ArticleRNA (New York, N.Y.)2010
On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 43 citations in OpenAlex.
- SARS-CoV-2 reshapes mNAR molecular medicine · 2025Article
- The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.PloS one · 2023Article
- RNA folding using quantum computers.PLoS computational biology · 2022Article
- PolyPurine Reverse Hoogsteen Hairpins Work as RNA Species for Gene Silencing.International journal of molecular sciences · 2021Article
- Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs.Nucleic acids research · 2020Article
- Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies.RNA (New York, N.Y.) · 2019Article
- Going beyond base-pairs: topology-based characterization of base-multiplets in RNA.RNA (New York, N.Y.) · 2019Article
- Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches.ACS omega · 2019Article
- The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN.Nature communications · 2018Article
- How Does MgBiophysical journal · 2017Article
- Structural landscape of base pairs containing post-transcriptional modifications in RNA.RNA (New York, N.Y.) · 2017Article
- An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.Nucleic acids research · 2015Article
- RNABP COGEST: a resource for investigating functional RNAs.Database : the journal of biological databases and curation · 2015Article
- Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs.Nucleic acids research · 2014Article
- Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position.Journal of molecular modeling · 2012Article
- Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?The journal of physical chemistry. B · 2010Article
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Authors and funding
4 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
We use a combination of database analysis and quantum chemical studies to investigate the role of cis and trans Hoogsteen:Hoogsteen (H:H) base pairs and associated higher-order structures in RNA. We add three new examples to the list of previously identified base-pair combinations belonging to these families and, in addition to contextual classification and characterization of their structural and energetic features, we compare their interbase interaction energies and propensities toward participation in triplets and quartets. We find that some base pairs, which are nonplanar in their isolated minimum energy geometries, attain planarity and stability upon triplet formation. A:A H:H trans is the most frequent H:H combination in RNA structures. This base pair occurs at many distinct positions in known rRNA structures, where it helps in the interaction of ribosomal domains in the 50S subunit. It is also present as a part of tertiary interaction in tRNA structures. Although quantum chemical studies suggest an intrinsically nonplanar geometry for this base pair in isolated form, it has the tendency to attain planar geometry in RNA crystal structures by forming higher-order tertiary interactions or in the presence of additional base-phosphate interactions. The tendency of this base pair to form such additional interactions may be helpful in bringing together different segments of RNA, thus making it suitable for the role of facilitator for RNA folding. This also explains the high occurrence frequency of this base pair among all H:H interactions.
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