title: G-ribo motif favors the formation of pseudoknots in ribosomal RNA.
abstract: Analysis of the pseudoknots existing in the ribosomal RNA showed that four of them are formed with the help of G-ribo, a recently identified RNA recurrent motif. The analysis of these pseudoknots revealed two major aspects in the G-ribo motif structure, which together provide the structural context favoring the formation of two different types of pseudoknots. The first aspect pertains to a particular side-by-side juxtaposition of two double helices that facilitates switches of the polynucleotide chain between different strands. The second aspect deals with the presence of an adenosine at a specific place where it can stabilize a particular arrangement of two quasicoaxial helices required for the pseudoknot formation. Additional analysis shows that the latter aspect is also present in other pseudoknots not related to the G-ribo motif or the ribosome, and thus represents a general structural element favoring the formation of pseudoknots.
authors.affiliation: Département de Biochimie, Université de Montréal, Montréal, QC, Canada. serguei.chteinberg@umontreal.ca
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Steinberg
authors.forename: Yury I
authors.initials: YI
authors.lastname: Boutorine
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D019143:Evolution, Molecular; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012335:RNA, Ribosomal / Q000032:analysis*; D050436:Regulatory Elements, Transcriptional; D017423:Sequence Analysis, RNA
chemical_list: D012335:RNA, Ribosomal