Conformational flexibility of cyclohexene residues
Luc Van Meervelt, Koen Robeyns · Acta Crystallographica Section A Foundations of Crystallography · 2008
How life emerged on Earth remains one of the great Mysteries for mankind.Molecules with backbones forming stable double helices, held by self-association, and capable of auto-replication -and more precisely nucleotides held by Watson-Crick base pairings -were considered as the seminal building blocks of life.Many scenarios involving extreme conditions were described, all of them dealing with the extreme pressure conditions of the "primary soup" that was present on earth at prebiotic stages.High-pressure molecular crystallography (HPMX) investigation of DNA was undertaken using crystals of the d(GGTATACC) octamer, in the range 0.2-2 GPa.This sequence crystallizes in the hexagonal P61 space group and is particularly interesting because it includes in a A-DNA crystal matrix, the B-form of DNA, leading us to simultaneously monitor the two forms of DNA under pressure.The 3D structure of d(GGTATACC) was recorded at ambient pressure, 0.55, 1.09 and 1.39 GPa and refined at 1.6 Å resolution.Fiber diagrams of the embedded B-DNA that superpose to the diffraction pattern of the A-DNA were analyzed from ambient pressure to up 1.9 GPa.A large axial compression of the DNA is observed (11 % at 1.39 GPa).The average base-step varies in A-DNA from 2.92 down to 2.73 Å, and in B-DNA from 3.40 to 3.10 Å. Surprisingly, in the case of A-DNA, the geometry of Watson-Crick base parings remains essentially invariant in the domain of pressure up to 1.39 GPa.Above 1.4 GPa, the crystal structure irreversibly deteriorates while the B-DNA fiber diagram still persists above 2 GPa.The remarkable stability and adaptation of d(GGTATACC) to high pressure is clearly associated with the base-paired double helix topology of the molecule by which it behaves as a molecular spring.