Modulation of RNA metal binding by flanking bases: 15N NMR evaluation of GC, tandem GU, and tandem GA sites

Abstract

(15)N NMR chemical shift changes in the presence of Mg(H(2)O)(6)(2+), Zn(2+), Cd(2+), and Co(NH(3))(6)(3+) were used to probe the effect of flanking bases on metal binding sites in three different RNA motifs. We found that: for GC pairs, the presence of a flanking purine creates a site for the soft metals Zn(2+) and Cd(2+) only; a GG.UU motif selectively binds only Co(NH(3))(6)(3+), while a UG.GU motif binds none of these metals; a 3' guanosine flanking the adenosine of a sheared GA.AG pair creates an unusually strong binding site that precludes binding to the cross-strand stacked guanosines within the tandem pair.

Figure 1

Specifically labeled RNA molecules 1–6 synthesized with the designated specifically labeled nucleosides a-f. Molecules 5 and 6 have previously been reported, and are included for comparison. The labeled nucleosides are: a, [1,7,NH₂-¹⁵N₃]-guanosine; b, [7-¹⁵N]-guanosine; c, [8-¹³C-7-¹⁵N]-guanosine; d, [2-¹³C-1,7,NH₂-¹⁵N₃]-guanosine; e, [8-¹³C-1,7,NH₂-¹⁵N₃]-guanosine; and f, [8-¹³C-1,7,NH₂-¹⁵N₃]-adenosine.