Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex

Locked nucleic acids (LNA), conformationally restricted nucleotide analogues, are known to enhance pairing stability and selectivity toward complementary strands. With the aim to contribute to a better understanding of the origin of these effects, the structure, thermal stability, hybridization thermodynamics, and base-pair dynamics of a full-LNA:DNA heteroduplex and of its isosequential DNA:DNA homoduplex were monitored and compared. CD measurements highlight differences in the duplex structures: the homoduplex and heteroduplex present B-type and A-type helical conformations, respectively. The pairing of the hybrid duplex is characterized, at all temperatures monitored (between 15 and 37 degrees C), by a larger stability constant but a less favorable enthalpic term. A major contribution to this thermodynamic profile emanates from the presence of a hairpin structure in the LNA single strand which contributes favorably to the entropy of interaction but leads to an enthalpy penalty upon duplex formation. The base-pair opening dynamics of both systems was monitored by NMR spectroscopy via imino protons exchange measurements. The measurements highlight that hybrid G-C base-pairs present a longer base-pair lifetime and higher stability than natural G-C base-pairs, but that an LNA substitution in an A-T base-pair does not have a favorable effect on the stability. The thermodynamic and dynamic data confirm a more favorable stacking of the bases in the hybrid duplex. This study emphasizes the complementarities between dynamic and thermodynamical studies for the elucidation of the relevant factors in binding events.

Ordering induced by chemical, thermal and mechanical constraints at solid interfaces

We know that classical thermodynamics even out of equilibrium always leads to stable situation which means degradation and consequently d sorder. Many experimental evidences in different fields show that gradation and order (symmetry breaking) during time and space evolution may appear when maintaining the system far from equilibrium. Order through fluctuations, stochastic processes which occur around critical points and dissipative structures are the fundamental background of the Prigogine-Glansdorff and Nicolis theory. The thermodynamics of macroscopic fluctuations to stochastic approach as well as the kinetic deterministic laws allow a better understanding of the peculiar fascinating behavior of organized matter. The reason for the occurence of this situation is directly related to intrinsic non linearities of the different mechanisms responsible for the evolution of the system. Moreover, when dealing with interfaces separating two immiscible phases (liquid - gas, liquid -liquid, liquid - solid, solid - solid), the situation is rather more complicated. Indeed coupling terms playing the major role in the conditions of instability arise from the peculiar singular static and dynamic properties of the surface and of its vicinity. In other words, the non linearities are not only intrinsic to classical steps involving feedbacks, but they may be imbedded with the non-autonomous character of the surface properties. In order to illustrate our goal we discuss three examples of ordering in far from equilibrium conditions: i) formation of chemical structures during the oxidation of metals and alloys; ii) formation of mechanical structures during the oxidation of metals iii) formation of patterns at a solid-liquid moving interface due to supercooling condition in a melt of alloy. © 1984, Walter de Gruyter. All rights reserved.

Surface area, porosity and water adsorption properties of fine volcanic ash particles

Our understanding on how ash particles in volcanic plumes react with coexisting gases and aerosols is still rudimentary, despite the importance of these reactions in influencing the chemistry and dynamics of a plume. In this study, six samples of fine ash (<100 μm) from different volcanoes were measured for their specific surface area, as, porosity and water adsorption properties with the aim to provide insights into the capacity of silicate ash particles to react with gases, including water vapour. To do so, we performed high-resolution nitrogen and water vapour adsorption/desorption experiments at 77 K and 303 K, respectively. The nitrogen data indicated as values in the range 1.1-2.1 m2/g, except in one case where as of 10 m2/g was measured. This high value is attributed to incorporation of hydrothermal phases, such as clay minerals, in the ash surface composition. The data also revealed that the ash samples are essentially non-porous, or have a porosity dominated by macropores with widths >500 Å All the specimens had similar pore size distributions, with a small peak centered around 50 Å These findings suggest that fine ash particles have relatively undifferentiated surface textures, irrespective of the chemical composition and eruption type. Adsorption isotherms for water vapour revealed that the capacity of the ash samples for water adsorption is systematically larger than predicted from the nitrogen adsorption as values. Enhanced reactivity of the ash surface towards water may result from (i) hydration of bulk ash constituents; (ii) hydration of surface compounds; and/or (iii) hydroxylation of the surface of the ash. The later mechanism may lead to irreversible retention of water. Based on these experiments, we predict that volcanic ash is covered by a complete monolayer of water under ambient atmospheric conditions. In addition, capillary condensation within ash pores should allow for deposition of condensed water on to ash particles before water reaches saturation in the plume. The total mass of water vapour retained by 1 g of fine ash at 0.95 relative water vapour pressure is calculated to be ∼10-2 g. Some volcanic implications of this study are discussed. © Springer-Verlag 2004.