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(A) Schematic representation of the mapping of four nucleotides with the nucleoside in blue and the phosphate in red. (B) The definition of the coordinate system from the oriented base, for two nucleotides. Dashed lines represent the projection of the vector that joins both bases in the x-y plane of each nucleoside. The base–base interactions, the base-phosphate interactions, and the interactions along the backbone are defined with respect to this reference frame.
