Symmetry and molecular structure of a DNA triple helix: d(T)n.cntdot.d(A)n.cntdot.d(T)n

Abstract

A structure for the triple helix d(T)n.d(A)n.d(T)n consistent with recent infrared spectral data is proposed, and its salient features are discussed. The present structure preserves the pseudodyad between the Watson-Crick base-paired adenine and thymine strands and in addition has a pseudorotational symmetry relating the Hoogsteen-paired adenine and thymine strands. The simultaneous presence of these two symmetries gives rise to a dyad between the two thymine polynucleotides. These symmetries result in identical backbone conformations for all three strands, unlike any previously proposed model for a triple helix. The proposed structure has an axial rise per residue of 3.26 A and 12 residues per turn obtained from X-ray fiber diffraction [Arnott S., & Selsing, E. (1974) J. Mol. Biol. 88, 509-521]. The present structure is structurally and conformationally similar to double helical B-form DNA and has sugar pucker in the C2'-endo region. This structure is fundamentally different from the one proposed by Arnott and co-workers, which was based on structural and conformational features similar to double helical A-form DNA with C3'-endo sugar pucker. It is stereochemically satisfactory, and it does not have the disallowed nonbonded distances present in the earlier model of Arnott and co-workers. It is energetically much more favorable than their structure. Coordinates of the present structure are given.