ArticleNucleic acids research2008
Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures.Scientific reports · 2025Article
- ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations.Genome biology · 2025Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs.RNA (New York, N.Y.) · 2024Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA 3D Modeling with FARFAR2, Online.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Importance of Anion-π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study.Journal of chemical theory and computation · 2021Article
- High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals.Crystals · 2021Article
- In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules.Nucleic acids research · 2021Article
- Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.Nucleic acids research · 2020Article
- Conformational adaptation of UNCG loops upon crowding.RNA (New York, N.Y.) · 2019Article
- Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers.Cold Spring Harbor perspectives in biology · 2019Review
- Rational Design of an Orthogonal Pair of Bimolecular RNase P Ribozymes through Heterologous Assembly of Their Modular Domains.Biology · 2019Article
- Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch.Nucleic acids research · 2019Article
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3 authors.
Funding
Abstract
Specific recognitions of GNRA tetraloops by small helical receptors are among the most widespread long-range packing interactions in large ribozymes. However, in contrast to GYRA and GAAA tetraloops, very few GNRA/receptor interactions have yet been identified to involve GGAA tetraloops in nature. A novel in vitro selection scheme based on a rigid self-assembling tectoRNA scaffold designed for isolation of intermolecular interactions with A-minor motifs has yielded new GGAA tetraloop-binding receptors with affinity in the nanomolar range. One of the selected receptors is a novel 12 nt RNA motif, (CCUGUG ... AUCUGG), that recognizes GGAA tetraloop hairpin with a remarkable specificity and affinity. Its physical and chemical characteristics are comparable to those of the well-studied '11nt' GAAA tetraloop receptor motif. A second less specific motif (CCCAGCCC ... GAUAGGG) binds GGRA tetraloops and appears to be related to group IC3 tetraloop receptors. Mutational, thermodynamic and comparative structural analysis suggests that natural and in vitro selected GNRA receptors can essentially be grouped in two major classes of GNRA binders. New insights about the evolution, recognition and structural modularity of GNRA and A-minor RNA-RNA interactions are proposed.
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