About: Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting

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About: Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting
Creator	Yu, Chien-Hung Noteborn, Mathieu Cornelis, W Olsthoorn, Pleij, René
Source	PMC
abstract	−1 Programmed ribosomal frameshifting (PRF) in synthesizing the gag-pro precursor polyprotein of Simian retrovirus type-1 (SRV-1) is stimulated by a classical H-type pseudoknot which forms an extended triple helix involving base–base and base–sugar interactions between loop and stem nucleotides. Recently, we showed that mutation of bases involved in triple helix formation affected frameshifting, again emphasizing the role of the triple helix in −1 PRF. Here, we investigated the efficiency of hairpins of similar base pair composition as the SRV-1 gag-pro pseudoknot. Although not capable of triple helix formation they proved worthy stimulators of frameshifting. Subsequent investigation of ∼30 different hairpin constructs revealed that next to thermodynamic stability, loop size and composition and stem irregularities can influence frameshifting. Interestingly, hairpins carrying the stable GAAA tetraloop were significantly less shifty than other hairpins, including those with a UUCG motif. The data are discussed in relation to natural shifty hairpins.
has issue date	2011-07-29(xsd:dateTime)
bibo:doi	10.1093/nar/gkr579
bibo:pmid	21803791
has license	cc-by-nc
sha1sum (hex)	1f3b676368e5c9a1582ab624cbf0884c383fddd2
schema:url	https://doi.org/10.1093/nar/gkr579
resource representing a document's title	Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting
has PubMed Central identifier	PMC3203594
has PubMed identifier	21803791
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:1f3b676368e5c9a1582ab624cbf0884c383fddd2#body_text
is schema:about of	named entity 'MUTATION' named entity 'INTERACTIONS' named entity 'SIMIAN RETROVIRUS' named entity 'BASE PAIR' named entity 'MOTIF' named entity 'REVEALED' named entity 'CLASSICAL' named entity 'CAPABLE' named entity 'INCLUDING' named entity 'PRF' named entity '2430' named entity 'LOOP' named entity 'DATA' named entity 'INVOLVING' named entity 'THERMODYNAMIC STABILITY' named entity 'POLYPROTEIN' named entity 'EFFICIENCY' named entity 'TETRALOOP' named entity 'RECENTLY' named entity 'INVOLVED' named entity 'carrying' named entity 'involving' named entity 'nucleotides' named entity 'investigation' named entity 'triple helix' named entity 'stimulated' named entity 'Stem-loop' named entity 'RIBOSOMAL' named entity 'STEM' named entity 'AFFECTED' named entity 'FORMATION' named entity 'NATURAL' named entity 'DIFFERENT' named entity 'PSEUDOKNOT' named entity 'BASE' named entity 'SUBSEQUENT' named entity 'INVESTIGATION' named entity 'SIZE' named entity 'PSEUDOKNOT' named entity 'RIBOSOMAL' named entity 'CARRYING' named entity 'ROLE' named entity 'NEXT TO' named entity 'HERE' named entity 'H-TYPE PSEUDOKNOT' named entity 'INFLUENCE' named entity 'RELATION' named entity 'STRUCTURES' named entity 'STEM-LOOP' named entity 'TRIPLE HELIX' named entity 'PRECURSOR' named entity 'TYPE' named entity 'PRO' named entity 'SUGAR' named entity 'SUBSTITUTE' named entity 'RNA' named entity 'STIMULATED' named entity 'FORMS' named entity 'NUCLEOTIDES' named entity 'INVESTIGATED' named entity 'EXTENDED' named entity 'COMPOSITION' named entity 'STIMULATORS' named entity 'STABLE' named entity 'SIMILAR' named entity 'SRV-1' named entity 'GAG' covid:arg/1f3b676368e5c9a1582ab624cbf0884c383fddd2 named entity 'formation' named entity 'ribosome' named entity 'Frameshifting' named entity 'frameshifting' named entity 'thermodynamic stability' named entity 'base pair' named entity 'frameshifting' named entity 'Human immunodeficiency virus' named entity 'DMEM'

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