Mc. Wahl et al., THE STRUCTURE OF R(UUCGCG) HAS A 5'-UU-OVERHANG EXHIBITING HOOGSTEEN-LIKE TRANS U-CENTER-DOT-U BASE-PAIRS, Nature structural biology, 3(1), 1996, pp. 24-31
The crystal structure of the RNA fragment, 5'-r(UUCGCG)-3', has been d
etermined at 1.4 Angstrom resolution by a combination of single isomor
phous replacement and molecular search methods. The 3'-terminal CGCG p
ortion of the hexamer engages in Watson-Crick hydrogen bonding while t
he 5'-terminal UU-overhang forms novel Hoogsteen-like U . U self-base
pairs with the overhang of an adjacent duplex. The U . U pairs display
a single conventional hydrogen bond between O4(U1) and N3 (U8) and a
CH-O hydrogen bond between C5-H (U1) and O4 (U8), through the Hoogstee
n face of the pyrimidine base U1. This unusual arrangement of one of t
he bases results in a trans U . U pair on antiparallel strands in cont
rast to the usual cis base pairs. The structure emphasizes the pronoun
ced polymorphism of U . U pairs and has implications for folding of RN
A molecules.