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.