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Figure 5
Relationship between the dinucleotide conformer and peak locations. (a) Classification of the region around P atoms. The region surrounded by P, O3′, OP1 and O5′ is referred to as subregion A. Similarly, the region surrounded by P, O3′, OP1 and OP2, the region surrounded by P, O3′, OP2 and O5′, and the region surrounded by P, OP1, OP2 and O5′ are referred to as subregions B, C and D, respectively. Subregions A and C are opposed to the minor and major grooves, respectively. (b) Peak frequency in each subregion for dinucleotide conformers. ZI and ZII were assigned to R–Y steps for Z-DNA. Z was assigned to Y–R steps. (c) Peaks in A/B, ZI and ZII. Yellow spheres indicate peak locations. Each dinucleotide is superimposed on a representative structure of each conformer (grey). The representative structures were PDB entries 460d (A3-A4) for A/B, 3p4j (B10-B11) for ZI and 3p4j (A4-A5) for ZII. (Letters in parentheses indicate chain IDs and residue IDs.) The representative structures were also superimposed on known multiple conformations: green, PDB entry 3wbo (B8-B9), and cyan, PDB entry 4ocb (A8-A9), for ZI; green, PDB entry 3wbo (A4-A5), and cyan, PDB entry 4ocb (A8-A9), for ZII; green, PDB entry 3ggk (A7-A8), and cyan, PDB entry 3ggk (A1-A2), for A/B. C3′, C4′ and O3′ in the residue and P, OP1, OP2, C5′ and O5′ in the next residue were used for superimposition. Only dinucleotides containing DA, DT, DG or DC in both steps were used to draw these figures. If several peaks were found at the location of an atom, the strongest peak was used to draw the figure.

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ISSN: 2059-7983
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