Structural studies on site-directed mutants of domain 3 of Xenopus laevis oocyte 5 S ribosomal RNA.
Base substitutions have been introduced into the highly conserved sequences of loops D and E within domain 3 of Xenopus laevis oocyte 5 S rRNA. The effects of these mutations on the solution structure of this 5 S rRNA have been studied by means of probing with nucleases, and with chemical reagents under native and semi-denaturing conditions. The data obtained with these mutants support the graphic model of Xenopus oocyte 5 S rRNA proposed by Westhof et al. In particular, our results rule out the existence of long-range base-pairing interactions between loop C and either loop D or loop E. The data also confirm that loops D and E in the wild-type 5 S RNA adopt unusual secondary structures and illustrate the importance of nucleotide sequence in the formation of intrinsic local loop conformations via non-canonical base-pairs and specific base-phosphate contacts. Consistent with this conclusion is our observation that the domain 3 fragment of Xenopus oocyte 5 S rRNA adopts the same conformation as the corresponding region in the full-length 5 S rRNA.
de Stevenson
I L
IL
Department of Biochemistry and Microbiology, University of Victoria, BC, Canada.
Romby
P
P
Baudin
F
F
Brunel
C
C
Westhof
E
E
Ehresmann
C
C
Ehresmann
B
B
Romaniuk
P J
PJ
D000818:Animals; D001483:Base Sequence; D005260:Female; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009865:Oocytes / Q000502:physiology*; D012341:RNA, Ribosomal, 5S / Q000235:genetics*; D012260:Ribonucleases; D014982:Xenopus laevis
D012341:RNA, Ribosomal, 5S; D012260:Ribonucleases