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Tertiary structure-based analysis of microRNA arget interactionsHIN HARK GAN1,3 and KRISTIN C.Pramipexole dihydrochloride GUNSALUS1,2,1Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA New York University, Abu Dhabi, United Arab EmiratesABSTRACT Current computational analysis of microRNA interactions is based largely on primary and secondary structure analysis.Lusutrombopag Computationally efficient tertiary structure-based methods are needed to enable more realistic modeling of the molecular interactions underlying miRNA-mediated translational repression.PMID:32695810 We incorporate algorithms for predicting duplex RNA structures, ionic strength effects, duplex entropy and free energy, and docking of duplex rgonaute protein complexes into a pipeline to model and predict miRNA arget duplex binding energies. To ensure modeling accuracy and computational efficiency, we use an all-atom description of RNA and a continuum description of ionic interactions using the PoissonBoltzmann equation. Our method predicts the conformations of two constructs of Caenorhabditis elegans let-7 miRNA arget duplexes to an accuracy of 3.8 root mean square distance of their NMR structures. We also show that the computed duplex formation enthalpies, entropies, and free energies for eight miRNA arget duplexes agree with titration calorimetry data. Analysis of duplex rgonaute docking shows that structural distortions arising from single-base-pair mismatches in the seed region influence the activity of the complex by destabilizing both duplex hybridization and its association with Argonaute. Collectively, these results demonstrate that tertiary structure-based modeling of miRNA interactions can reveal structural mechanisms not accessible with current secondary structure-bas.