Paranemic Crossover DNA: There and Back Again.

Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology.

Structural stability and length of I-motif of G-quartet in DNA octaplex.

To confirm that longer DNA strands with sequences gcGA[G](n)Agc can form an octaplex, X-ray analyses at n>1 have been performed. Several crystals of d(gcGA[G]2Agc) are obtained under different conditions. It has been found that the crystal obtained with cobalt hexamine suggests a hexaplex formation, while the crystal obtained with Mg2+ and Na+ ions suggests an octaplex formation.

Crystal structure of d(gcGXGAgc) with X=G: a mutation at X is possible to occur in a base-intercalated duplex for multiplex formation.

DNA fragments with the sequences d(gcGX[Y]n Agc) (n=1, X=A, and Y=A, T, or G)form base-intercalated duplexes, which is a basic unit for formation of multiplexes such as octaplex and hexaplex. To examine the stability of multiplexes, a DNA with X=Y=G and n=1 was crystallized under conditions different from those of the previously determined sequences, and its crystal structure has been determined. The two strands are coupled in an anti-parallel fashion to form a base-intercalated duplex, in which the first and second residues form Watson-Crick type G:C pairs and the third and sixth residues form a sheared G:A pairs at both ends of the duplex.