Two Dimensional DNA Array Modification

We have learned how to modify the patterns produced by 2-D arrays from antiparallel double crossover molecules. We can modify these arrays in two ways. The first way entails restricting the hairpins that produce the patterns:

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At the top of this drawing are four double crossover molecules, A B, C and D*, which are shown schematically. The pattern results from hairpins directed out of the plane of the array from molecules B and D*. Hairpin B contains a restriction site missing on D*. When the array is treated with the restriction enzyme, this hairpin is removed. Thus, the 32 nm pattern on the top is converted to a 64 nm pattern after restriction.

The second modificaton entails performing the reverse operation, as shown below:

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The components of the array here are similar to those above. However, we have replaced B with a different component double crossover tile, B. This tile contains a sticky end, that can pair with a sticky end on a hairpin in solution. Thus, the upper array produces a 64 nm pattern, but when a hairpin is ligated to it, or even just hydrogen bonded to it, a 32 nm pattern results, as shown in the bottom array.

Thus, we can modify specific structural features created by self-assembly techniques.

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