Sequence-dependent structural changes in a self-assembling DNA oligonucleotide

Abstract

DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson–Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg2+through a combination of Watson–Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson–Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A–G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G–A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson–Crick duplex region. These results provide important new insights into the sequence–structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson–Crick and noncanonical base pairs that is responsible for crystallization fate.