We presented our work on isotopically labeled RNA hairpins used as model complexes between let-7 miRNA and the binding sites on lin-41 mRNA. The 3D structures of RNA constructs were determined with the use of standard 2D and 3D NMR techniques. Phages were used to align the RNA constructs and to acquire residual dipolar couplings. NMR restraint computer simulations showed that RNAs fold into stable structures consisting of two stem regions separated by an asymmetric internal loop. Stems were stabilized by Watson-Crick base pairs. The asymmetric internal loop from second binding site (LCS2) adopted a well-defined structure. Three uracils formed a base triple, while the two adenines formed AA base pair. The asymmetric internal loop from first binding site (LCS1) was less defined. These interesting structural elements make complex between miRNA and mRNA different in comparison to a common A-form RNA.
B.03 Paper at an international scientific conference
COBISS.SI-ID: 4204058Work focused on let-7 miRNAs that imperfectly binds two times to 3’-UTR of lin-41 mRNAs (LCS1 and LCS2) and regulates developmental timing of nematode C. elegans. 13C,15N-labeled RNA hairpins were prepared for both binding sites. Their structures in solution were determined with the use of standard NMR techniques. Simulated annealing with restrained molecular dynamics showed that RNA folded into stable structures consisting of two stems separated by an asymmetric internal loop. The asymmetric internal loop of a RNA mimicking second binding site (LCS2) adopted a well defined structure. Three uracils formed a base triple, while the two adenines formed AA base pair. The analysis of helical parameters of the both stems showed that internal loop induced bend between stems, which leaded to increase in the wideness of the major groove. The asymmetric internal loop of RNA mimicking first binding site (LCS1) was less defined. All these structural elements of both binding sites are important for recognition inside the ribonucleoprotein complexes (miRNPs).
B.03 Paper at an international scientific conference
COBISS.SI-ID: 4266778