Figure 2.

Overall structure of the aptamer within the aptamer–hFc1 complex. (a) Tertiary (left) and secondary (right) structures of the bound aptamer. Ca²⁺ is shown as green sphere. The nucleotide sequences are color coded as follows: adenine, red; guanine, cyan; 2′-fluoro uridine, green; and 2′-fluoro cytidine, yellow. (b) U6:A18:U9 base triple. The interactions are indicated with thin dashed lines and the distances (Å) are given in black. RNA atoms are colored, red, blue, light blue and orange for oxygen, nitrogen, fluorine and phosphorus, respectively. The color coding of the carbon is the same as in Figure 2 a. (c) Interaction between the H8 of G7 and the 2′-fluoro of U6. The H8 atom is shown at the calculated ideal positions. (d) Functional annotation of base substitutions and ribose 2′ modifications in the anti-hFc1 aptamer. Base substitutions described previously (19) and those newly manipulated in this study are indicated in the M-fold structure of Apt8-2 (19), a functional derivative of the aptamer used for crystallization. Each oligonucleotide with the indicated substitutions were chemically synthesized and examined for affinity to hIgG1 by SPR. Nucleotide symbols: N (black), RNA; n (green), DNA; fN (blue), 2′-fluoro modification; and mN (orange), 2′ O-methyl modification. All substitutions shown here completely abrogated binding activity.