Two inequivalent folding isomers of the three-way DNA junction with unpaired bases: sequence-dependence of the folded conformation.

The global structures of three-way helical junctions in DNA that contain two unpaired bases at the point of strand exchange have been studied. All such junctions examined undergo a folding in the presence of metal ions, to a structure in which there is coaxial stacking of two helices, with the third at an acute angle. However there are potentially two isomers of this structure possible, which are stereochemically inequivalent. We find that the majority of sequences studied by us fold into the isomer in which the polarity of the bulge-containing strand passing from the unstacked to the stacked helix is 5' to 3'. However, some sequences adopt the alternative stacking isomer, in which the polarity of the bulged strand is 3' to 5'. These isomeric differences are in complete agreement with the findings from two other studies by NMR. In addition to the isomeric differences, we find significant sequence-dependent differences within series of junctions that adopt the same isomeric form in the presence of ions. We conclude that the folding of bulged three-way DNA junctions is highly sequence-dependent.