Kinetics of protein-release by an aptamer-based DNA nanodevice

A recently introduced DNA nanodevice can be used to selectively bind or release the protein thrombin triggered by DNA effector strands. The release process is not well described by simple first or second order reaction kinetics. Here, fluorescence resonance energy transfer and fluorescence correlation spectroscopy experiments are used to explore the kinetics of the release process in detail. To this end the influence of concentration variations and also of temperature is determined. The relevant kinetic parameters are extracted from these experiments and the kinetic behavior of the system is simulated numerically using a set of rate equations. The hydrodynamic radii of the aptamer device alone and bound to thrombin are determined as well as the dissociation constant for the aptamer device-thrombin complex. The results from the experiments and a numerical simulation support the view that the DNA effector strand first binds to the aptamer device followed by the displacement of the protein.     

Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: scaling behavior of average quantities

We study numerically the effect of sequence heterogeneity on the thermodynamic properties of a Poland-Scheraga model for DNA denaturation taking into account self-avoidance, i.e. with exponent c_p = 2.15 for the loop length probability distribution. In complement to previous on-lattice Monte Carlo like studies, we consider here off-lattice numerical calculations for large sequence lengths, relying on efficient algorithmic methods. We investigate finite size effects with the definition of an appropriate intrinsic length scale x, depending on the parameters of the model. Based on the occurrence of large enough rare regions, for a given sequence length N, this study provides a qualitative picture for the finite size behavior, suggesting that the effect of disorder could be sensed only with sequence lengths diverging exponentially with x. We further look in detail at average quantities for the particular case x = 1.3, ensuring through this parameter choice the correspondence between the off-lattice and the on-lattice studies. Taken together, the various results can be cast in a coherent picture with a crossover between a nearly pure system like behavior for small sizes , as observed in the on-lattice simulations, and the apparent asymptotic behavior indicative of disorder relevance, with an (average) correlation length exponent ν_r ≥2/d (=2).     

Modeling phase behavior for quantifying micro-pervaporation experiments

We present a theoretical model for the evolution of mixture concentrations in a micro-pervaporation device, similar to those recently presented experimentally. The described device makes use of the pervaporation of water through a thin PDMS membrane to build up a solute concentration profile inside a long microfluidic channel. We simplify the evolution of this profile in binary mixtures to a one-dimensional model which comprises two concentration-dependent coefficients. The model then provides a link between directly accessible experimental observations, such as the widths of dense phases or their growth velocity, and the underlying chemical potentials and phenomenological coefficients. It shall thus be useful for quantifying the thermodynamic and dynamic properties of dilute and dense binary mixtures.     

Multiple ionization and fragmentation of the DNA base thymine by interaction with C q+ ions

Ionization and fragmentation of the DNA base thymine upon interaction with keV C^q+ ions (q = 1 - 6) has been studied. By means of time-of-flight spectrometry of two or more thymine fragments in coincidence with an ejected electron we could investigate particular dissociation channels by means of their associated kinetic-energy-release. The fragmentation dynamics are strongly influenced by the C^q+ charge state: for low q values mainly fragmentation due to direct collisions is observed. With increasing q, electron capture becomes more important. For larger q we could identify several Coulomb explosion channels, leading to very energetic fragments.     

Free energy landscape from path-sampling: application to the structural transition in LJ38

We introduce a path-sampling scheme that allows equilibrium state-ensemble averages to be computed by means of a biased distribution of non-equilibrium paths. This non-equilibrium method is applied to the case of the 38-atom Lennard-Jones atomic cluster, which has a double-funnel energy landscape. We calculate the free energy profile along the Q₄ bond orientational order parameter. At high or moderate temperature the results obtained using the non-equilibrium approach are consistent with those obtained using conventional equilibrium methods, including parallel tempering and Wang-Landau Monte Carlo simulations. At lower temperatures, the non-equilibrium approach becomes more efficient in exploring the relevant inherent structures. In particular, the free energy agrees with the predictions of the harmonic superposition approximation.     

