| 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.;The remarkable consequence of this type of crossover structure is that the strands of the two interwrapped helices are completely unlinked and the paranemic nature of the PX structure suggests that it can be used to produce a new form of DNA cohesion. We have demonstrated that it is possible to combine large, topologically closed, DNA triangle molecules through paranemic cohesion by gel electrophoresis. Further evidences come from the Atomic Force Microscopy (AFM) visualization of one-dimensional periodic chains and small two-dimensional lattices. The use of PX motifs enables one to join two topologically closed molecules.;The structure features of PX molecules suggest that supercoiled homologous DNA regions could associate to form PX-DNA. The basis for this suggestion is that the twist of PX-DNA is roughly half that of conventional DNA. However, not all DNA can form PX-DNA. The DNA must have true homology (the entire DNA in two regions must be identical), or at least it must have ‘PX homology’, wherein every other unit tangle is homologous. Two-dimensional agarose gel results show the structural transitions for head-to-head true and PX homology molecules, which are absent for non-homology and head-to-tail true homology molecules. Preliminary crosslinking and AFM imaging results show the expected patterns for the head-to-head true and PX homology molecules, but not for the non-homology and head-to-tail pure homology molecules. It is evident that PX DNA could provide a molecular framework for the DNA-based recognition of homology in cellular processes, including homologous recombination. |
