Structural domains of DNA mesojunctions

Holliday junctions are central intermediates in the process of genetic recombination. These DNA molecules contain four double helices that flank a central branch point, so that each of the four strands that constitute the junction is associated with two different helices. Previously, we have shown that such branched junctions are a special subset of the class of DNA molecules containing multiple strands, in which each strand is associated with two double helices [Du, S. M., Zhang, S., & Seeman, N. C. (1992) Biochemistry 31, 10955-10963]. Conventional branched molecules, such as the Holliday junction, contain helices whose axes can all be drawn to radiate from a central point. The other molecules of the class contain helices whose axes are circumferential about the central point. If all of the helices are circumferential, the molecule is called an antijunction; if the molecule contains a mixture of radial and circumferential helices, it is called a mesojunction. The properties of the molecule are a function of the even or odd nature of the number of helical half-turns in the circumferential helices. Previously, a four-strand antijunction and three-strand and four-strand mesojunctions containing three half-turns (16 nucleotide pairs) per helix were constructed and characterized. Here, we have attempted to construct the analogous molecules containing two half-turns (10 nucleotide pairs) in each helix. The three-strand mesojunction and the four-strand antijunction are not stable under conditions suitable for analysis. We have characterized the two four-strand mesojunctions that are stable by Ferguson analysis, thermal denaturation, and Fe(II)EDTA2- autofootprinting. In addition, we have characterized a four-strand mesojunction containing 14 nucleotide pairs in its circumferential helices and have shown that its favored conformer is different from that of a closely related molecule containing 16 nucleotide pairs in its circumferential helices.