B-form to A-form conversion by a 3 '-terminal ribose: crystal structure ofthe chimera d(CCACTAGTG)r(G)

The crystal structure of the chimerical decamer d(CCACTAGTG)r(G), bearing a 3'-terminal riboguanidine, has been solved and refined at 1.8 Angstrom res olution (R-factor 16.6%; free R-factor 22.8%). The decamer crystallizes in the orthorhombic space group P2(1)2(1)2(1) with unit cell constants a = 23. 90 Angstrom, b = 45.76 Angstrom and c = 49.27 Angstrom. The structure was s olved by molecular replacement using the coordinates of the isomorphous chi mera r(GCG)d(TATACGC). The final model contains one duplex and 77 water mol ecules per asymmetric unit. Surprisingly, all residues adopt a conformation typical for A-form nucleic acids (C3'-endo type sugar pucker) although the all-DNA analog, d(CCACTAGTGG), has been crystallized in the B-form. Compar ing circular dichroism spectra of the chimera and the corresponding all-DNA sequence reveals a similar trend of the former molecule to adopt an A-like conformation in solution. The results suggest that the preference of ribon ucleotides for the A-form is communicated into the 5'-direction of an oligo nucleotide strand, although direct interactions of the 2'-hydroxyl group ca n only be discerned with nucleotides in the 3'-direction of a C3'-endo puck ered ribose. These observations imply that forces like water-mediated conta cts, the concerted motions of backbone torsion angles, and stacking prefere nces, are responsible for such long-range influences. This bi-directional s tructural communication originating from a ribonucleotide can be expected t o contribute to the stability of the A-form within all-RNA duplexes.