The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3′-end adenine overhangs

Ke Shi, Baocheng Pan, Muttaiya Sundaralingam

Research output: Contribution to journalReview articlepeer-review

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1392-1397
Number of pages6
JournalNucleic acids research
Volume31
Issue number5
DOIs
StatePublished - Mar 1 2003

Bibliographical note

Funding Information:
We gratefully thank the NIH for grant GM-17378 and the Board of Regents of Ohio for an Ohio Eminent Scholar Chair and Endowment to M.S. We also acknowledge the Hays Consortium Investment Fund by the Regions of Ohio for partial support for purchasing the Raxis IIc imaging plate system.

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