Structure of an RNA double helix including uracil-uracil base pairs in an internal loop

Abstract

The crystal structure of the RNA dodecamer 5'-GGACUUUGGUCC-3' has been determined from X-ray diffraction data to 2.6 A resolution. This oligomer forms an asymmetric double helix in the crystal. Four consecutive non-Watson-Crick base-pairs are formed in the middle of the duplex including the first intrahelical U-U (or T-T) pairs observed in an oligonucleotide crystal structure. Two different conformations of U-U pairs are observed in the context of the surrounding sequence. One of these pairs is highly twisted, allowing a bound water to bridge across strands in the major groove. The crystal packing illustrates a new form of RNA helix-helix interaction.

Probing the Role of a Secondary Structure Element at the 5‘- and 3‘-Splice Sites in Group I Intron Self-Splicing: The Tetrahymena L-16 ScaI Ribozyme Reveals a New Role of the G·U Pair in Self-Splicing

“…As noted above, previous structural data with model duplexes suggested that stacking is disrupted by an internal G•U wobble pair, so that stacking between the P1 and the P1 extension helices might not be expected to be continuous (66)(67)(68)70). This structural picture is supported by the recent x-ray structures of the group I intron (65,71).…”

Imperfect CAG Repeats Form Diverse Structures in SCA1 Transcripts

“…It appears that the RNA duplex containing two tandem U-C mismatches in its central positions is very unstable compared with a similar duplex with the U-U mismatches (43). The presence of eight water molecules, four per each U-C pair, bound to stabilize these pairs may be the factor that causes a severe nearly 2-fold widening of the major groove as compared with A-RNA, resulting in duplex destabilization (43). It is tempting to speculate that a similar effect may be the driving force for the CAG repeat duplex destabilization in the SCA1 transcripts.…”

“…Which of the postulated two geometries of the U-C pairs occurs in the RNAs: the U-Cϩ (with the neighboring carbonyl and imino groups involved in the formation of hydrogen bonds) or the neutral U-C pair (with N3-imino proton of U forming a watermediated hydrogen bond to the N3 of C)? Some answers to these questions come from the crystal structures of RNA duplexes containing the U-C pairs (43)(44)(45). It appears that the RNA duplex containing two tandem U-C mismatches in its central positions is very unstable compared with a similar duplex with the U-U mismatches (43).…”

“…Some answers to these questions come from the crystal structures of RNA duplexes containing the U-C pairs (43)(44)(45). It appears that the RNA duplex containing two tandem U-C mismatches in its central positions is very unstable compared with a similar duplex with the U-U mismatches (43). The presence of eight water molecules, four per each U-C pair, bound to stabilize these pairs may be the factor that causes a severe nearly 2-fold widening of the major groove as compared with A-RNA, resulting in duplex destabilization (43).…”

Crystals of the chemically synthesized acceptor stem of tRNAAlafromEscherichia colidiffracting to high resolution

“…Moreover, only a few short RNA molecules were analyzed by X-ray crystallography (Baeyens, De Bondt & Holbrook, 1995;Betzel et al, 1994;Cruse et al, 1994;Leonard et al, 1994;Holbrook, Cheong, Tinoco & Kim, 1991;Dock-Bregeon et al, 1988;Schindelin et al, 1995;Portmann, Usman & Egli, 1995). One reason for few structural investigations of short RNA's was the lack of a suitable method to produce large amounts of RNA tbr a long time.…”