Nature Communications, 2023 T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box ...
Xiaolin Niu +5 more
doaj +1 more source
A hepatitis C virus cis-acting replication element forms a long-range RNA-RNA interaction with upstream RNA sequences in NS5B [PDF]
, 2008 The genome of hepatitis C virus (HCV) contains cis-acting replication elements (CREs) comprised of RNA stem-loop structures located in both the 5' and 3' non-coding regions (NCR), and in the NS5B coding sequence.
Diviney, Sinéad +22 more
core +1 more source
On the predictibility of A-minor motifs from their local contexts
RNA Biology, 2022 This study investigates the importance of the structural context in the formation of a type I/II A-minor motif. This very frequent structural motif has been shown to be important in the spatial folding of RNA molecules.
Coline Gianfrotta +4 more
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Coupling Between Production of Ribosomal RNA and Maturation: Just at the Beginning
Frontiers in Molecular Biosciences, 2021 Ribosomal RNA (rRNA) production represents the most active transcription in the cell. Synthesis of the large rRNA precursors (35S/47S in yeast/human) is achieved by up to hundreds of RNA polymerase I (Pol I) enzymes simultaneously transcribing a single ...
Chaima Azouzi +7 more
doaj +1 more source
Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses:Implications for virus evolution and host persistence [PDF]
, 2004 Discrete RNA secondary and higher-order structures, typically local in extent, play a fundamental role in RNA virus replication. Using new bioinformatics analysis methods, we have identified genome-scale ordered RNA structure (GORS) in many genera and ...
Evans, David J +5 more
core +1 more source
RNA folding on the 3D triangular lattice
BMC Bioinformatics, 2009 Background Difficult problems in structural bioinformatics are often studied in simple exact models to gain insights and to derive general principles. Protein folding, for example, has long been studied in the lattice model.
Mayne Martin +2 more
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Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells
RNA Biology, 2023 RNA aptamers are structured RNAs that can bind to diverse ligands, including proteins, metabolites, and other small molecules. RNA aptamers are widely used as in vitro affinity reagents.
Qian Hou, Samie R. Jaffrey
doaj +1 more source
RNA Movies 2: sequential animation of RNA secondary structures [PDF]
, 2007 Kaiser A, Krüger J, Evers DJ. RNA Movies 2: sequential animation of RNA secondary structures. NUCLEIC ACIDS RESEARCH.
Krüger, Jan +2 more
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Fine-tuning structural RNA alignments in the twilight zone [PDF]
, 2010 Bremges A, Schirmer S, Giegerich R. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics. 2010;11(1): 222.Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence ...
Bremges Andreas +8 more
core +1 more source
Pseudoknots in RNA folding landscapes [PDF]
Bioinformatics, 2015 Abstract Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model
Marcel Kucharík +3 more
openaire +5 more sources