Models of double-stranded nucleic acids. Top row, end-on view of the indicated double-stranded nucleic acid. Bottom row, view oriented to highlight the major and minor grooves. Phosphate groups (PO3) = yellow, Ribose 2′ O = magenta, 2′ H = black. Note that in dsRNA the yellow phosphate groups are oriented into the major groove, whereas in DNA and RNA:DNA hybrid molecules they are oriented toward the surface. Conversely, the magenta and black ribose 2′ hydroxyl are oriented toward the surface in dsRNA such that they are accessible along the length of the helix (end on view), whereas in RNA:DNA hybrid molecules they are displaced into the minor groove. Nucleic acid models generated using PDB files 1ZF0 for dsDNA, 280D for dsRNA, and 1FIX for the RNA:DNA hybrid from RSCB Protein Data Bank (http://www.pdb.org).
