Figure 2.

Molecular models of 32 base pair immobilized HJs. (A) Full atom representation of J1 showing the geometrical relationships between the crossover isomers. In the I/II crossover isomer, arm I is stacked on arm II, and arm III on arm IV. The alternate I/IV crossover isomer has arm I stacked on arm IV, and arm II on arm III. Strand 1 is yellow, strand 2 is green, strand 3 is magenta, and strand 4 is cyan. (B) Ribbon diagrams showing the location of the FRET and NMR probes used in these studies. The F1R4 dye-labeled junction for FRET experiments is shown in the two crossover isomers, with fluorescein attached to arm I (F1) in orange and tetramethylrhodamine attached to arm IV (R4) in white. The full molecular structure of the base pair containing the labeled T₉ residue for the NMR experiments is also shown, with the ¹⁵N-enriched nitrogen atom in red.