Reports

RNA Tertiary Structure Mediation by Adenosine Platforms

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Science  20 Sep 1996:
Vol. 273, Issue 5282, pp. 1696-1699
DOI: 10.1126/science.273.5282.1696

Figures

  • Fig. 1.

    (A) Schematic secondary structure of the P4-P6 domain, with adenosine platforms in boldface. The noncanonical base pair below each platform is also shown. (B) Location of adenosine platforms in the crystal structure. The structure is shown in the same orientation as that of (A); adenosines of the platforms are highlighted in blue and green, while the backbone positions of the wobble base pairs below the platforms are indicated in red. Blue adenosines are accessible to dimethyl sulfate in the presence and absence of the docking partner associated with the platform; green adenosines are protected from dimethyl sulfate modification when the docking partner is present (see text and Fig. 3 for details). (C) Another view of the crystal structure, rotated 90° about the long axis of the molecule. The conserved core region is to the right in (A) and (B) and the core faces the reader in (C). This figure was prepared by means of the molecular graphics program RIBBONS (24).

  • Fig. 2.

    (A) View of an adenosine platform looking down the helix axis. N3 of the 5′ A and N6 of the 3′ A are within hydrogen bonding distance (2.8 to 3.4 Å). Closed arrow, N1 position of the 5′ A, which is protected from dimethyl sulfate when the long-range contact is formed; open arrow, N1 position of the 3′ A which shows variable dimethyl sulfate protection (see 18). (B) The adenosine platform in the tetraloop receptor; color scheme as in Fig. 1. (C) Stereo view from underneath the platform, looking up the helix axis. Figure prepared with RIBBONS (24).

  • Fig. 3.

    The different kinds of long-range interactions that occur near the adenosine platforms. At left and in the center, reciprocal interactions occur between L5c and J6/6a in the two molecules in the asymmetric unit of the crystal; at right, the tetraloop docks above the platform in the tetraloop receptor. The docking partner for each platform is shaded. Blue adenosines (circles) are accessible to dimethyl sulfate in the presence and absence of the docking partner associated with the platform. Green adenosines (squares) are protected from dimethyl sulfate modification when the docking partner is present. The noncanonical base pair below each platform is highlighted in red.