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Article

Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures

1
Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
2
Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
3
Biotechnology Center, Department of Genomics, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
4
Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Present address: Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.
Academic Editor: Ramon Eritja
Molecules 2020, 25(21), 5099; https://doi.org/10.3390/molecules25215099
Received: 29 September 2020 / Revised: 28 October 2020 / Accepted: 30 October 2020 / Published: 3 November 2020
(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)
Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. Furthermore, we also evaluate the potential of Redβ to anneal sticky-end modified Holliday junctions into hierarchical assemblies. We demonstrate the Redβ-mediated annealing of Holliday junction dimers, multimers, and extended networks several microns in size. While these hybrid DNA–protein nanostructures may find applications in the crystallization of DNA–protein complexes, our work shows the great potential of Redβ to aid in the synthesis of functional DNA nanostructures under mild reaction conditions. View Full-Text
Keywords: DNA nanotechnology; Holliday junctions; atomic force microscopy; single-strand annealing proteins; Redβ DNA nanotechnology; Holliday junctions; atomic force microscopy; single-strand annealing proteins; Redβ
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MDPI and ACS Style

Ramakrishnan, S.; Subramaniam, S.; Kielar, C.; Grundmeier, G.; Stewart, A.F.; Keller, A. Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures. Molecules 2020, 25, 5099. https://doi.org/10.3390/molecules25215099

AMA Style

Ramakrishnan S, Subramaniam S, Kielar C, Grundmeier G, Stewart AF, Keller A. Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures. Molecules. 2020; 25(21):5099. https://doi.org/10.3390/molecules25215099

Chicago/Turabian Style

Ramakrishnan, Saminathan, Sivaraman Subramaniam, Charlotte Kielar, Guido Grundmeier, A. F. Stewart, and Adrian Keller. 2020. "Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures" Molecules 25, no. 21: 5099. https://doi.org/10.3390/molecules25215099

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