Is there a special function for U.G basepairs in ribosomal RNA?
U.G basepairs are well-established elements of RNA structure. The geometry of this pair is different, however, from classical Watson-Crick basepairs. This leads to an unusual stacking of the basepair: overlap with the basepair at the 5' side of the U (and the 3' side of the G) is strong (stacked) while it is weak with the basepair on the other side (destacked). The closure of an RNA helix by a U.G pair will be energetically unfavourable when the U residue occupies the 5' end. In transfer RNA there is a strong selection against a 'destacked' U.G pair at helix ends. In the 16S rRNA model of Escherichia coli there are 72 U.G pairs of which 36 or 22 occupy a helix end, depending on how such an end is defined. There is a slight preference for 'stacked' U.G's in these positions. It is remarkable, however, that of 13 very conserved U.G pairs in the 16S (-like) rRNA, 7 occur at helix ends and that 5 of these have the 'destacked' configuration. It is suggested that these pairs, if they exist at all in a hydrogen-bounded form, are stabilized by co-axial stacking with other helices or by interaction with a protein.
van Knippenberg
P H
PH
Department of Biochemistry, Gorlaeus Laboratories, University of Leiden, The Netherlands.
Formenoy
L J
LJ
Heus
H A
HA
D001482:Base Composition; D001483:Base Sequence; D006147:Guanine; D006860:Hydrogen Bonding; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D014498:Uracil
D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D014498:Uracil; D006147:Guanine