Flexibility defines structure in crystals of amphiphilic DNA nanostars

Abstract

DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and bond directionality have been recognised as key design features for DNA motifs to sustain long-range order in 3D, but the practical challenges associated with prescribing building-block geometry with sufficient accuracy have limited the variety of available designs. We have recently introduced a novel platform for the one-pot preparation of crystalline DNA frameworks supported by a combination of Watson-Crick base pairing and hydrophobic forces [Nano Lett., 17(5):3276-3281, 2017]. Here we use small angle X-ray scattering and coarsegrained molecular simulations to demonstrate that, as opposed to available all-DNA approaches, amphiphilic motifs do not rely on structural rigidity to support long-range order. Instead, the flexibility of amphiphilic DNA building-blocks is a crucial feature for successful crystallisation.

Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation

“…Together, these results reveal that Mg 2+ binds closely to the DNA origami and is more likely to bind specific locations near crossovers, which has been shown to rigidify crossovers, 64,65 whereas Na + binds at a larger distance from the origami and rapidly exchanges with the bulk solvent. Spm 4+ binds closely to the DNA origami grooves, aligning with the backbone phosphates and shows, together with Mg 2+ ions, the highest charge compensation near crossovers, while K 10 is able to stabilize DNA origami without binding deeply in the grooves.…”

I22: SAXS/WAXS beamline at Diamond Light Source – an overview of 10 years operation

“…This can be used in tension, compression and bending modes. A millisecond pressure-jump cell (1 to 5000 bar) for use in X-ray scattering experiments has been developed in collaboration with Imperial College London, and is now routinely available on I22 (Brooks et al, 2010). For higher pressure, a diamond anvil cell is available for use with the microfocus beam (Almax-easyLab, Diksmuide, Belgium; Boehler-Almax PlateDAC).…”

“…From its inception, I22 was designed to accommodate the wide-ranging scientific requirements of the UK SAXS community. This covers most areas of science from biology and medicine through to advanced materials (O'Sullivan et al, 2011;Inamdar et al, 2017;Brady et al, 2019;Bots et al, 2014;Besselink et al, 2016;Lutz-Bueno et al, 2016). It has successfully shown its flexibility by accommodating a wide array of diverse sample environments during its years of operation.…”

“…Of particular note in this area is the P-jump cell developed in collaboration with Imperial College (Brooks et al, 2010). Due to the collaborative development of the cell its functionality has been fully embedded into the beamline control system which has enabled an integrated approach to data collection from the outset.…”

A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

“…Another significant application area for oxDNA has been the simulation of large structures to assess their conformation, stability and flexibility ( Fernandez-Castanon et al, 2016 ; Schreck et al, 2016 ; Sharma et al, 2017 ; Shi et al, 2017 ; Benson et al, 2018 ; Choi et al, 2018 ; Coronel et al, 2018 ; Berengut et al, 2019 ; Brady et al, 2019 ; Hoffecker et al, 2019 ; Snodin et al, 2019 ; Berengut et al, 2020 ; Chhabra et al, 2020 ; Poppleton et al, 2020 ; Tortora et al, 2020 ; Yao et al, 2020 ).…”