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Default NMR Characterization of an Oligonucleotide Model of the MiR-21 Pre-Element.

NMR Characterization of an Oligonucleotide Model of the MiR-21 Pre-Element.

Related Articles NMR Characterization of an Oligonucleotide Model of the MiR-21 Pre-Element.

PLoS One. 2014;9(9):e108231

Authors: Chirayil S, Wu Q, Amezcua C, Luebke KJ

Abstract
We have used NMR spectroscopy to characterize an oligonucleotide stem loop structure based on the pre-element of an oncogenic microRNA, miR-21. This predicted stem-loop structure is cleaved from the precursor of miR-21 (pre-miR-21) by the nuclease Dicer. It is also a critical feature recognized by the protein complex that converts the primary transcript (pri-miR-21) into the pre-miRNA. The secondary structure of the native sequence is poorly defined by NMR due to rapid exchange of imino protons with solvent; however, replacement of two adjacent putative GU base pairs with GC base pairs retains the conformation of the hairpin observed by chemical probing and stabilizes it sufficiently to observe most of the imino proton resonances of the molecule. The observed resonances are consistent with the predicted secondary structure. In addition, a peak due to a loop uridine suggests an interaction between it and a bulged uridine in the stem. Assignment of non-exchangeable proton resonances and characterization of NOEs and coupling constants allows inference of the following features of the structure: extrahelicity of a bulged adenosine, deviation from A-form geometry in a base-paired stem, and consecutive stacking of the adenosines in the 5' side of the loop, the guanosine of the closing base pair, and a cross-strand adenosine. Modeling of the structure by restrained molecular dynamics suggests a basis for the interaction between the loop uridine, the bulged uridine in the stem, and an AU base pair in the stem.


PMID: 25250627 [PubMed - as supplied by publisher]



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