Figure 2.

The experimental approach of Millar, Chazin, et al. (2). (A) The modifications made to the junction in its extended form. In the FRET experiments, donor and acceptor fluorophore pairs were attached to the ends of two different helical arms (indicated by the oval shapes). In one stacking conformer (B) these are relatively close together across the narrow angle of the stacked X-structure, while in the other they are at opposite ends of a stacked pair of helices (C). For the NMR experiments a thymine base at the point of strand exchange (indicated by the red block) was modified by substitution of ring nitrogen atoms by the spin 1/2 ¹⁵N. In conformer B the substituted thymine is located on the continuous strand, whereas in C it is on the exchanging strand. The central sequences of the three junctions studied are shown in D with the modified thymine highlighted in open type.