Ligation of DNA triangles containing double crossover molecules

An antiparallel DNA double crossover molecule has been incorporated into one edge of a DNA triangle. The goal in this work is to combine a rigid geometrical motif, the triangle, with a rigid DNA motif, the double crossover, incorporating the properties of branched DNA. The triangle has been designed to contain 3 turns of DNA in each edge. The double crossover molecule produces an extra domain along its edge. The extra domain can be restricted by Bbs I to produce two complementary sticky ends separated by 4.5 turns of DNA. Ligation-closure experiments performed on the restricted triangle yield very long reporter strands and no indications of cyclization, suggesting that the double crossover molecule retains its stiffness when incorporated in the triangle. These experiments are evaluated through the use of denaturing gel electrophoresis. The ligation products have been visualized by atomic force microscopy, under nondenaturing conditions. Clear zigzag species can be identified as triangles ligated in one di...