Engineering DNA Crystals toward Studying DNA–Guest Molecule Interactions

Abstract

Sequence-selective recognition of DNA duplexes is important for a wide range of applications including regulating gene expression, drug development, and genome editing. Many small molecules can bind DNA duplexes with sequence selectivity. It remains as a challenge how to reliably and conveniently obtain the detailed structural information on DNA–molecule interactions because such information is critically needed for understanding the underlying rules of DNA–molecule interactions. If those rules were understood, we could design molecules to recognize DNA duplexes with a sequence preference and intervene in related biological processes, such as disease treatment. Here, we have demonstrated that DNA crystal engineering is a potential solution. A molecule-binding DNA sequence is engineered to self-assemble into highly ordered DNA crystals. An X-ray crystallographic study of molecule–DNA cocrystals reveals the structural details on how the molecule interacts with the DNA duplex. In this approach, the DNA will serve two functions: (1) being part of the molecule to be studied and (2) forming the crystal lattice. It is conceivable that this method will be a general method for studying drug/peptide–DNA interactions. The resulting DNA crystals may also find use as separation matrices, as hosts for catalysts, and as media for material storage.

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

“…(i) The component (one 8-mer DNA strand) is arguably the smallest, unique DNA component for assembly of any DNA nanostructure, thus pushing the boundary of the minimalist approach for DNA nanotechnology. − (ii) The 8-mer DNAs simultaneously form two different structural motifs, and both motifs together assemble into the final crystals. In prior studies, one set of strands always forms only one particular motif under one specific assembly condition; − ,− instead, the DNA strands form two different types of motifs in this study, thus leading to higher structural complexity. Such an integration of divergent and convergent assembly is a fundamentally new concept for increasing structural complexity and reducing the number of unique, component DNA strands.…”

“…Our findings may provide a strategy for guiding the self-assembly of DNA strands into one particular structure when there are multiple potential structures. In the applied side, the high resolution of the DNA crystals may allow structural studies of small guest molecules that can be incorporated into the DNA crystal lattices, or organize molecules in 3D with Å level precision for other applications, such as photonic devices, cascade catalysis, − and information processing and storages. − …”

“…In the course of the study of tensegrity triangle-based DNA crystals, one phenomenon became obvious: small and symmetric motifs resulted in high resolution crystals. 13,19 The same phenomenon was also observed in a DNA crystal system containing parallel DNA duplexes. 20 Herein, following this principle, we have designed an 8-mer DNA (8 nucleotides, nts, long) to assemble into 3D DNA crystals with a resolution of 2.17 Å.…”

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 ).…”

Site-specific arrangement and structure determination of minor groove binding molecules in self-assembled three-dimensional DNA crystals

“…To this end, an expanding toolbox of these lattices containing a wide variety of crystal symmetries, tunable pore volumes and sizes, and programmable sequences have been developed, including a recently reported 3D double crossover motif that demonstrated that the crystals were viable for binding of Hoechst 33342 for structural studies. 9,15,21-30…”