We describe a biophysical approach that enables changes in the structure of DNA to be followed during nucleosome formation in in vitro reconstitution with either the canonical “Widom” sequence or a judiciously mutated sequence. The rapid non-perturbing photochemical analysis presented here provides ‘snapshots’ of the DNA configuration at any given moment in time during nucleosome formation under a very broad range of reaction conditions. Changes in DNA photochemical reactivity upon protein binding are interpreted as being mainly induced by alterations in individual base pair roll angles. The results strengthen the importance of the role of an initial (H3/H4)2 histone tetramer-DNA interaction and highlight the modulation of this early event by the DNA sequence. (H3/H4)2 binding precedes and dictates subsequent H2A/H2B-DNA interactions, which are less affected by the DNA sequence, leading to the final octameric nucleosome. Overall, our results provide a novel, exciting way to investigate those biophysical properties of DNA that constitute a crucial component in nucleosome formation and stabilization.

The anisotropic shape of DNA molecules allows them to form lyotropic liquid crystals (LCs) at high concentrations. This liquid crystalline arrangement is also found in vivo (e.g., in bacteriophage capsids, bacteria or human sperm nuclei). However, the role of DNA liquid crystalline organization in living organisms still remains an open question. Here we show that in vitro, the DNA spatial structure is significantly changed in mesophases compared to non-organized DNA molecules. DNA LCs were prepared from pBluescript SK (pBSK) plasmid DNA and investigated by photochemical analysis of structural transitions (PhAST). We reveal significant differences in the probability of UV-induced pyrimidine dimer photoproduct formation at multiple loci on the DNA indicative of changes in major groove architecture.

Diamond could be an excellent support for nanodevices utilizing biomolecules if it is covered with a polymer layer immobilizing a variety of biomolecules. We report a wet method to form a 3-aminopropyltriethoxysilane (APTES) multilayer with a controlled hardness, roughness, and capacity for immobilizing protein. The method is feasible in typical biochemical laboratories where biomolecules are prepared. Atomic force microscopy (AFM) revealed that the surface geometries and nanoscopic hardness of the multilayers on an oxygen-terminated single-crystalline diamond surface depended on the dielectric constant of the solvent; the smaller the constant, the harder the layer. The hard multilayers had holes and APTES aggregates on the surfaces, while less hard ones had homogeneous surfaces with rare holes and little aggregates. The secondary deposition of APTES in a solvent with a large dielectric constant on a hard multilayer removed the holes, and further treatment of the multilayer in acidic ethanol solution diminished the aggregates. Such a surface can immobilize streptavidin with enough specificity against nonspecific adsorption using a combination of polyethylene glycol reagents. The results of a scratching test and nanoindentation test with AFM provided consistent results, suggesting some universality of the scratching test independent of the tip structure of the cantilever. The mechanism of formation of multilayers on the diamond surface and their binding to it is discussed.