Abstract
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs' folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg(2+)-dependent, furthermore, the Mg(2+)-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg(2+) to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg(2+), and tolerate mutations at key tertiary motifs at high Mg(2+), which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.