Correlation in a Gaussian chain with the ends fixed

We consider an ideal chain whose ends are fixed without fluctuation at different points, possibly by optical tweezers. We derive a two-point probability distribution of a corresponding random walk and explicitly calculate the scattering function. We find that the contour plot of the resulting function shows a kind of normal butterfly pattern, contaminated by wavy texture. These results are compared with some representative previous models.     

Gene delivery process in a single animal cell after femtosecond laser microinjection

Microinjection of extracellular molecules into a single animal cell was performed by an amplified femtosecond laser irradiation. When a single-shot laser pulse was focused on the plasma membrane of a single fibroblast from the mouse cell line NIH3T3 with a high-numerical aperture objective lens, a transient hole with a diameter of 1 μm was formed. The delivery process of extracellular molecules immediately after the hole formation was monitored by a fluorescence staining with fluoresceinisothiocyanate-dextran (FITC-dextran). Then the gene expression was confirmed using a DNA plasmid of an enhanced green fluorescent protein (EGFP). The gene expression was observed when the laser pulse was focused first on the cellular membrane and then on the nuclear membrane, while the gene was not expressed when the laser was focused only on the cellular membrane. On the basis of these results, the efficiency of gene delivery by the femtosecond laser microinjection and the subsequent gene expression were clarified.     

Tautomer contributions to the near UV spectrum of guanine: towards a refined picture for the spectroscopy of purine molecules

By using depopulation laser techniques, like IR-UV population labeling coupled to mass-selected R2PI detection, we confirm that four tautomers are responsible for the near UV spectroscopy (310-280 nm) of guanine: two enol and two keto forms, each pair having a 7NH and a 9NH form. Besides the UV spectroscopy of each tautomer, additional information on the excited state nature and dynamics is obtained from fluorescence studies. In particular, the quenching of fluorescence beyond 285 nm, the existence of a background absorption, as well as the existence of a strongly red-shifted component in the fluorescence emission provides evidence for a strong electronic mixing in the excited state together with an efficient non-radiative process. The details of these features are found to be tautomer-dependent. Comparison of the present results with literature data on other purine molecules, like adenine or 9-substituted guanines, enables us to propose a new insight on the spectroscopy and dynamics of the purine molecules. First, a large variability of the tautomer distribution in the gas phase is found within the purine family, in particular a molecular change, as simple as a 9-methylation on guanine, can reduce the tautomer distribution to a single species (enol form). Since the absorption spectrum is tautomer-dependent as well as substituent-dependent, it turns out that the tautomer population is one of the major parameters that control the overall shape of the UV spectrum. Second, the excited state model, often evoked in the literature, which involves electronic coupling between excited states of different natures, namely ππ^* and nπ^* states, might account for the present fluorescence measurements on guanine, providing an extensive excited state electronic mixing is assumed for these systems. Received 24 June 2002 Published online 13 September 2002     

Systematic field-theory for the hard-core one-component plasma

A continuous liquid flow in a vacuum (a liquid beam) of an aqueous solution of adenine salt containing hydrochloric acid or sodium hydroxide was irradiated with an intense pulsed IR laser at 3 μm, which is resonant to a vibrational mode related to the OH stretch vibration of H₂O. Neutral species isolated into the vacuum were ionized by a pulsed UV laser at 270 nm, and the product ions were mass-analyzed by a time-of-flight mass spectrometer. It is found that AH ₂ ^{2 + .} 2Cl^- and [A-iH] ^{i - .} iNa⁺ (i = 1-3) are isolated in the vacuum from the aqueous acidic and alkaline solutions, respectively, under irradiation of the IR laser, and undergo four-photon ionization involving decomposition and proton transfer of the intermediate species under irradiation of the UV laser. Received 1st May 2002 Published online 13 September 2002     

Solvent evaporation of spin cast films: “crust” effects

When a glassy polymer film is formed by evaporation, the region near the free surface is polymer rich and becomes glassy first, as noticed long ago by Scriven et al. We discuss the thickness of this “crust” and the time interval where it is present --before freezing of the whole film. We argue that the crust is under mechanical tension, and should form some cracks. This may be the source of the roughness observed on the final, dry films, when the solvent vapor pressure is high (and leads to thin crusts). Received 13 November 2001