The crystal structure of the octamer [r(guauaca)dC](2) with six Watson-Crick base-pairs and two 3 ' overhang residues

The crystal structure of an alternating RNA octamer, r(guauaca)dC (RNA base s are in lower case while the only DNA base is in upper case), with two 3' overhang residues one of them a terminal deoxycytosine and the other a ribo se adenine, has been determined at 2.2 Angstrom resolution. The refined str ucture has an R-work 18.6% and R-free 26.8%. There are two independent dupl exes (molecules I and II) in the asymmetric unit cell, a = 24.95, b = 45.25 and c = 73.67 Angstrom, with space group P2(1)2(1)2(1). Instead of forming a blunt end duplex with two a(+).c mispairs and six Watson-Crick base-pair s, the strands in the duplex slide towards the 3' direction forming a two-b ase overhang (radC) and a six Watson-Crick base-paired duplex. The duplexes are bent (molecule I, 20 degrees; molecule II, 25 degrees) and stack head- to-head to form a right-handed superhelix. The overhang residues are looped out and the penultimate adenines of the two residues at the top end (A15) are anti and at the bottom (A7) end are syn. The syn adenine bases form min or groove A,(GC) base triples with C8-H ... N2 hydrogen bonds. The anti ade nine in molecule II also forms a triple and a different C2-H ... N3 hydroge n bond, while the other anti adenine in molecule I does not, it stacks on t he looped out overhang base dC. The 3' terminal deoxycytosines form two sta cked hemiprotonated trans d(C.C)(+) base-pairs and the pseudo dyad related molecules form four consecutive deoxyribose and ribose zipper hydrogen bond s in the minor groove. (C) 2000 Academic Press.