Base Orientation of Second DNA in RecA·DNA Filaments. Analysis by combination of linear dichroism and small angle neutron scattering in flow-oriented solution

To gain insight into the mechanism of pairing two complementary DNA strands by the RecA protein, we have determined the nucleobase orientation of the first and the second bound DNA strands in the RecA·DNA filament by combined measurements of linear dichroism and small angle neutron scattering on flow-oriented samples. An etheno-modified DNA, poly(depsilon A) was adapted as the first DNA and an oligo(dT) as the second DNA, making it possible to distinguish between the linear dichroism signals of the two DNA strands. The results indicate that binding of the second DNA does not alter the nucleobase orientation of the first bound strand and that the bases of the second DNA are almost coplanar to the bases of the first strand although somewhat more tilted (60 degrees relative to the fiber axis compared with 70 degrees for the first DNA strand). Similar results were obtained for the RecA·DNA complex formed with unmodified poly(dA) and oligo(dT). An almost coplanar orientation of nucleobases of two DNA strands in a RecA-DNA filament would facilitate scanning for, and recognition of, complementary base sequences. The slight deviation from co-planarity could increase the free energy of the duplex to facilitate dissociation in case of mismatching base sequences

Multi-lamellar vesicle formation in a long-chain nonionic surfactant: C16E4/D2O system

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Structure and enzymatic accessibility of leaf and stem from wheat straw before and after hydrothermal pretreatment

BACKGROUND: Biomass recalcitrance is affected by a number of chemical, physical and biological factors. In this study we looked into the differences in recalcitrance between two major anatomical fractions of wheat straw biomass, leaf and stem. A set of twenty-one wheat cultivars was fractionated and illustrated the substantial variation in leaf-to-stem ratio between cultivars. The two fractions were compared in terms of chemical composition, enzymatic convertibility, cellulose crystallinity and glucan accessibility. The use of water as a probe for assessing glucan accessibility was explored using low field nuclear magnetic resonance and infrared spectroscopy in combination with hydrogen-deuterium exchange. RESULTS: Leaves were clearly more degradable by lignocellulolytic enzymes than stems, and it was demonstrated that xylose removal was more linked to glucose yield for stems than for leaves. Comparing the locations of water in leaf and stem by low field NMR and FT-IR revealed that the glucan hydroxyl groups in leaves were more accessible to water than glucan hydroxyl groups in stems. No difference in crystallinity between leaf and stem was observed using wide angle x-ray diffraction. Hydrothermal pretreatment increased the accessibility towards water in stems but not in leaves. The results in this study indicate a correlation between the accessibility of glucan to water and to enzymes. CONCLUSIONS: Enzymatic degradability of wheat straw anatomical fractions can be indicated by the accessibility of the hydroxyl groups to water. This suggests that water may be used to assess glucan accessibility in biomass samples