Abstract
DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5′-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.
Highlights
The ability for DNA oligonucleotides with complementary sequences to recognize each other in a complex sequence environment has made DNA one of the most widely used molecules for programmed molecular self-assembly
The DNA nanotechnology field originated from the idea that 3D DNA crystals could be used as molecular scaffolds to determine protein structures [18] and creating periodic 3D DNA arrays has remained one of the major challenges of the field
Because the duplex is inherently linear on short length scales, all DNA crystal designs must include some type of branching motif to propagate the lattice into 3D
Summary
The ability for DNA oligonucleotides with complementary sequences to recognize each other in a complex sequence environment has made DNA one of the most widely used molecules for programmed molecular self-assembly. Each oligonucleotide strand forms a ps duplex with a crystallographically equivalent strand, resulting in the first example of a DNA crystal structure that contains four different symmetric homo base pairs.
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