ArticleJournal of computer-aided molecular design
Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis.
Article in Journal of computer-aided molecular design. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- NMR structures of small molecules bound to a model of a CUG RNA repeat expansion.Bioorganic & medicinal chemistry letters · 2024Review
- NMR structures and magnetic force spectroscopy studies of small molecules binding to models of an RNA CAG repeat expansion.bioRxiv : the preprint server for biology · 2024Article
- NMR structures of small molecules bound to a model of an RNA CUG repeat expansion.bioRxiv : the preprint server for biology · 2024Article
- RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.Interdisciplinary sciences, computational life sciences · 2022Article
- The effect of mutation in the stem of the MicroROSE thermometer on its thermosensing ability: insights from molecular dynamics simulation studies.RSC advances · 2022Article
- Novel mechanisms of the conformational transformations of the biologically important G·C nucleobase pairs in Watson-Crick, Hoogsteen and wobble configurationsRSC advances · 2021Article
- Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches.Journal of computer-aided molecular design · 2020Article
- Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs.Biochemistry · 2019Article
- Evidence for Hidden Involvement of N3-Protonated Guanine in RNA Structure and Function.ACS omega · 2019Article
- Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies.Journal of molecular modeling · 2017Article
- Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation.Journal of molecular modeling · 2017Article
- Melting of polymeric DNA double helix at elevated temperature: a molecular dynamics approach.Journal of molecular modeling · 2017Article
- How Does MgBiophysical journal · 2017Article
- Structural landscape of base pairs containing post-transcriptional modifications in RNA.RNA (New York, N.Y.) · 2017Article
- RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.Journal of computer-aided molecular design · 2017Article
- Role of indirect readout mechanism in TATA box binding protein-DNA interaction.Journal of computer-aided molecular design · 2015Article
- RNABP COGEST: a resource for investigating functional RNAs.Database : the journal of biological databases and curation · 2015Article
- Analysis of stacking overlap in nucleic acid structures: algorithm and application.Journal of computer-aided molecular design · 2014Article
- Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs.Journal of computer-aided molecular design · 2014Article
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3 authors.
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Abstract
Non-canonical base pairs contribute immensely to the structural and functional variability of RNA, which calls for a detailed characterization of their spatial conformation. Intra-base pair parameters, namely propeller, buckle, open-angle, stagger, shear and stretch describe structure of base pairs indicating planarity and proximity of association between the two bases. In order to study the conformational specificities of non-canonical base pairs occurring in RNA crystal structures, we have upgraded NUPARM software to calculate these intra-base pair parameters using a new base pairing edge specific axis system. Analysis of base pairs and base triples with the new edge specific axis system indicate the presence of specific structural signatures for different classes of non-canonical pairs and triples. Differentiating features could be identified for pairs in cis or trans orientation, as well as those involving sugar edges or C-H-mediated hydrogen bonds. It was seen that propeller for all types of base pairs in cis orientation are generally negative, while those for trans base pairs do not have any preference. Formation of a base triple is seen to reduce propeller of the associated base pair along with reduction of overall flexibility of the pairs. We noticed that base pairs involving sugar edge are generally more non-planar, with large propeller or buckle values, presumably to avoid steric clash between the bulky sugar moieties. These specific conformational signatures often provide an insight into their role in the structural and functional context of RNA.
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