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Abstract
G•U wobble base pair frequently occurs in RNA structures. The unique chemical, thermodynamic, and structural properties of the G•U pair are widely exploited in RNA biology. In several RNA molecules, the G•U pair plays key roles in folding, ribozyme catalysis, and interactions with proteins. G•U may occur as a single pair or in tandem motifs with different geometries, electrostatics, and thermodynamics, further extending its biological functions. The metal binding affinity, which is essential for RNA folding, catalysis, and other interactions, differs with respect to the tandem motif type due to the different electrostatic potentials of the major grooves. In this work, we present the crystal structure of an RNA 8-mer duplex r[UCGUGCGA]2, providing detailed structural insights into the tandem motif I (5′UG/3′GU) complexed with Ba2+ cation. We compare the electrostatic potential of the presented motif I major groove with previously published structures of tandem motifs I, II (5′GU/3′UG), and III (5′GG/3′UU). A local patch of a strongly negative electrostatic potential in the major groove of the presented structure forms the metal binding site with the contributions of three oxygen atoms from the tandem. These results give us a better understanding of the G•U tandem motif I as a divalent metal binder, a feature essential for RNA functions.
Highlights
Watson–Crick (WC) base pairs shape the RNA double-helical landscape
GU pairs have been found in multiple classes of RNA, including messenger RNA (Benard et al, 1998), ribosomal RNA (Woese et al, 1983; Gutell et al, 1994), transfer RNA (Ladner et al, 1975), small nuclear RNA (Wu and Manley, 1992; Sashital et al, 2004; Sashital et al, 2007), and ribozymes [such as group I and II introns, and in hepatitis delta virus (HDV)] (Cech et al, 1981; Allain and Varani, 1995; Strobel and Cech, 1995; Been and Wickham, 1997; Nishikawa et al, 1997; Colmenarejo and Tinoco, 1999)
While several structures including such pairs have been reported, this work presents the first detailed analysis based on an experimental model of the motif I GU tandem complexed with a divalent metal cation
Summary
Watson–Crick (WC) base pairs shape the RNA double-helical landscape. multiple nonWC interactions (Leontis et al, 2002) have been distinguished in RNA structures and implicated in various biological functions of RNA (Westhof and Fritsch, 2000; Chandrasekhar and Malathhi, 2003; Brown, 2020). GU pairs have been found in multiple classes of RNA, including messenger RNA (mRNA) (Benard et al, 1998), ribosomal RNA (rRNA) (Woese et al, 1983; Gutell et al, 1994), transfer RNA (tRNA) (Ladner et al, 1975), small nuclear RNA (Wu and Manley, 1992; Sashital et al, 2004; Sashital et al, 2007), and ribozymes [such as group I and II introns, and in hepatitis delta virus (HDV)] (Cech et al, 1981; Allain and Varani, 1995; Strobel and Cech, 1995; Been and Wickham, 1997; Nishikawa et al, 1997; Colmenarejo and Tinoco, 1999)
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