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Understanding the Binding Affinity and Specificity of miRNAs: A Molecular Dynamics Study

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Advances in Computational Modeling and Simulation

Part of the book series: Lecture Notes in Mechanical Engineering ((LNME))

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Abstract

MicroRNAs (miRNA) are endogenously produced small (21–27 nucleotides long) non-coding RNA molecules that can play post-transcriptional regulation of gene expression either by cleavage of the mRNA strand or by translational repression. However, recognizing mRNA targets by miRNAs is not clearly understood. It is observed that one miRNA molecule can target hundreds of different mRNA sites and different miRNAs can target a single mRNA site. The majority of miRNA target prediction algorithms mainly consider the complementarity on the seed region of miRNA for their target selection. To explore the role of different regions of miRNA for target selection, explicit solvent unrestrained molecular dynamics simulation has been performed on miRNA-RNA duplex. Our studies revealed that seed region complementary base pairing is sufficient to maintain the integrity of the duplex, whereas bulge and 3′ end regions are highly flexible which can interact with target mRNA through non-canonical hydrogen bonds and regulate translational repression.

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Acknowledgements

We would like to acknowledge the HPC facilities of BITS-Pilani, Pilani campus.

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Authors and Affiliations

  1. Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani Campus, Pilani, RJ, 333031, India

    Swarnima Kushwaha, Ayushi Mandloi & Shibasish Chowdhury

Authors
  1. Swarnima Kushwaha
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  2. Ayushi Mandloi
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  3. Shibasish Chowdhury
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Corresponding author

Correspondence to Shibasish Chowdhury .

Editor information

Editors and Affiliations

  1. Department of Civil Engineering, Birla Institute of Technology and Scienc, Pilani, Rajasthan, India

    Rallapalli Srinivas

  2. Department of Mathematics, Birla Institute of Technology and Scienc, Pilani, Rajasthan, India

    Rajesh Kumar

  3. Department of Biotechnology, Birla Institute of Technology and Scienc, Dubai, United Arab Emirates

    Mainak Dutta

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This research did not receive any specific grant from funding agencies.

Author Contributions

SC conceived, designed, and supervised the overall project; AM carried out initial modeling work; and SK, AM, and SC performed data analysis and wrote the manuscript. All authors have approved the final version of the manuscript.

Conflict of Interest

All the authors declare no conflict of interest.

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Kushwaha, S., Mandloi, A., Chowdhury, S. (2022). Understanding the Binding Affinity and Specificity of miRNAs: A Molecular Dynamics Study. In: Srinivas, R., Kumar, R., Dutta, M. (eds) Advances in Computational Modeling and Simulation. Lecture Notes in Mechanical Engineering. Springer, Singapore. https://doi.org/10.1007/978-981-16-7857-8_19

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  • DOI: https://doi.org/10.1007/978-981-16-7857-8_19

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-16-7856-1

  • Online ISBN: 978-981-16-7857-8

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