Selective structural change of bulged-out region of double-stranded RNA containing bulged nucleotides by spermidine

Polyamines are essential for cell growth due to effects mainly at the level of translation. These effects likely involve a structural change, induced by polyamines, of the bulged-out region of double-stranded RNA that is different from changes induced by Mg2+. Structural changes were studied using U6–34, a model RNA of U6 small nuclear RNA containing bulged nucleotides. Binding of NS1–2 peptide derived from the RNA binding site of NS1 protein, to U6–34 was inhibited by spermidine but not by Mg2+. A selective conformational change of the bases in the bulged-out region of U6–34 induced by spermidine was observed by NMR. The selective effect of spermidine was lost when the bulged-out region of U6–34 was removed in U6–34(Δ5). The binding of NS1–2 peptide to U6–34(Δ5) was inhibited both by spermidine and Mg2+. The selective structural change of U6–34 by spermidine was confirmed by circular dichroism.