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In this study, we investigate the topological adaptability and structural resilience of periodic soft matter entanglements using the DNA tensegrity triangle, a foundational motif in structural DNA nanotechnology, as a model system. By simulating the Reidemeister moves from knot theory, which describe a series of “moves” by which the knot equivalence is preserved, we demonstrate that many variants of the tensegrity triangle maintain their lattice geometry, underscoring the motif’s inherent topological robustness. Using granular deformations in a series of closely related motifs, we systematically twist the helices and slide their ends relative to junction crossings to yield 48 distinct crystal structures. Notably, we Identify a novel poke-DX feature (PDX), which introduces rigid crossover configurations with enhanced crystallographic resolution and site-specific metal ion coordination. Further exploration reveals the formation of semi-junctions – a new class of four-arm junctions held together by a single rotatable bond, which feature relaxed torsional strain and altered crossover geometries. These configurations support lattice transformations into tetragonal and distorted rhombohedral forms as well as facilitate topological inversion between left- and right- handed triangles. Altogether, these findings illustrate how controlled topological operations at the molecular level can tune local flexibility and stiffness at key sites to affect long-range lattice geometry. This work positions DNA-based frameworks as a programmable platform for the design of architected materials, topological metamaterials, and nanoscale devices with tunable structural and functional properties. 

Self-assembling DNA crystals have emerged over the last two decades as an efficient and effective means of organizing matter at the nanoscale, but functionalization of these lattices has proved challenging as physiological buffer conditions are required to maintain structural integrity. In this manuscript, we demonstrate the silicification of porous DNA crystals using sol-gel chemistry. We identify reaction conditions that produce the minimum coating thickness to confer environmental protection, and subsequently measure the protective ability of the silica coating to various stressors, including heat, low ionic strength solution, organic solvents, and unprotected flash freezing. By soaking ions and dyes into the lattice after silica coating, we demonstrate that the crystals maintain their pores, and that the major groove of the DNA can still be used as a site-specific template for chemical modifications. We image a library of different crystal motifs by electron microscopy and confirm the presence of silica using energy dispersive spectroscopy. Finally, we perform X-ray diffraction on these crystals, both with and without cryoprotection and determine the structure of the DNA frame, underscoring the conserved molecular order after coating. We anticipate these mesoporous silica composites for use in applications involving extreme, non-physiological conditions and for experiments which utilize the DNA glass described here as a template for surface science. 

Topology has emerged as a field for describing and controlling order and matter, and thereby the physical properties of materials. There are several largely disparate fields focused on examining and manipulating topology. One of these arenas is in the realm of real space, manipulating systems in terms of their spatial properties, to control the corresponding structural, mechanical, and self- assembling responses. Much of the work in soft matter topology falls within this domain. A second arena is in the domain of momentum or k-space wherein topology controls the features of the electronic band structure of materials, and topologically non-trivial features result in the development of materials with truly unique properties. This work focuses squarely on the realm of condensed matter physics. Here, we review concepts of real- and k-space topology and propose areas for convergence between these two disparate fields. 

DNA nanotechnology leverages the molecular design resolution of the DNA double helix to fold and tile matter into designer architectures. Recent advances in bioinorganic chemistry have exploited the affinity of soft nucleobase functional groups for silver ions in order to template the growth of silver nanoclusters by templated reduction. The coupling of the spatial resolution of DNA nanotechnology and the atomic precision of DNA-based nanocluster synthesis has not been realized. Here we develop a method using 3D DNA crystals to employ silver-ion-mediated base pairs as nucleation sites for atomically-precise nanocluster growth. By leveraging the topology of DNA tensegrity triangles, we provide a mesoporous 3D lattice that is robust to reducing conditions, enabling precise spatial templating. Use of in situ confocal fluorescence microscopy allows for the direct observation of reaction kinetics and reconstruction of the optical bandgap. Control over reaction time and stoichiometry, base pair identity, and buffer composition enable precise tuning of the atomic composition and optical properties of the ensuing nanoclusters. The resulting crystals are of diffraction quality, yielding molecular structures of Ag4 and Ag6 in 3D. Inter-cluster distances of less than 2 nm show strong plasmonic coupling, with red shifting observed relative to literature standards. We anticipate that these results will yield advances in materials synthesis, DNA-based plasmonic crystals, and optically-active nanoelectronics. 

Nuclear spin singlet states are often found to allow long-lived storage of nuclear magnetization, which can form the basis of novel applications in spectroscopy, imaging, and in studies of dynamic processes. Precisely how long such polarization remains intact, and which factors affect its lifetime is often difficult to determine and predict. We present a combined experimental/computational study to demonstrate that molecular dynamics simulations and ab initio calculations can be used to fully account for the experimentally observed proton singlet lifetimes in ethyl-d 5 -propyl-d 7 -maleate in deuterated chloroform as solvent. The correspondence between experiment and simulations is achieved without adjustable parameters. These studies highlight the importance of considering unusual and difficult-to-control mechanisms, such as dipolar couplings to low-gamma solvent nuclei, and to residual paramagnetic species, which often can represent lifetime limiting factors. These results also point to the power of molecular dynamics simulations to provide insights into little-known NMR relaxation mechanisms. 

The examination and optimized preparation of nuclear spin singlet order has enabled the development of new types of applications that rely on potentially long-term polarization storage. Lifetimes several orders of magnitude longer than T 1 have been observed. The efficient creation of such states relies on special pulse sequences. The extreme cases of very large and very small magnetic equivalence received primary attention, while relatively little effort has been directed towards studying singlet relaxation in the intermediate regime. The intermediate case is of interest as it is relevant for many spin systems, and would also apply to heteronuclear systems in very low magnetic fields. Experimental evidence for singlet–triplet leakage in the intermediate regime is sparse. Here we describe a pulse sequence for efficiently creating singlets in the intermediate regime in a broad-band fashion. Singlet lifetimes are studied with a specially synthesized molecule over a wide range of magnetic fields using a home-built sample-lift apparatus. The experimental results are supplemented with spin simulations using parameters obtained from ab initio calculations. This work indicates that the chemical shift anisotropy (CSA) mechanism is relatively weak compared to singlet–triplet leakage for the proton system observed over a large magnetic field range. These experiments provide a mechanism for expanding the scope of singlet NMR to a larger class of molecules, and provide new insights into singlet lifetime limiting factors.