Sites of high local frustration in DNA origami

Richard Kosinski, Ann Mukhortava, Wolfgang Pfeifer, Andrea Candelli, Philipp Rauch and Barbara Saccà ()
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Richard Kosinski: ZMB, University of Duisburg-Essen
Ann Mukhortava: LUMICKS, De Boelelaan 1085
Wolfgang Pfeifer: ZMB, University of Duisburg-Essen
Andrea Candelli: LUMICKS, De Boelelaan 1085
Philipp Rauch: LUMICKS, De Boelelaan 1085
Barbara Saccà: ZMB, University of Duisburg-Essen

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: Abstract The self-assembly of a DNA origami structure, although mostly feasible, represents indeed a rather complex folding problem. Entropy-driven folding and nucleation seeds formation may provide possible solutions; however, until now, a unified view of the energetic factors in play is missing. Here, by analyzing the self-assembly of origami domains with identical structure but different nucleobase composition, in function of variable design and experimental parameters, we identify the role played by sequence-dependent forces at the edges of the structure, where topological constraint is higher. Our data show that the degree of mechanical stress experienced by these regions during initial folding reshapes the energy landscape profile, defining the ratio between two possible global conformations. We thus propose a dynamic model of DNA origami assembly that relies on the capability of the system to escape high structural frustration at nucleation sites, eventually resulting in the emergence of a more favorable but previously hidden state.

Date: 2019
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DOI: 10.1038/s41467-019-09002-6

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