Summary information and primary citation
- PDB-id
-
4rp0;
DSSR-derived features in text and
JSON formats
- Class
- DNA
- Method
- X-ray (2.19 Å)
- Summary
- Sequence and structure of a self-assembled 3-d DNA
crystal: d(ggataattaggag)
- Reference
-
Saoji M, Zhang D, Paukstelis PJ (2015): "Probing
the role of sequence in the assembly of three-dimensional
DNA crystals." Biopolymers,
103, 618-626. doi: 10.1002/bip.22688.
- Abstract
- DNA is a widely used biopolymer for the construction of
nanometer-scale objects due to its programmability and
structural predictability. One long-standing goal of the
DNA nanotechnology field has been the construction of
three-dimensional DNA crystals. We previously determined
the X-ray crystal structure of a DNA 13-mer that forms a
continuously hydrogen bonded three-dimensional lattice
through Watson-Crick and non-canonical base pairs. Our
current study sets out to understand how the sequence of
the Watson-Crick duplex region influences crystallization
of this 13-mer. We screened all possible self-complementary
sequences in the hexameric duplex region and found 21
oligonucleotides that crystallized. Sequence analysis
showed that one specific Watson-Crick pair influenced the
crystallization propensity and the speed of crystal
self-assembly. We determined X-ray crystal structures for
13 of these oligonucleotides and found sequence-specific
structural changes that suggests that this base pair may
serve as a structural anchor during crystal assembly.
Finally, we explored the crystal self-assembly and
nucleation process. Solution studies indicated that these
oligonucleotides do not form base pairs in the absence of
cations, but that the addition of divalent cations leads to
rapid self-assembly to higher molecular weight complexes.
We further demonstrate that crystals grown from mixtures of
two different oligonucleotide sequences contain both
oligonucleotides. These results suggest that crystal
self-assembly is nucleated by the formation of the
Watson-Crick duplexes initiated by a simple chemical
trigger. This study provides new insight into the role of
sequence for the assembly of periodic DNA structures.
