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Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation

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Abstract

The structure of a hairpin loop—in particular its large accessible surface area and its exposed hydrogen-bonding edges—facilitate an inherent possibility for interactions. Just like higher-order RNA macromolecules, pre-microRNAs possess a hairpin loop, and it plays a crucial role in miRNA biogenesis. Upon inspecting the crystal structures of RNAs with various functions, we noticed that, along with a fairly long double helix, the RNAs contained sequentially different hairpin loops comprising four residues. We therefore applied molecular dynamics simulation to analyze six of these previously unexplored tetraloops, along with GNRA (where N is any nucleotide and R is a purine nucleotide) tetraloops, to understand their structural and functional characteristics. A number of analyses quantifying loop stability by examining base–base stacking, base–sugar and base–phosphate hydrogen bonding, and backbone variability were performed. Importantly, we determined the different interbase stacking preferences of the single-stranded unpaired bases of the hairpin loops, which had not previously been quantified in any form. Furthermore, our study indicates that canonical GNRA structural properties are exhibited by some structures containing non-GNRA loop sequences.

Stacking overlap at loop region

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Acknowledgements

We would like to thank the Bioinformatics Resources and Applications Facility (BRAF), C-DAC, Pune for providing computation facilities.

Funding

This work was supported by the Department of Atomic Energy, India through the BARD project and the Department of Biotechnology, Govt. of India.

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  1. Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India

    Debasish Mukherjee & Dhananjay Bhattacharyya

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Mukherjee, D., Bhattacharyya, D. Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation. J Mol Model 23, 300 (2017). https://doi.org/10.1007/s00894-017-3470-1

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