Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions**

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Abstract

DNA has become a prime material for assembling complex three-dimensional objects that promise utility in various areas of application. However, achieving user-defined goals with DNA objects has been hampered by the difficulty to prepare them at arbitrary concentrations and in user-defined solution conditions. Here, we describe a method that solves this problem. The method is based on poly(ethylene glycol)-induced depletion of species with high molecular weight. We demonstrate that our method is applicable to a wide spectrum of DNA shapes and that it achieves excellent recovery yields of target objects up to 97 %, while providing efficient separation from non-integrated DNA strands. DNA objects may be prepared at concentrations up to the limit of solubility, including the possibility for bringing DNA objects into a solid phase. Due to the fidelity and simplicity of our method we anticipate that it will help to catalyze the development of new types of applications that use self-assembled DNA objects.

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Rapid planetesimal formation in turbulent circumstellar discs

Anders Johansen, Jeffrey S. Oishi, Mordecai-Mark Mac Low … (2007)

The initial stages of planet formation in circumstellar gas discs proceed via dust grains that collide and build up larger and larger bodies (Safronov 1969). How this process continues from metre-sized boulders to kilometre-scale planetesimals is a major unsolved problem (Dominik et al. 2007): boulders stick together poorly (Benz 2000), and spiral into the protostar in a few hundred orbits due to a head wind from the slower rotating gas (Weidenschilling 1977). Gravitational collapse of the solid component has been suggested to overcome this barrier (Safronov 1969, Goldreich & Ward 1973, Youdin & Shu 2002). Even low levels of turbulence, however, inhibit sedimentation of solids to a sufficiently dense midplane layer (Weidenschilling & Cuzzi 1993, Dominik et al. 2007), but turbulence must be present to explain observed gas accretion in protostellar discs (Hartmann 1998). Here we report the discovery of efficient gravitational collapse of boulders in locally overdense regions in the midplane. The boulders concentrate initially in transient high pressures in the turbulent gas (Johansen, Klahr, & Henning 2006), and these concentrations are augmented a further order of magnitude by a streaming instability (Youdin & Goodman 2005, Johansen, Henning, & Klahr 2006, Johansen & Youdin 2007) driven by the relative flow of gas and solids. We find that gravitationally bound clusters form with masses comparable to dwarf planets and containing a distribution of boulder sizes. Gravitational collapse happens much faster than radial drift, offering a possible path to planetesimal formation in accreting circumstellar discs.

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The Dicke Quantum Phase Transition with a Superfluid Gas in an Optical Cavity

Ferdinand Brennecke, Tilman Esslinger, Christine Guerlin … (2009)

A phase transition describes the sudden change of state in a physical system, such as the transition between a fluid and a solid. Quantum gases provide the opportunity to establish a direct link between experiment and generic models which capture the underlying physics. A fundamental concept to describe the collective matter-light interaction is the Dicke model which has been predicted to show an intriguing quantum phase transition. Here we realize the Dicke quantum phase transition in an open system formed by a Bose-Einstein condensate coupled to an optical cavity, and observe the emergence of a self-organized supersolid phase. The phase transition is driven by infinitely long-ranged interactions between the condensed atoms. These are induced by two-photon processes involving the cavity mode and a pump field. We show that the phase transition is described by the Dicke Hamiltonian, including counter-rotating coupling terms, and that the supersolid phase is associated with a spontaneously broken spatial symmetry. The boundary of the phase transition is mapped out in quantitative agreement with the Dicke model. The work opens the field of quantum gases with long-ranged interactions, and provides access to novel quantum phases.

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Self-assembly of DNA into nanoscale three-dimensional shapes

Shawn M. Douglas, Hendrik Dietz, Tim Liedl … (2009)

Molecular self-assembly offers a ‘bottom-up’ route to fabrication with subnanometre precision of complex structures from simple components1. DNA has proven a versatile building block2–5 for programmable construction of such objects, including two-dimensional crystals6, nanotubes7–11, and three-dimensional wireframe nanopolyhedra12–17. Templated self-assembly of DNA18 into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase ‘scaffold strand’ that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide ‘staple strands’19, 20. Here we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six shapes — monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross — with precisely controlled dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and of heterotrimeric wireframe icosahedra. Proper assembly requires week-long folding times and calibrated monovalent and divalent cation concentrations. We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometer scale.

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Author and article information

Journal

Journal ID (nlm-ta): Angew Chem Int Ed Engl

Journal ID (iso-abbrev): Angew. Chem. Int. Ed. Engl

Journal ID (publisher-id): anie

Title: Angewandte Chemie (International Ed. in English)

Publisher: WILEY-VCH Verlag (Weinheim )

ISSN (Print): 1433-7851

ISSN (Electronic): 1521-3773

Publication date (Print): 17 November 2014

Publication date (Electronic): 24 October 2014

Volume: 53

Issue: 47

Pages: 12735-12740

Affiliations

[* ]Physik Department, Walter Schottky Institute Technische Universität München, Am Coulombwall 4a, 85748 Garching (Germany) http://bionano.physik.tu-muenchen.de

Author notes

** We thank Christian Wachauf for designing the 4- and 10-helix bundle, Fabian Kilchherr for designing the 18-helix bundle, Jonas Funke for designing the “hinge” object, Matthias Schickinger for designing the “flake”, Philip Ketterer for designing the 100-helix bundle, and Dominik Renn for technical assistance. This work was supported by the Deutsche Forschungsgemeinschaft through the Excellence Cluster Center for Integrated Protein Science, Nano Initiative Munich, the Sonderforschungsbereich SFB863, and the TUM International Graduate School of Science and Engineering (IGSSE). Additional funding came from a European Research Council Starting Grant 256270 (to H.D.).

Article

DOI: 10.1002/anie.201405991

PMC ID: 4253120

PubMed ID: 25346175

SO-VID: 90a2733f-b1dc-45e4-bcb6-f3fa1773a09b

Copyright © © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes

History

Date received : 06 June 2014

Date revision received : 29 August 2014

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