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 spermicline was observed by NMR. The selective effect of spermidine was lost when the bulged-out region of U6-34 was removed in U6-34(Delta 5). The binding of NS1-2 peptide to U6-34(Delta 5) was inhibited both by spermidine and Mg2+. The selective structural change of U6-34 by spermidine was confirmed by circular dichroism. (c) 2008 Elsevier Inc. All rights reserved.