International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 22.2, p. 551
Section 22.2.6.2. RNA
aSchool of Biological Sciences, University of Auckland, Private Bag 92-109, Auckland, New Zealand |
In contrast to DNA, RNA molecules generally form single-stranded structures, which are correspondingly much more complex and less regular. This means that catalytic and other activities can be generated in addition to their information-carrying roles. Current knowledge of detailed RNA three-dimensional structure is limited to transfer RNAs and several ribozymes, including a large ribosomal RNA domain (Cate et al., 1996). Even from this small sample, however, it is clear that a great diversity of hydrogen-bonding interactions exists; RNA molecules contain regions of double-helical structure, often with classical Watson–Crick A–U and G–C base pairing, but these regions are interspersed with loops and bulges and tertiary interactions between the various secondary-structural (double-helical) elements. These interactions include many unconventional base pairings (e.g. see Fig. 22.2.6.1).
Some RNA structural motifs may prove to be of widespread general importance in RNA molecules. One example is a sharp turn with sequence CUGA in the hammerhead ribozyme that exactly matches turns in tRNAs (Pley et al., 1994). Another is the GNRA tetraloop structure (N = any base, R = purine). This loop has a well defined structure, stabilized by hydrogen bonding and stacking involving its own bases, and it also presents further hydrogen-bonding groups that can dock into `receptor' structures in other parts of the RNA molecule. This results in triple or quadruple base interactions (Fig. 22.2.6.1) that tie different parts of the RNA structure together; the parallel with hydrogen-bonding side chains in proteins is very strong. The 2′-hydroxyls of ribose groups are also used in some of these interactions (Fig. 22.2.6.1). Further ribose interactions involve interdigitated ribose groups that line the interfaces between adjacent helices such that pairs of riboses interact by hydrogen bonding through their 2′-hydroxyl groups, forming `ribose zippers' As many more RNA structures are determined experimentally, it is likely that more hydrogen-bonding motifs will be recognized, and their full role in RNA structure can be better assessed than at our present, imperfect state of knowledge.
References
Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R. & Doudna, J. A. (1996). Crystal structure of a group I ribozyme domain: principles of RNA packing. Science, 273, 1678–1685.Google ScholarPley, H. W., Flaherty, K. M. & McKay, D. B. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature (London), 372, 68–74.Google Scholar