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The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6CI3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two GNU and two C U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G U pair is a wobble base pair analogous to the GOT pair found in DNA fragments. The CU mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit ofthe base pair in the RNA helix. The BrU BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.Tertiary structure is essential to the biological function of many single-stranded RNAs. Base pairing between complementary segments in a sequence generates a series of doublehelical stems that connect unpaired regions or loops. These can fold further into compact assemblies stabilized by additional hydrogen bonds and by hydrophobic and electrostatic interactions (1). The various levels of structural order are most completely characterized in tRNAs, for which a number of crystal structures have been determined (2-4). In the case of larger and more complex RNA species, including ribosomal components and RNase P, present understanding of secondary structure relies heavily on assumptions about the relative stabilities of possible base-pairing arrangements (5). These follow the specificities of adenine for uracil and guanine for cytosine observed in both ribonucleotides and deoxyribonucleotides during replication and transcription and are also mirrored in the experimentally measured stabilities of short oligonucleotide duplexes. Although the double helix is a central feature of these systems, none is a conspicuously direct model of the environment within a globular RNA structure.The present analysis of an RNA double helix is the second to be reported for an oligonucleotide containing a "tetraloop" sequence. Tetraloops are common in natural singlestranded RNA and, although the stems of such structural elements are variable, the unpaired regions are found to be tetranucleotides of mainly two types: a group with the general sequence r(GNRA) and the specific r(UUCG). Examples of both classes have been examined extensively in solution, where they exist as monomeric, thermally stable, looped species which parallel the behavior of the parent sequences in RNA of higher molecular weight (6,7).In crystals of both the present sequence and a dodecamer studied by Holbrook et al. (8), where r(UUCG) is embedded in se...

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This analysis provides a rare example of an experimentally determined non-duplex DNA structure. It provides conformational detail relevant to the tight packaging or folding of a DNA strand and illustrates how a cation might modulate phosphate-phosphate repulsion in a tightly packed structure. The observation of base quartets involving G.C base pairs suggests a further structure to be considered in DNA-DNA interactions. The structure also provides detailed geometries for A.A and T.T base pairs.

The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was refined to a resolution of 1.7 A using combined diffractometer and synchrotron data. The analysis was carried out independently in two laboratories using different procedures. Although the final results are identical the comparison of the two approaches highlights potential problems in the refinement of oligonucleotides when only limited data are available. As part of the analysis the positions of 84 solvent molecules in the asymmetric unit were established. The DNA molecule is highly solvated, particularly the phosphate-sugar back-bone and the functional groups of the bases. The major groove contains, in the central BrU-A-BrU-A region, a ribbon of water molecules forming closed pentagons with shared edges. These water molecules are linked to the base O and N atoms and to the solvent chains connecting the O-1 phosphate oxygen atoms on each strand. The minor groove is also extensively hydrated with a continuous network in the central region and other networks at each end. The pattern of hydration is briefly compared with that observed in the structure of a B-dodecamer.

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The GAAA consensus sequence can dimerise into a stable zipper-like duplex as well as forming a hairpin loop. The arrangement closes the minor groove and exposes the intercalated, unpaired, adenines to the solvent and DNA-binding proteins. Such a motif, which can transform into a hairpin, should be considered as a structural option in modelling DNA and as a potential binding site, where it could have a role in DNA replication, nuclease resistance, ssDNA genome packaging and centromere function.

No abstract