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arXiv · 2401.00318

A self-assembled periodic nanoporous framework in aqueous solutions of the DNA tetramer GCCG

Gregory P. Smith·Tommaso P. Fraccia·Chenhui Zhu·Tommaso Bellini·Noel A. Clark
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Abstract

The collective behavior of the shortest DNA oligomers in high concentration aqueous solutions is an unexplored frontier of DNA science and technology. Here we broaden the realm of DNA nanoscience by demonstrating that single-component aqueous solutions of the DNA 4-base oligomer GCCG can spontaneously organize into three-dimensional (3D) periodic mesoscale frameworks. This oligomer can form B-type double helices by Watson-Crick (WC) pairing, into tiled brickwork-like duplex strands, which arrange into mutually parallel arrays and form the nematic and columnar liquid crystal phases, as is typical for long WC chains. However, at DNA concentrations above 400mg/mL, these solutions nucleate and grow an additional mesoscale framework phase, comprising a periodic network on a three dimensional body-centered cubic (BCC) lattice. This lattice is an array of nodes (valence-8, each formed by a pair of quadruplexes of GCCG terminal Gs), connected with a separation of 6.6 nm by struts (6-GCCG-long WC duplexes). This 3D-ordered DNA framework is of low density (DNA volume fraction ~0.2), but, due to its 3D crystal structure, is osmotically incompressible over its phase range. Atomistic simulations confirm the stability of such structures, which promise to form the basis of novel families of simply and inexpensively made nanoscale frameworks for templating and selection applications.

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Gregory P. Smith, Tommaso P. Fraccia, Chenhui Zhu, Tommaso Bellini, Noel A. Clark. 2023-12-30. A self-assembled periodic nanoporous framework in aqueous solutions of the DNA tetramer GCCG. https://arxiv.org/abs/2401.00318

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