Structure of a small RNA hairpin

Abstract

The hairpin stem-loop form of the RNA oligonucleotide rCGC(UUU)GCG has been studied by NMR spectroscopy. In 10 mM phosphate buffer this RNA molecule forms a unimolecular hairpin with a stem of three base pairs and a loop of three uridines, as judged by both NMR and UV absorbance melting behavior. Distance and torsion angle restraints were determined using homonuclear proton-proton and heteronuclear proton-phosphorus 2-D NMR. These values were used in restrained molecular dynamics to determine the structure of the hairpin. The stem has characteristics of A-form geometry, although distortion from A-form occurs in the 3'-side of the stem, presumably to aid in accommodating the small loop. The loop nucleotides adopt C2'-endo conformations. NOE's strongly suggest stacking of the uracils with the stem, especially the first uracil on the 5'-side of the loop. The reversal of the chain direction in the loop seems to occur between U5 and U6. Loop structures produced by molecular dynamics simulations had a wide range of conformations and did not show stacking of the uracils. A flexible loop with significant dynamics is consistent with all the data.

Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain

“…Furthermore, recent studies of the dynamics of pyrimidine-rich tetraloops indicate that these motifs are conformationally extremely dynamic. 47,48 The J2/3 loop is likely to behave in a similar manner, as the bulk of the bases (46)(47)(48)(49)(50)(51)(52) are in fact pyrimidines. Thus, this region would be a flexible gateway, allowing the ligand into the interior of the binding pocket for recognition by Y74, which would be preorganized for ligand binding.…”

The Hairpin Elements of Nucleic Acid Structure: DNA and RNA Folding

“…The RNA sequences r(GCGAUU-UCU-GACCGCC) (Puglisi et al 1990) and r(CGC-UUU-GCG) (Davis et al 1993) form hairpins with a three-membered loop. The NOE data suggested stacking of the first two loop nucleotides on the 3' end of the helix and a turn between the second and third loop nucleotides.…”

On the structural features of hairpin triloops in rRNA: From nucleotide to global conformational change upon ligand binding

“…The RNA-protein interactions can be considered as being a consequence of induced fit between flexible loops (Hainzl et al, 2005). Whereas triloops are common in a variety of naturally occurring RNAs, they may possess some particularly useful structural characteristics (Davis et al, 1993). Several solution structures of hairpin triloops in various RNAs have been reported in the literature (Kim and Tinoco, 2001;Leeper et al, 2003).…”