Divergence and Convergence: Complexity Emerges in Crystal Engineering from an 8-mer DNA

Abstract

Biology provides plenty of examples on achieving complicated structures out of minimal numbers of building blocks. In contrast, structural complexity of designed molecular systems is achieved by increasing the numbers of component molecules. In this study, the component DNA strand assembles into a highly complex crystal structure via an unusual path of divergence and convergence. This assembly path suggests a route to minimalists for increasing structural complexity. The original purpose of this study is to engineer DNA crystals with high resolution, which is the primary motivation and a key objective for structural DNA nanotechnology. Despite great efforts in the last 40 years, engineered DNA crystals have not yet consistently reached resolution better than 2.5 Å, limiting their potential uses. Our research has shown that small, symmetrical building blocks generally lead to high resolution crystals. Herein, by following this principle, we report an engineered DNA crystal with unprecedented high resolution (2.17 Å) assembled from one single DNA component: an 8-base-long DNA strand. This system has three unique characteristics: (1) It has a very complex architecture, (2) the same DNA strand forms two different structural motifs, both of which are incorporated into the final crystal, and (3) the component DNA molecule is only an 8-base-long DNA strand, which is, arguably, the smallest DNA motif for DNA nanostructures to date. This high resolution opens the possibility of using these DNA crystals to precisely organize guest molecules at the Å level, which could stimulate a range of new investigations.

Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals

“…The predictability of Watson–Crick base pairing has allowed for the construction of a variety of DNA nanostructures. − The discovery and design of alternate base pairs, such as the 8-letter “hachimoji” DNA, have increased the size and complexity of DNA motif design. , In this manner, the incorporation of metals into pyrimidine pairs through the two classical examples of dT:Hg 2+ :dT and dC:Ag + :dC allows for a targeted expansion of the DNA programming language toward the introduction of bioinorganic behavior into DNA motifs that would lead to enhanced electron conduction . These two transition metal ions can selectively fill the gap between two pyrimidine nucleobases at the center N3 position of both nucleobases with a high ion specificity and orthogonality (Figure ).…”