General Strategy for the Design of DNA Coding Sequences Applied to Nanoparticle Assembly.

The DNA-directed assembly of nano-objects has been the subject of many recent studies as a means to construct advanced nanomaterial architectures. Although much experimental in silico work has been presented and discussed, there has been no in-depth consideration of the proper design of single-strand sticky termination of DNA sequences, noted as ssST, which is important in avoiding self-folding within one DNA strand, unwanted strand-to-strand interaction, and mismatching. In this work, a new comprehensive and computationally efficient optimization algorithm is presented for the construction of all possible DNA sequences that specifically prevents these issues. This optimization procedure is also effective when a spacer section is used, typically repeated sequences of thymine or adenine placed between the ssST and the nano-object, to address the most conventional experimental protocols. We systematically discuss the fundamental statistics of DNA sequences considering complementarities limited to two (or three) adjacent pairs to avoid self-folding and hybridization of identical strands due to unwanted complements and mismatching. The optimized DNA sequences can reach maximum lengths of 9 to 34 bases depending on the level of applied constraints. The thermodynamic properties of the allowed sequences are used to develop a ranking for each design. For instance, we show that the maximum melting temperature saturates with 14 bases under typical solvation and concentration conditions. Thus, DNA ssST with optimized sequences are developed for segments ranging from 4 to 40 bases, providing a very useful guide for all technological protocols. An experimental test is presented and discussed using the aggregation of Al and CuO nanoparticles and is shown to validate and illustrate the importance of the proposed DNA coding sequence optimization.

The electrostatic probe: a tool for the investigation of the Aß(1-16) peptide deformations using the static modes.

We investigate the conformational changes of the Amyloid ß(1-16) peptide induced by moving Zn(2+) ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn(2+) ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.

Elementary surface chemistry during CuO/Al nanolaminate-thermite synthesis: copper and oxygen deposition on aluminum (111) surfaces.

The surface chemistry associated with the synthesis of energetic nanolaminates controls the formation of the critical interfacial layers that dominate the performances of nanothermites. For instance, the interaction of Al with CuO films or CuO with Al films needs to be understood to optimize Al/CuO nanolaminates. To that end, the chemical mechanisms occurring during early stages of molecular CuO adsorption onto crystalline Al(111) surfaces are investigated using density functional theory (DFT) calculations, leading to the systematic determination of their reaction enthalpies and associated activation energies. We show that CuO undergoes dissociative chemisorption on Al(111) surfaces, whereby the Cu and O atoms tend to separate from each other. Both Cu and O atoms form islands with different properties. Copper islanding fosters Cu insertion (via surface site exchange mechanism) into the subsurface, while oxygen islands remain stable at the surface. Above a critical local oxygen coverage, aluminum atoms are extracted from the Al surface, leading to oxygen-aluminum intermixing and the formation of aluminum oxide (γ-alumina). For Cu and O co-deposition, copper promotes oxygen-aluminum interaction by oxygen segregation and separates the resulting oxide from the Al substrate by insertion into Al and stabilization below the oxide front, preventing full mixing of Al, Cu, and O species.

Toward in silico biomolecular manipulation through static modes: atomic scale characterization of HIV-1 protease flexibility.

Probing biomolecular flexibility with atomic-scale resolution is a challenging task in current computational biology for fundamental understanding and prediction of biomolecular interactions and associated functions. This paper makes use of the static mode method to study HIV-1 protease considered as a model system to investigate the full biomolecular flexibility at the atomic scale, the screening of active site biomechanical properties, the blind prediction of allosteric sites, and the design of multisite strategies to target deformations of interest. Relying on this single calculation run of static modes, we demonstrate that in silico predictive design of an infinite set of complex excitation fields is reachable, thanks to the storage of the static modes in a data bank that can be used to mimic single or multiatom contact and efficiently anticipate conformational changes arising from external stimuli. All along this article, we compare our results to data previously published and propose a guideline for efficient, predictive, and custom in silico experiments.

Atomic scale determination of enzyme flexibility and active site stability through static modes: case of dihydrofolate reductase.

A Static Mode approach is used to screen the biomechanical properties of DHFR. In this approach, a specific external stimulus may be designed at the atomic scale granularity to arrive at a proper molecular mechanism. In this frame, we address the issues related to the overall molecular flexibility versus loop motions and versus enzymatic activity. We show that backbone motions are particularly important to ensure DHFR domain communication and notably highlight the role of a α-helix in Met20 loop motion. We also investigate the active site flexibility in different bound states. Whereas in the occluded conformation the Met20 loop is highly flexible, in the closed conformation backbone motions are no longer significant, the Met20 loop is rigidified by new intra- and intermolecular weak bonds, which stabilizes the complex and promotes the hydride transfer. Finally, while various simulations, including I14 V and I14A mutations, confirm that Ile14 is a key residue in catalytic activity, we isolate and characterize at the atomic scale how a specific intraresidue chemical group makes it possible to assist ligand positioning, to direct the nicotinamide ring toward the folate ring.

Nanoscale actuation of electrokinetic flows on thermoreversible surfaces.

We report on a novel approach for controlling nanohydrodynamic properties at the solid-liquid interfaces through the use of stimuli-responding polymer coatings. The end-tethered polymers undergo a phase separation upon external activation. The reversible change in the thickness and polarity of the grafted polymers yields in a dynamic control of the surface-generated, electrokinetic phenomena. Nonactivated, swollen polymers are thicker than the electrical double layer (EDL) and prohibit the development of an EOF even on charged surfaces. On the other hand, activated polymer chains shrink and become thinner than the EDL and allow for the EOF to build up unimpeded. We show here that, for given experimental conditions, the EOF velocity on the shrunken surface is 35 times greater than the one on the nonactivated surface. Furthermore, we reveal that coupling of such surfaces with dense arrays of thermal actuators developed in our laboratory can lead to novel micro- and nanofluidic devices.