Structure of four-way DNA junctions containing a nick in one strand

We have investigated the structure of the four-way helical DNA junction containing a single covalent discontinuity (nick) in one strand. These could result from either unitary strand exchange processes, or the action of nucleases upon a complete junction. We have employed gel electrophoresis methods to study the global configuration of arms in these junctions. We find that the junction carrying a nick in one strand undergoes a folding process in the presence of magnesium ion concentrations greater than 200 microM. Comparison of the electrophoretic mobilities of the six possible derivative junctions with two long and two shortened arms suggests that the folding occurs by coaxial stacking of pairs of helical arms, which is supported by the suppression of reactivity to osmium tetroxide of thymine bases at the centre of the junction. However, unlike the complete junction (i.e. the junction without nicked strands), the two stacked pairs of helices lie at a mutual angle of approximately 90 degrees. The folding process generates two kinds of strands; two continuous strands and two exchanging strands. Two isomers of the right-angled stacked structure are possible, depending on the selection of stacking partners; it appears that the critical factor determining the relative stabilities of these isomers is the location of the nick. Thus the nicked junctions fold into the isomer that locates the nick on the exchanging strand. However, if the nick is not located at the point of strand exchange, the junction reverts to the stacked X-structure of the complete junction, even if the nick is moved by a single base-pair. These results suggest that the exchanging strands may be significantly strained in the structure of the complete four-way junction, such that an interruption to the continuity at this position allows the two stacked helices to disengage, and rotate to an angle where the overall electrostatic repulsion may be lower.