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. 2012 May 28;40(16):8111–8118. doi: 10.1093/nar/gks426

Figure 3.

Figure 3.

Crystal structure comparisons. The red and yellow balls represent the oxygen and selenium atoms of the modified moieties, respectively. (A) The superimposed duplex structures of 5′-G(SedU)G(mo5dU)ACAC-3′ (3a; in red; PDB ID: 3LTR; 1.30 Å resolution) and the corresponding native (in green; PDB ID: 1DNS; 2.0 Å resolution). (B) The superimposed single-strand structures of 3a (5-OMe-DNA; in red), 3b (5-SMe-DNA; in blue; PDB ID: 3IKI; 1.38 Å resolution), 3c (5-SeMe-DNA; in yellow; PDB ID: 3LTU; 1.40 Å resolution) and the corresponding native (in green; PDB ID: 1DNS). This high-resolution structure of 5-SeMe-DNA (3c), indicating no H-bond formation between the 5-SeMe and 5′-phosphate groups, updates the lower-resolution structure (PDB ID: 3BM0). (C) Superimposed modified dU4 and T4 residues in these four DNAs. (D) Superimposed local structures of dG3 in these four DNAs. (C and D are in the same color code as B). (E) The superimposed structures of mo5dU4/dA base pair of 3a (3LTR; in red), T4/dA of the native (1DNS; in green], and the native T4/dA base pair of 5′-G(SedU)GTACAC-3′ (1Z7I; in cyan; 1.28 Å resolution). The native T4 of 5′-G(SedU)GTACAC-3′ (PDB ID: 1Z7I; 1.28 Å resolution) is displayed, since the resolution of the native structure (1DNS; 2.0 Å resolution) is low and the highly ordered water molecules at T4 are not demonstrated. These two structures (1Z7I and 1DNS) are virtually identical.