A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail

Simmons, C.R.; MacCulloch, T.; Zhang, Fei; Liu, Yan; Stephanopoulos, Nicholas

doi:10.1002/anie.202005505

Cited by 23 publications

(21 citation statements)

References 51 publications

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“…Rationally designed crystals based upon the “tensegrity” motif 13 which self-assemble with designed four-arm junction crossover points and “sticky end” cohesion have also been shown to be capable of being converted into nanodevices 14 . Recently, several unique motifs with distinctive crystal symmetries, improved resolution, and in one case, a unique junction nucleotide sequence, have been reported 15 – 18 .…”

Section: Introductionmentioning

confidence: 99%

“…Theoretically, there are 36 base pair combinations of immobile sequences. “J1” was the earliest to be designed 42 , 43 , and has been used nearly exclusively in the construction of self-assembled 3D crystals 13 , 15 – 17 with a single exception where “J10” was used 18 . Some early work explored the sequence influence on packing of stacked-X junctions using theoretical 44 , 45 or experimental methods 46 , 47 , but to our knowledge, no systematic study of the immobile HJs has been performed.…”

Section: Introductionmentioning

confidence: 99%

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The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

et al. 2022

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The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

et al. 2022

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“…This observation conforms with the expectation that the immobile junction reported in 1983 forms the characteristic stacked “H” shape rather than a cross-like motif . However, the large variation in bending for the junction found in the hexagonal motif is a surprising discovery, since branched junctions have specific angles that they favor, which has been exploited by others to prescribe certain crystal structures . We also see significant tilt differences at other locations in the structure and at the sticky end, as shown in Table S3.…”

Section: Results and Discussionmentioning

confidence: 99%

3D Hexagonal Arrangement of DNA Tensegrity Triangles

Vecchioni

Ohayon

et al. 2021

ACS Nano

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The tensegrity triangle motif utilizes Watson–Crick sticky end cohesion to self-assemble into a rhombohedral crystal lattice using complementary 5′-GA and 5′-TC sticky ends. Here, we report that using noncanonical 5′-AG and 5′-TC sticky ends in otherwise isomorphic tensegrity triangles results in crystal self-assembly in the P63 hexagonal space group as revealed by X-ray crystallography. In this structure, the DNA double helices bend at the crossover positions, a feature that was not observed in the original design. Instead of propagating linearly, the tilt between base pairs of each right-handed helix results in a left-handed superstructure along the screw axis, forming a microtubule-like structure composed of three double helices with an unbroken channel at the center. This hexagonal lattice has a cavity diameter of 11 nm and a unit cell volume of 886 000 Å3far larger than the rhombohedral counterpart (5 nm, 330 000 Å3).

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“…7 c). The 3D DNA crystals proposed in 1982 have been reported using a rationally designed tensegrity triangle [ 123 ], various 4 × N motifs [ 124 – 126 ], a six-fold symmetric motif [ 127 ], and a layer-crossed motif [ 128 ] (Fig. 7 d).…”

Section: Dna Nanotechnologymentioning

confidence: 99%

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

2022

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Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide. Graphical Abstract

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A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail

Cited by 23 publications

References 51 publications

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

3D Hexagonal Arrangement of DNA Tensegrity Triangles

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

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