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Figure 4.
Figure 4. General Rules for Cation Binding in the Major
Groove of G•U Motifs
(A) Schematic of the arrangement of
major groove functional groups for PM01, PM05, and PM09. These
three variants vary only in the orientation of flanking G-C
pairs relative to the tandem G•U pairs. Blue circles are
amine, red are carbonyls, and orange are purine N7 groups. In
PM01, the two major groove amines (from cytosine) are placed
away from the binding site due to the turn of the helix. In PM05
and PM09, the amines are placed in position to limit the
mobility of the ion (shown in green). In addition, the location
of carbonyls and N7 groups in the flanking sequences and close
to the binding site make the ion more mobile as it attempts to
satisfy multiple potential hydrogen binding partners.
(B)
Schematic of the arrangement of major groove functional groups
in the four single G•U pair containing variants. In single
G•U pairs, the amines are best placed in the 3′ positions to
withdraw them from the pocket.
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