Adaptation of the base-paired double-helix molecular architecture to extreme pressure

Abstract

The behaviour of the d(GGTATACC) oligonucleotide has been investigated by X-ray crystallography at 295 K in the range from ambient pressure to 2 GPa (∼20 000 atm). Four 3D-structures of the A-DNA form (at ambient pressure, 0.55, 1.09 and 1.39 GPa) were refined at 1.60 or 1.65 Å resolution. In addition to the diffraction pattern of the A-form, the broad meridional streaks previously explained by occluded B-DNA octamers within the channels of the crystalline A-form matrix were observed up to at least 2 GPa. This work highlights an important property of nucleic acids, their capability to withstand very high pressures, while keeping in such conditions a nearly invariant geometry of base pairs that store and carry genetic information. The double-helix base-paired architecture behaves as a molecular spring, which makes it especially adapted to very harsh conditions. These features may have contributed to the emergence of a RNA World at prebiotic stage.

Hydrostatic and osmotic pressure study of the RNA hydration

“…FTIR spectra of yeast tRNA Phe recorded up to 1,400 MPa showed an increase of molecule hydration and some conformational changes [33]. Similarly analysis of DNA at pressure up to 1,380 MPa showed only subtle changes in its structure and increase of the number of bound water molecules from 57 to 76 [34]. However, change in the number of water molecules associated with tRNA Phe must be accompanied by change in the nucleic acid conformation.

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The many twists and turns of DNA: template, telomere, tool, and target

“…In the first, the structure of the duplex [d(GGTATACC)] 2 was determined at 295K at ambient pressure as well as at 0.55, 1.09 and 1.39 GPa to ca. 1.6 Å resolution [39] (2pkv, 2pl4, 2pl8 and 2plb). The only notable change was a continuous and smooth shortening of the duplex that could be monitored even in the 1.5 to 2 GPa range where the crystalline order was eventually lost.…”

“…However, the overall relatively minor consequences provide an indication of the capability of nucleic acid duplexes to withstand even high-level pressures. Although we have no precise knowledge of the conditions that RNA duplexes were exposed to at the prebiotic stage, the picture of RNA as a molecular spring that is able to adapt to harsh conditions is an attractive one [39]. …”

High pressure macromolecular crystallography for structural biology: a review

“…Crystals of the d(GGTATACC) oligonucleotide were investigated by X-ray crystallography from ambient pressure to 2 GPa [72]. Four structures of the A-DNA form (at ambient pressure, 0.55, 1.09 and 1.39 GPa) were refined at 1.60 or 1.65 Å resolution in P6 1 space group.…”