Parallel nucleic acid helices with Hoogsteen base pairing: symmetry and structure.

Molecular structures for parallel DNA and RNA double helices with Hoogsteen pairing are proposed for the first time. The DNA helices have sugars in the C2'-endo region and the phosphodiester conformations are (trans, gauche-), and the RNA helices have sugars in the C3'-endo region and the phosphodiester conformations are (gauche-, gauche-). A pseudorotational symmetry relates the two parallel strands of DNA helices and a screw symmetry relates the two strands of RNA helices, which have an associated tilt of the bases. The conformational space of parallel helices with Hoogsteen base pairing, unlike the Watson-Crick duplex, is highly restricted due to the unique positioning of the symmetry axis in the former case. The features of the parallel double helix with Hoogsteen pairing are compared with the Watson-Crick duplex and the corresponding triple helix.