ArticleNucleic acids research2011
Structural characterization of naturally occurring RNA single mismatches.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- RNA tertiary structure and conformational dynamics revealed by BASH MaP.bioRxiv : the preprint server for biology · 2024Article
- An RNA excited conformational state at atomic resolution.Nature communications · 2023Article
- pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31.Biophysical chemistry · 2022Article
- Electronic Circular Dichroism of the Cas9 Protein and gRNA:Cas9 Ribonucleoprotein Complex.International journal of molecular sciences · 2021Article
- Identification of key sequence features required for microRNA biogenesis in plants.Nature communications · 2020Article
- RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures.Database : the journal of biological databases and curation · 2020Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- Enhancing potency of siRNA targeting fusion genes by optimization outside of target sequence.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- A Tandem Oligonucleotide Approach for SNP-Selective RNA Degradation Using Modified Antisense Oligonucleotides.PloS one · 2015Article
- Hybridization Properties of RNA Containing 8-Methoxyguanosine and 8-Benzyloxyguanosine.PloS one · 2015Article
- Hierarchy of RNA functional dynamics.Annual review of biochemistry · 2014Review
- Effect of sodium ions on RNA duplex stability.Biochemistry · 2013Article
- A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations.Journal of the American Chemical Society · 2013Article
- Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site.Biochemistry · 2013Article
- RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures.Nucleic acids research · 2012Article
- A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA.RNA (New York, N.Y.) · 2011Article
- Molecular recognition of 6'-N-5-hexynoate kanamycin A and RNA 1x1 internal loops containing CA mismatches.Biochemistry · 2011Article
- NMR spectroscopy and molecular dynamics simulation of r(CCGCUGCGG)₂ reveal a dynamic UU internal loop found in myotonic dystrophy type 1.Biochemistry · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence-structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.
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