Fig. 4.Surface potentials of common mismatches found in double stranded RNA. In each case the mismatches are found in A-form RNA with the major groove shown on the left and the minor groove shown on the right. [top] A-RNA with tandem G-U wobble pairs. The major groove displays more negative potential and the minor groove displays more positive potential. [middle] A-RNA with tandem G-A mismatches in the sheared conformation. Again the major groove has increased negative potential but the minor groove is not significantly different as seen in wild-type RNA (see Fig .3, middle). Sheared G-A base pairs are well-known metal-binding sites. [bottom] A-RNA with tandem G-A mismatches in the imino-hydrogen bonded conformation. The major groove has strong negative and positive potentials and the minor groove has increased positive potential.
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