Paranemic Crossover DNA: A Generalized Holliday Structure with Applications in Nanotechnology

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Abstract
Paranemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson−Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of five nucleotide pairs and major groove separations of six, seven, or eight nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13, or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26, or 28 nucleotides). Nondenaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions.