strong luminescence in water and show long term chemical and photo-chemical stability.

Single Particle Tracking reveals two distinct environments for CD4 receptors at the surface of living T lymphocytes

We investigated the lateral diffusion of the HIV receptor CD4 at the surface of T lymphocytes at 20°C and 37°C by Single Particle Tracking using Quantum Dots. We found that the receptors presented two major distinct behaviors that were not equally affected by temperature changes. About half of the receptors showed a random diffusion with a diffusion coefficient increasing upon raising the temperature. The other half of the receptors was permanently or transiently confined with unchanged dynamics on raising the temperature. These observations suggest that two distinct subpopulations of CD4 receptors with different environments are present at the surface of living T lymphocytes.

How does temperature impact the conformation of single DNA molecules below melting temperature

Abstract The double stranded DNA molecule undergoes drastic structural changes during biological processes such as transcription during which it opens locally under the action of RNA polymerases. Local spontaneous denaturation could contribute to this mechanism by promoting it. Supporting this idea, different biophysical studies have found an unexpected increase in the flexibility of DNA molecules with various sequences as a function of the temperature, which would be consistent with the formation of a growing number of locally denatured sequences. Here, we take advantage of our capacity to detect subtle changes occurring on DNA by using high throughput tethered particle motion to question the existence of bubbles in double stranded DNA under physiological salt conditions through their conformational impact on DNA molecules ranging from several hundreds to thousands of base pairs. Our results strikingly differ from previously published ones, as we do not detect any unexpected change in DNA flexibility below melting temperature. Instead, we measure a bending modulus that remains stable with temperature as expected for intact double stranded DNA.