Skip to main content
. Author manuscript; available in PMC: 2013 Jan 10.
Published in final edited form as: J Chem Theory Comput. 2011 Dec 8;8(1):335–347. doi: 10.1021/ct200712b

Figure 11.

Figure 11

Atomic-level representation of the two-layered GpUpA/GpA miniduplex from the Escherichia coli 23S rRNA sarcin/ricin domain (PDB ID: 3dvz36) showing the anti-parallel 5′→3′ GpUpA trinucleotide (G2655pU2656pA2657) and the non-adjacent GpA dinucleotide (G2664pA2665). The O2′…O2P (purple dashed line) forms an out-of-plane edge above the GpU platform submotif that is specifically recognized by the non-adjacent G2664 (green and black dashed lines). The nucleotides in the lower plane (the GpU platform and the non-adjacent A2665) are depicted with filled sugar and nucleobase rings, while those in the upper plane (A2657 and the non-adjacent G2664) are represented by stick models with unfilled rings. Left, view perpendicular to the GpU platform plane; right, view in the platform (lower) plane.