Intrusion of MPD into the minor groove of 2′- O-Me(CGCGCG) 2 is discussed with respect to RNA dehydration, a prerequisite of Z-RNA formation. Comparison of the 2′- O-Me(CGCGCG) 2 structure in the P3 212 and P6 122 crystals delineates stability of the water network within the minor groove to dehydration by MPD and is of interest for evaluating factors governing small molecule binding to RNA. The two MPD molecules intrude into the hydration network in the minor groove, each forming hydrogen bonds between their secondary hydroxyl group and exo-amino functions of guanosine residues. This work provides the first example of molecular interactions of nucleic acids with MPD, which was used as a precipitant, cryo-solvent and resolution enhancing agent.
Two are in the major groove and interact with O 6 and N 7 of guanosine and N 4 of cytidine residues through their hydration spheres. As many as five magnesium ions are located in the structure. Only a single row of water molecules is observed in the minor groove due to the presence of hydrophobic 2′- O-methyl groups. The structure includes 65 ordered water molecules. The duplex is overwound with an average value of 9.7 bp per turn, characterised as having a C3′- endo sugar pucker, very low base pair rise and high helical twist and inclination angles. The structure in space group P3 212 is a half-turn right-handed helix that includes two 2-methyl-2,4-pentanediol (MPD) molecules bound in the minor groove. The crystal and molecular structure of 2′- O-Me(CGCGCG) 2 has been determined at 1.19 Å resolution, at 100 K, using synchrotron radiation.
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