Nucleic Acids Research, 2003, Vol. 31, No. 5 1392-1397
© 2003 Oxford University Press
The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs
Department of Chemistry and Department of Biochemistry, The Ohio State University, 200 Johnston Laboratory, Columbus, OH 43210, USA
*To whom correspondence should be addressed. Tel: +1 614 2922925; Fax: +1 614 2922524; Email: sundaral{at}chemistry.ohio-state.edu
The crystal structure of an alternating RNA heptamer r(GUAUACA) has been determined to 2.0 Å resolution and refined to an Rwork of 17.1% and Rfree of 18.5% using 2797 reflections. The heptamer crystallized in the space group C222 with a unit cell of a = 25.74, b = 106.58, c = 30.26 Å and two independent strands in the asymmetric unit. Each heptamer forms a duplex with its symmetry-related strand and each duplex contains six Watson–Crick base pairs and 3'-end adenosine overhangs. Therefore, two kinds of duplex (duplex 1 and duplex 2) are formed. Duplexes 1 stack on each other forming a pseudo-continuous column, which is typical of the RNA packing mode, while duplex 2 is typical of A-DNA packing with its termini in abutting interactions. Overhang adenine residues stack within the duplexes with C3'-endo sugar pucker and C2'-endo sugar pucker in duplexes 1 and 2, respectively. A Na+ ion in the crystal lattice is water bridged to two N1 atoms of symmetry-related A7 bases.