A Specific Quadrílateral Synthesized from DNA Branched Junctions

Four different three-arm branched DNA junctions have been synthesized and covalently linked together in a prescribed arrangement to form a macrocycle of previously specified sequence. One end of each individual junction is closed by a hairpin loop. Each open arm of the four junctions terminates in a unique single-stranded cohesive (“sticky”) end; there are four pairs of complementary sticky ends among the eight arms, two pairs with 3' overhangs, and two pairs with 5' overhangs. The associations between junctions are directed by the sequences of these cohesive ends. The junctions that associate in this fashion are enzymatically joined together by the use of bacteriophage T4 DNA ligase. The final product is a “quadrilateral” the sides of which are each 16 nucleotide pairs long, approximately 1.5 turns of DNA. The quadrilateral is designed to be composed of two hextuply linked circles of DNA.