The spectral characteristics (wavelength and line width) and the optical extinction cross-section of the longitudinal localized surface plasmon resonance (LSPR) of individual gold nanobipyramids have ...been quantitatively measured using the spatial modulation spectroscopy technique. The morphology of the same individual nanoparticles has been determined by transmission electron microscopy (TEM). The experimental results are thus interpreted with a numerical model using the TEM measured sizes of the particles as an input, and either including the substrate or assuming a mean homogeneous environment. Results are compared to those obtained for individual nanorods and also show the importance of the local environment of the particle on the detailed description of its spectral position and extinction amplitude.
The acoustic vibrations of metal nanoparticles encapsulated in a dielectric shell (Ag@SiO2) were investigated using a time-resolved femtosecond technique. The measured vibration periods significantly ...differ from those predicted for the bare metal cores and, depending on the relative core and shell sizes, were found to be either larger or smaller than them. These results show that the vibration of the whole core–shell particle is excited and detected. Moreover, vibrational periods are in excellent agreement with the predictions of a model based on continuum thermoelasticity. However, such agreement is obtained only if a good mechanical contact of the metal and dielectric parts of the core–shell particle is assumed, providing a unique way to probe this contact in multimaterial or hybrid nano-objects.
Generation of ultra high frequency acoustic waves in water is key to nano resolution sensing, acoustic imaging and theranostics. In this context water immersed carbon nanotubes (CNTs) may act as an ...ideal optoacoustic source, due to their nanometric radial dimensions, peculiar thermal properties and broad band optical absorption. The generation mechanism of acoustic waves in water, upon excitation of both a single-wall (SW) and a multi-wall (MW) CNT with laser pulses of temporal width ranging from 5 ns down to ps, is theoretically investigated via a multiscale approach. We show that, depending on the combination of CNT size and laser pulse duration, the CNT can act as a thermophone or a mechanophone. As a thermophone, the CNT acts as a nanoheater for the surrounding water, which, upon thermal expansion, launches the pressure wave. As a mechanophone, the CNT acts as a nanopiston, its thermal expansion directly triggering the pressure wave in water. Activation of the mechanophone effect is sought to trigger few nanometers wavelength sound waves in water, matching the CNT acoustic frequencies. This is at variance with respect to the commonly addressed case of water-immersed single metallic nano-objects excited with ns laser pulses, where only the thermophone effect significantly contributes. The present findings might be of impact in fields ranging from nanoscale non-destructive testing to water dynamics at the meso to nanoscale.
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•Carbon nanotubes are suggested as ultrafast photoacoustic generators of high frequency sound waves in water.•Nanoparticles thermal expansion can generate acoustic waves in ultrafast photoacoustic processes.•Light pulse duration can switch from thermophone to mechanophone photoacoustic wave generation.
Investigations of the ultrafast acoustic response of metal nanosystems yield important information on the validity of continuous elastic mechanics at the nanoscale and also provide an optical way to ...probe nanoobject morphologies. In this context, we used femtosecond time-resolved pump–probe spectroscopy to study two classes of bimetallic nanoparticles: chemically synthesized AuAg nanospheres in water in the 20–45 nm size range, both with alloyed and segregated core–shell morphologies, and mass-selected glass-embedded PtAu core–shell nanospheres in the very small size range (2.3–2.5 nm), synthesized by physical methods. The analysis of the corresponding breathing mode periods demonstrates validity of the predictions of the continuous elastic model for bimetallic nanoobjects with the investigated sizes, morphologies and composition. Moreover, discrimination of nanoparticles internal structure (alloy or core–shell) by measurement of their acoustic response is also demonstrated.
