STRUCTURE OF D(T)N.D(A)N.D(T)N - THE DNA TRIPLE HELIX HAS B-FORM GEOMETRY WITH C2'-ENDO SUGAR PUCKER

The polynucleotide helix d(T)n.d(A)n.d(T)n is the only deoxypolynucleotide triple helix for which a structure has been published, and it is generally assumed as the structural basis for studies of DNA triplexes. The helix has been assigned to an A-form conformation with C3'-endo sugar pucker by Arnott and Selsing [1974; cf. Arnott et al. (1976)]. We show here by infrared spectroscopy in D2O solution that the helix is instead B-form and that the sugar pucker is in the C2'-endo region. Distamycin A, which binds only to B-form and not to A-form helices, binds to the triple helix without displacement of the third strand, as demonstrated by CD spectroscopy and gel electrophoresis. Molecular modeling shows that a stereochemically satisfactory structure can be built using C2'-endo sugars and a displacement of the Watson-Crick base-pair center from the helix axis of 2.5 angstrom. Helical constraints of rise per residue (h = 3.26 angstrom) and residues per turn (n = 12) were taken from fiber diffraction experiments of Arnott and Selsing (1974). The conformational torsion angles are in the standard B-form range, and there are no short contacts. In contrast, we were unable to construct a stereochemically allowed model with A-form geometry and C3'-endo sugars. Arnott et al. (1976) observed that their model had short contacts (e.g., 2.3 angstrom between the phosphate-pendent oxygen on the A strand and O2 in the Hoogsteen-paired thymine strand) which are generally known to be outside the allowed range. We conclude that the triple helix d(T)n.d(A)n.d(T)n has a conformation of the B-form with sugar pucker near C2'-endo geometry. We note that since the two T strands are antiparallel, identical conformations of the two strands will result in a dyad relating the T strands.