Fig. 7 Motif generation by reciprocal exchange. (a) The fundamental operation. The basic
operation of reciprocal exchange is shown: A red strand and a blue strand become a red–blue
and a blue–red strand following the operation. (b) Motifs that can result from reciprocal exchange
of DNA molecules. The DX motif results from two reciprocal exchanges between double helical
motifs. The DX + J motif contains another DNA domain. Usually this domain is oriented
perpendicular to the plane of the two helix axes in the DX part of the motif. When this orientation
is achieved, the extra domain can behave as a topographic marker for 2D arrays containing the
DX + J motif. In the TX motif , a third domain has been added to a DX motif; again the exchanges
take place between strands of opposite polarity. The PX molecule is formed by exchanges between
strands of identical polarity at every possible position. The JX 2 molecule is one of the topoisomers
of the PX motif and lacks two of these exchanges, leading to its bottom being flipped a half-turn,
relative to its top
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N.C. Seeman