No abstract

The crystal structure of the RNA duplex [r(CCCCGGGG)]2 has been refined to 1.46 A resolution with room temperature synchrotron diffraction data. This represents the highest resolution reported to date for an all-RNA oligonucleotide and is well beyond the best resolution ever achieved with an A-form DNA duplex. The analysis of the ordered hydration around the octamer duplex reveals conserved regular arrangements of water molecules in both grooves. In the major groove, all located first shell water molecules can be fitted into a pattern that is repeated through all eight base pairs, involves half the phosphate oxygens, and joins the two strands. In the minor groove, roughly across its narrowest dimension, tandem water molecules link the 2'-hydroxyl groups of adjacent nucleotides in base-pair steps in a similarly regular fashion. The structure provides evidence for an important role of the 2'-hydroxyl groups in the thermodynamic stabilization of RNA, beyond their known functions of locking the sugar pucker and mediating 3' --> 5' intrastrand O2'...O4' hydrogen bonds. The ribose 2'-hydroxyls lay the foundation for the enthalpic stability of the RNA relative to the DNA duplex, both as a scaffold for the water network in the minor groove and through their extensive individual hydration.

We report an accurate ab initio study of the effects of chirality on the intermolecular interactions between two small chiral molecules bound by a single hydrogen bond. The methods used are second-order Møller–Plesset theory (MP2), as well as density functional theory with the B3LYP functional. The differential interaction energy between two homochiral molecules, e.g., R⋅⋅⋅R′ and the analogous heterochiral molecules R⋅⋅⋅S′ measures the degree of chiral discrimination, termed the chirodiastaltic energy, ΔEchir. Formation of the O–H⋅⋅⋅O hydrogen bond between the chiral H-bond donor HOOH and the chiral H acceptor 2-methyl oxirane leads to four diastereomeric complexes. There are two distinct contributions to the chirodiastaltic energies, the diastereofacial contribution which controls the face or side of the acceptor to which the H bond is formed, and the diastereomeric contribution, which is the energy difference between two complexes formed by (M)- and (P)-HOOH to the same face. The largest chirodiastaltic energy is ΔEchir=0.46 kcal/mol (6% of the binding energy) between the syn-(M)- and syn-(P)-HOOH⋅2-methyl oxirane complexes. The chiral 2,3-dimethyloxirane acceptor is C2 symmetric and hence offers two identical faces. Here the chirodiastaltic energy is identical to the diastereomeric energy, and is calculated to be ΔEchir=0.36 kcal/mol or 4.5% of the binding energy.

Single adenosine bulges cause a marked opening of the normally narrow RNA major groove in both crystal structures, rendering the bases more accessible to interacting molecules compared with an intact stem. The geometries around the looped-out adenosines are different in the two crystal forms, indicating that bulges can confer considerable local plasticity on the usually rigid RNA double helix. The results provide a conformational basis for the preferential, metal-assisted self-cleavage of RNA at bulged sites.