ArticleBMC research notes2014
Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps.
Article in BMC research notes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 14 citations in OpenAlex.
- Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.Scientific reports · 2019Article
- Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation.Journal of molecular modeling · 2017Article
- Structure of RNA Stem Loop B from the Picornavirus Replication Platform.Biochemistry · 2017Article
- RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.Journal of computer-aided molecular design · 2017Article
- 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
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSequence determines the three-dimensional structure of RNAs, and thereby plays an important role in carrying out various biological functions. RNA duplexes containing Watson-Crick (WC) basepairs, interspersed with non-Watson-Crick basepairs, are the dominant structural unit and form the scaffold for the 3-dimensional structure of RNA. It is therefore crucial to understand the geometric variation in the dinucleotide steps that form the helices. We have carried out a detailed analysis of the dinucleotide steps formed by AU and GC Watson-Crick basepairs in RNA structures (both free and protein bound) and compared the results to that seen in DNA. Further, the effect of protein binding on these steps was examined by comparing steps in free RNA structures with protein bound RNA structures.
resultsCharacteristic sequence dependent geometries are observed for the RR, RY and YR type of dinucleotide steps in RNA. Their geometric parameters show correlated variations that are different from those observed in B-DNA helices. Subtle, but statistically significant differences are seen in roll, slide and average propeller-twist values, between the dinucleotide steps of free RNA and protein bound RNA structures. Many non-canonical cross-strand and intra-strand hydrogen bonds were identified that can stabilise the RNA dinucleotide steps, among which YR steps show presence of many new unreported interactions.
conclusionsOur work provides for the first time a detailed analysis of the conformational preferences exhibited by Watson-Crick basepair containing steps in RNA double helices. Overall, the WC dinucleotide steps show considerable conformational variability. Furthermore, we have identified hydrogen bond interactions in several of the dinucleotide steps that could play a role in determining the preferred geometry, in addition to the intra-basepair hydrogen bonds and stacking interactions. Protein binding affects the conformation of the steps that are in direct contact, as well as allosterically affect the steps that are not in direct physical contact.
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