Behavior of B- and Z-DNA Crystals under High Hydrostatic Pressure

Abstract

Single crystals of B-DNA and Z-DNA oligomers were analyzed under high hydrostatic pressure and their behavior was compared to the A-DNA crystals already known. The amplitude of the base compression, when compared to the A-form of DNA (0.13 Å/GPa), was higher for the Z-DNA (0.32 Å/GPa) and was the highest for the B-DNA (0.42 Å/GPa). The B-DNA crystal degraded rapidly around 400–500 MPa, while the Z-structure was more resistant, up to 1.2 GPa.

The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF

“…1; Collins et al, 2011;Barstow et al, 2008Barstow et al, , 2009van der Linden et al, 2014). Similarly, we also found that the application of pressure to some protein-ligand complexes in crystals allows a shift in the thermodynamic equilibrium towards saturation of ligand occupancies in protein binding sites, but also, in the same manner, enables the population of less stable secondary ligand-binding sites that are unpopulated at atmospheric pressure (Prange ´et al, 2022). This effect of pressure proves to be essential for dissecting enzymatic reaction intermediates in crystals and highlighting intermediate stages of ligand-protein binding processes.…”

“…In some cases, pressure also modifies the protein-protein interactions involved in crystal packing and thereby induces a change of symmetry (i.e. phase transitions; see Section 4.4; Prange ´et al, 2022).…”

“…A recent structural study involving urate oxidase (UOX) carried out at the HPMX laboratory shows that pressure can be a profitable tool to explore functional structural changes in proteins (Prange ´et al, 2022). UOX is an enzyme that catalyzes the oxidation of uric acid and is used as treatment for acute hyperuricemia.…”

A high-pressure single-crystal X-ray diffraction study of potassium guaninate hydrate, K+·C5H4N5O−·H2O

“…The A-DNA structure is less compact as compared to the two other DNA conformations because of the presence of a large central channel filled with water molecules. The more densely packed B-DNA and Z-DNA crystals collapsed when ÁV/V 0 reached 4% (at P = 0.45 GPa) and 6% (at P = 1.1 GPa), respectively (Girard et al, 2007;Prange ´et al, 2022). The pressure range of structural stability for DNA crystals is much lower than those for guaninates, especially for the potassium salt, probably because of a larger complexity and possible flexibility of structural units in the structures of DNA.…”

“…Detailed information on the effect of pressure and temperature on the intermolecular distances in biomolecules helps to rationalize the stability of extremophiles, to develop the techniques for inactivating pathogens (important for food and pharmaceutical industries), and to model the conformational changes that occur when the biomolecules are involved in biochemical reactions (Kahn et al, 2007;Fourme et al, 2009;Ascone et al, 2010;Cioni & Gabellieri, 2011;Boldyreva, 2012;Fourme et al, 2012;Wang et al, 2014;Kurpiewska et al, 2016;Colloc'h et al, 2017;Prange ´et al, 2022;Girard et al, 2022). High-pressure small-molecule crystallography can also contribute to understanding and predicting the response of biological macromolecules from model studies of crystals composed of their fragments (Boldyreva, 2012).…”