Holliday Junction Parallelogram DNA Arrays

In a solution containing Mg(+2) cations, the Holliday junction takes on a stacked structure, whereby its four arms assort themselves into a pair of double helical stacking domains. Two strands are roughly helical in structure, and two are involved in crossing over between the domains. The helical strands are roughly antiparallel to each other, although rotated by about 60 degrees from ideal antiparallelism. This structure is shown in (a) below.

Although this structure is known to be somewhat floppy, it is possible to make a useful tile for one and two dimensional arrays by taking four such junctions and making a parallelogram from them, as shown in (b) above. It is possible to use these tiles to make 1D arrays, as shown in (c), or 2D arrays, as shown in (d). It is possible to change the dimensions of the parallelograms and their overhangs, so that a series of tunable cavities can be produced from this motif. A sample AFM picture is shown below

In addition to making 1-D and 2-D arrays from conventional Holliday junctions, it is also possible to make them from Bowtie junctions.

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