The dynamics of supercoiled DNA play an important role in various cellular processes such as transcription and replication that involve DNA supercoiling. We present experiments that enhance our ...understanding of these dynamics by measuring the intrinsic response of single DNA molecules to sudden changes in tension or torsion. The observed dynamics can be accurately described by quasistatic models, independent of the degree of supercoiling initially present in the molecules. In particular, the dynamics are not affected by the continuous removal of the plectonemes. These results set an upper bound on the hydrodynamic drag opposing plectoneme removal, and thus provide a quantitative baseline for the dynamics of bare DNA.
Observation of DNA–protein interactions by single molecule fluorescence microscopy is usually performed by using fluorescent DNA binding agents. However, such dyes have been shown to induce cleavage ...of the DNA molecule and perturb its interactions with proteins. A new method for the detection of surface-attached DNA molecules by fluorescence microscopy is introduced in this paper. Biotin- and/or digoxigenin-modified DNA fragments are covalently linked at both extremities of a DNA molecule via sequence-specific hybridization and ligation. After the modified DNA molecules have been stretched on a glass surface, their ends are visualized by multicolor fluorescence microscopy using conjugated quantum dots (QD). We demonstrate that under carefully selected conditions, the position and orientation of individual DNA molecules can be inferred with good efficiency from the QD fluorescence signals alone. This is achieved by selecting QD pairs that have the distance and direction expected for the combed DNA molecules. Direct observation of single DNA molecules in the absence of DNA staining agent opens new possibilities in the fundamental study of DNA–protein interactions. This work also documents new possibilities regarding the use of QD for nucleic acid detection and analysis.
Dynamics of phosphodiester synthesis by DNA ligase Crut, Aurélien; Nair, Pravin A; Koster, Daniel A ...
Proceedings of the National Academy of Sciences - PNAS,
05/2008, Letnik:
105, Številka:
19
Journal Article
Recenzirano
Odprti dostop
Ligases are essential actors in DNA replication, recombination, and repair by virtue of their ability to seal breaks in the phosphodiester backbone. Ligation proceeds through a nicked DNA-adenylate ...intermediate (AppDNA), which must be sealed quickly to avoid creating a potentially toxic lesion. Here, we take advantage of ligase-catalyzed AMP-dependent incision of a single supercoiled DNA molecule to observe the step of phosphodiester synthesis in real time. An exponentially distributed number of supercoils was relaxed per successful incision-resealing event, from which we deduce the torque-dependent ligation probability per DNA swivel. Premature dissociation of ligase from nicked DNA-adenylate accounted for almost equal to10% of the observed events. The ability of ligase to form a C-shaped protein clamp around DNA is a key determinant of ligation probability per turn and the stability of the ligase-AppDNA intermediate. The estimated rate of phosphodiester synthesis by DNA ligase (400 s⁻¹) is similar to the high rates of phosphodiester synthesis by replicative DNA polymerases.
Modification of the plasmonic response of a metal nano‐object due to interaction with a substrate is experimentally investigated measuring the quantitative optical extinction spectra of individual ...nano‐objects with various elongated shapes (bipyramids and rods) deposited on a dielectric (silica) or absorbing (carbon) membrane. Apart from the expected dependence of the nanoparticle surface plasmon resonance (SPR) frequency on the nature of the substrate, large substrate and particle shape dependent modifications of its SPR width are demonstrated. These dependencies are ascribed to strong localization of the electromagnetic field associated with the longitudinal SPR of an elongated nano‐object around its tips, leading to different interaction with the substrate depending on the particle shape and 3D orientation relative to the substrate. Both parameters have been precisely determined by electron tomography, permitting excellent reproduction of the experimental data. Experiments performed on silver‐encapsulated bipyramids, whose shape evolves from a pyramidal one towards a cylindrical one, further confirm this effect.
By combining spatial modulation spectroscopy, 3D electron tomography, and numerical simulations, the plasmonic response of individual elongated nanoparticles deposited on a dielectric or absorbing substrate is quantitatively investigated. The nanoparticle interaction with the underlying substrate is strongly affected by particle shape, the particle–substrate distance, and the 3D particle orientation relative to the substrate.
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