Manganese ion binding sites at RNA duplexes

In an X-ray analysis of the yeast tRNA , a specific magnesium-binding site in the vicinity of a G4-U69 wobble base pair was foimd. Thus it seemed attractive to study if a G-U pair is a specific binding site for magnesium ions. Addition of the diamagnetic Mg cation has only little, though measurable, effects on the chemical shifts of the imino resonances ( 0.05 ppm). Since it is known from a number of biological and biochemical studies that 

Indeed, specific imino line broadenings were found upon addition of manganese ions for the tRNA acceptor stem duplexes with and without ACCA terminus (Fig. 19.3). 

These manganese ion-binding studies have been extended by analyzing several other RNA duplexes that were derived from tRNA acceptor stems [33]. These included sequence variants of the E. coli tRNA (with G3-C70 and I3-U70 base pairs), E. coli tRNA°, tRNA acceptor duplexes, as well as yeast tRNA , and tRNA acceptor stems. 

It could be concluded that G-U pairs indeed have a potential for specific binding of divalent cations. However, similar broadening effects for the tRNA acceptor stem variant with a G3-C70 instead of the G3-U70 base pair were also observed. There the largest Une width increase is likewise observed for the G imino proton of base pair 2, followed by a slightly smaller broadening for the G3 imino resonance [33]. Analysis of several fiirther duplexes led to the conclusion that stretches of four consecutive purines also create sites of preferred binding of manganese ions. 

Though one-dimensional H NMR studies of the tRNA acceptor arm gave hints to the special role of the G-U base pair, detailed information on the possible modifications of the local helical geometry in the vicinity of the G-U pair caimot be obtained by these experiments. 

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