NMR spectroscopic determination of the solution structure of a branched nucleic acid from residual dipolar couplings by using isotopically labeled nucleotides.

Branched nucleic acids play important biological roles, and well-known examples such as the Hammerhead ribozyme, the all-RNA enzyme, a three-way junction (3H according to IUPAC nomenclature), and the Holliday junctions or DNA four-way junctions (J6, Figure 1a; 4H according to IUPAC nomenclature) have recently been reviewed. The Holliday junctions form the central intermediates in both homologous and site-specific recombination. In solution, in the presence of multivalent ions and thus under physiological salt conditions, their structure consists of two quasi-continuously stacked helices in an essentially canonical conformation (Figure 1c). Four recent crystal structures of 4H confirm these structural features, but no coherence is observed in the value of the interhelix angle y (defined in Figure 1b); three structures show right-handed interhelix