From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal

By Jianping Zheng, J. Birktoft, Yi Chen, Tong Wang, R. Sha, P. Constantinou, S. Ginell, C. Mao, Nadrian C. Seeman. Nature, 2009

889 citations recorded by the source corpus.

We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4 Å resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/478c12c00b5cc246e041445a60e3a9b878a3b2d7

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Citations in the corpus

The Emerging Field of RNA Nanotechnology (2010, positive): “Continuous growth of the tensegrity triangle in the periodic DNA module has resulted in the formation of DNA crystals diffracting to 4-A resolutio”
Nanomaterials Based on DNA (2010, methodology): “constructs in 3D (250 μm in extent) is now 4-Å resolution, but other crystals (up to 1 mm in dimension) are readily available to 10-Å resolution (51).”
Materials perspective on Casimir and van der Waals interactions (2015, background): “…such as filamentous graphitic systems of metallic and semiconducting single-walled CNTs (Rajter et al., 2013, 2007; Siber et al., 2009), multiple composites of DNA (Sontz et al., 2012; Young et al., 2014; Zheng et al., 2009), type I collagen (Cheng et al., 2008), and polystyrene (Jin et al., 2005).”
Generation of protein lattices by fusing proteins with matching rotational symmetry. (2011, methodology): “We note that a thermal annealing approach has been used to grow 3D crystals of a designed DNA lattic”
Computational design of a protein crystal (2012, background): “The structures and functions of these previously studied self-assembled systems are limited, however, to those achievable with DNA hybridization or preexisting protein domains.”
Nanotechnology in agri-food production: an overview (2014, positive): “This technique helps in improving important crops by organizing and linking carbohydrates, lipids, proteins, and nucleic acids to this crystal.(118) Chemically coated mesoporous silica nanoparticles help in delivering DNA and chemicals into isolated plant cells.”
Challenges and opportunities for structural DNA nanotechnology (2011, methodology): “A landmark of periodic DNA structure assembly was achieved by Seeman and co-worker”
Programmable materials and the nature of the DNA bond (2015, methodology): “Only the tensegrity triangle (41), with three linearly independent helix axes, has produced substantial 3D crystals thus far (43).”