Summary information and primary citation
- PDB-id
-
7jld;
DSSR-derived features in text and
JSON formats
- Class
- DNA
- Method
- X-ray (3.163 Å)
- Summary
- Self-assembly of a 3d DNA crystal lattice (4x6 scramble
duplex version) containing the j22 immobile holliday
junction with r3 symmetry
- Reference
-
Simmons CR, MacCulloch T, Krepl M, Matthies M, Buchberger
A, Crawford I, Sponer J, Sulc P, Stephanopoulos N, Yan H
(2022): "The
influence of Holliday junction sequence and dynamics on
DNA crystal self-assembly." Nat Commun,
13, 3112. doi: 10.1038/s41467-022-30779-6.
- Abstract
- The programmable synthesis of rationally engineered
crystal architectures for the precise arrangement of
molecular species is a foundational goal in nanotechnology,
and DNA has become one of the most prominent molecules for
the construction of these materials. In particular,
branched DNA junctions have been used as the central
building block for the assembly of 3D lattices. Here,
crystallography is used to probe the effect of all 36
immobile Holliday junction sequences on self-assembling DNA
crystals. Contrary to the established paradigm in the
field, most junctions yield crystals, with some enhancing
the resolution or resulting in unique crystal symmetries.
Unexpectedly, even the sequence adjacent to the junction
has a significant effect on the crystal assemblies. Six of
the immobile junction sequences are completely resistant to
crystallization and thus deemed "fatal," and molecular
dynamics simulations reveal that these junctions invariably
lack two discrete ion binding sites that are pivotal for
crystal formation. The structures and dynamics detailed
here could be used to inform future designs of both
crystals and DNA nanostructures more broadly, and have
potential implications for the molecular engineering of
applied nanoelectronics, nanophotonics, and catalysis
within the crystalline context.
