Three-Dimensional DNA
Crystals with pH-Responsive
Noncanonical Junctions
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Abstract
Three-dimensional (3D) DNA crystals have been envisioned
as programmable
biomaterial scaffolds for creating ordered arrays of biological and
nonbiological molecules. Despite having excellent programmable properties,
the linearity of the Watson–Crick B-form duplex imposes limitations
on 3D crystal design. Predictable noncanonical base pairing motifs
have the potential to serve as junctions to connect linear DNA segments
into complex 3D lattices. Here, we designed crystals based on a template
structure with parallel-stranded noncanonical base pairs. Depending
on pH, the structures we determined contained all but one or two of
the designed secondary structure interactions. Surprisingly, a conformational
change of the designed Watson–Crick duplex region resulted
in crystal packing differences between the predicted and observed
structures. However, the designed noncanonical motif was virtually
identical to the template when crystals were grown at pH 5.5, highlighting
the motif’s predictability. At pH 7.0 we observed a structurally
similar variation on this motif that contains a previously unobserved
C–G•G–C quadruple base pair. We demonstrate that
these two variants can interconvert <i>in crystallo</i> in
response to pH perturbations. This study spotlights several important
considerations in DNA crystal design, describes the first 3D DNA lattice
composed of A-DNA helical sheets, and reveals a noncanonical DNA motif
that has adaptive features that may be useful for designing dynamic
crystals or biomaterial assemblies