The modified nucleotide queuosine (Q) is almost universally found in the anticodon wobble position of specific tRNAs. In many bacteria, biosynthesis of Q is modulated by a class of regulatory mRNA elements called riboswitches. The preQ(1) riboswitch, found in the 5'UTR of bacterial genes involved in synthesis of the Q precursors preQ(0) and preQ(1), contains the smallest known aptamer domain. W...

Secondary and tertiary structures in the 3' untranslated region (UTR) of plus-strand RNA viruses have been postulated to function as control elements in RNA replication, transcription, and translation. Here we describe a 54-nucleotide (nt) hairpin-type pseudoknot within the 288-nt 3' UTR of the bovine coronavirus genome and show by mutational analysis of both stems that the pseudoknotted struct...

We have used bioinformatics approaches to identify a potential case of -1 ribosomal frame shifting in the mRNAs of the three variants of human SEMA6C protein. The mRNAs contain a heptanucleotide slippery sequence followed by a compact H-type pseudoknot. Unlike -1 frameshifting signals in viral or viral-like mRNAs, the slippery sequence and downstream pseudoknot in SEMA6C mRNAs locate 423 nucleo...

Pseudoknots are abundant in RNA structures. Many computational analyses require pseudoknot-free structures, which means that some of the base pairs in the knotted structure must be disregarded to obtain a nested structure. There is a surprising diversity of methods to perform this pseudoknot removal task, but these methods are often poorly described and studies can therefore be difficult to rep...

We examined mutationally a two-hairpin structure (nucleotides 57 to 70 and 76 to 110) in a region of domain I of Escherichia coli 23S rRNA that has been implicated in specific functions in protein synthesis by other studies. On the basis of the observed covariance of several nucleotides in each loop in Bacteria, Archaea, and chloroplasts, the two hairpins have been proposed to form a pseudoknot...

Dual graphs have been applied to model RNA secondary structures. The purpose of the paper is two-fold: we present new graph-theoretic properties of dual graphs to validate the further analysis and classification of RNAs using these topological representations; we also present a linear-time algorithm to partition dual graphs into topological components called blocks and determine if each block c...

Here we investigated ribosomal pausing at sites of programmed -1 ribosomal frameshifting, using translational elongation and ribosome heelprint assays. The site of pausing at the frameshift signal of infectious bronchitis virus (IBV) was determined and was consistent with an RNA pseudoknot-induced pause that placed the ribosomal P- and A-sites over the slippery sequence. Similarly, pausing at t...

In this paper we enumerate k-noncrossing RNA pseudoknot structures with given minimum arc-and stack-length. That is, we study the numbers of RNA pseudoknot structures with arc-length ≥ 3, stack-length ≥ σ and in which there are at most k − 1 mutually crossing bonds, denoted by T [3] k,σ (n). In particular we prove that the numbers of 3, 4 and 5-noncrossing RNA structures with arc-length ≥ 3 and...

Folding messenger RNA into specific structures is a common regulatory mechanism involved in translation. In Escherichia coli, the operator of the rpsO gene transcript folds into a pseudoknot or double-hairpin conformation. S15, the gene product, binds only to the pseudoknot, thereby repressing its own synthesis when it is present in excess in the cell. The two RNA conformations have been propos...