Modulating transformation of DNA origami nanoarray via sequence design

Dongfang Wang, Fiona Cole, Martina Pfeiffer, Mengting Cao, Tim Schröder, Philip Tinnefeld () and Yonggang Ke ()
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Dongfang Wang: University of Science and Technology of China
Fiona Cole: Ludwig-Maximilians-Universität München
Martina Pfeiffer: Ludwig-Maximilians-Universität München
Mengting Cao: University of Science and Technology of China
Tim Schröder: Ludwig-Maximilians-Universität München
Philip Tinnefeld: Ludwig-Maximilians-Universität München
Yonggang Ke: Emory University and Georgia Institute of Technology

Nature Communications, 2025, vol. 16, issue 1, 1-9

Abstract: Abstract The four-way DNA junction is the most prevalent structural motif in DNA nanotechnology. Recently, a reconfigurable DNA nanoarray (domino array) was created with this basic motif to realize intricate, stepwise transformation by the information relay between neighboring four-way junction units. Here, we generate a DNA domino array with same sequences at every junction, and use it as a platform to study how the design of DNA bases at junctions influences the kinetics and thermodynamics of transformation of four-way junctions in reconfigurable DNA nanoarrays. By regulating the energy difference and thus the conversion between the two configurations of four-way junctions, we show the transformation of DNA nanoarray can be modulated in a designable manner. The coordinated transformation of four-way junctions in the DNA domino array enables a detailed investigation on array transformation by using Atomic Force Microscopy (AFM) imaging and single-molecule Förster resonance energy transfer (FRET) microscopy.

Date: 2025
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DOI: 10.1038/s41467-025-61421-w

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