Overcoming the speed limit of four-way DNA branch migration with bulges in toeholds
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Author(s)
Type
Journal Article
Abstract
Dynamic DNA nanotechnology creates programmable reaction networks and nanodevices using DNA strands.
The key reaction in dynamic DNA nanotechnology is the exchange of DNA strands between different molecular species, achieved through three-way and four-way strand exchange reactions. While both reactions have been widely used, the fourway exchange reaction has traditionally been slower and less efficient than the three-way reaction. In this paper, we describe a new mechanism to optimise the kinetics of the four-way strand exchange reaction by adding bulges to the toeholds of the four-way DNA complexes involved in the reaction. These bulges facilitate an alternative branch migration mechanism and destabilise the four-way DNA junction, increasing the four-way strand exchange rate by an order of magnitude. This advancement has the potential to expand the field of dynamic DNA nanotechnology by enabling efficient four-way strand exchange reactions for in-vivo applications.
The key reaction in dynamic DNA nanotechnology is the exchange of DNA strands between different molecular species, achieved through three-way and four-way strand exchange reactions. While both reactions have been widely used, the fourway exchange reaction has traditionally been slower and less efficient than the three-way reaction. In this paper, we describe a new mechanism to optimise the kinetics of the four-way strand exchange reaction by adding bulges to the toeholds of the four-way DNA complexes involved in the reaction. These bulges facilitate an alternative branch migration mechanism and destabilise the four-way DNA junction, increasing the four-way strand exchange rate by an order of magnitude. This advancement has the potential to expand the field of dynamic DNA nanotechnology by enabling efficient four-way strand exchange reactions for in-vivo applications.
Date Issued
2025-09-17
Date Acceptance
2025-08-08
Citation
Nano Letters, 2025, 25 (37), pp.13772-13779
ISSN
1530-6984
Publisher
American Chemical Society
Start Page
13772
End Page
13779
Journal / Book Title
Nano Letters
Volume
25
Issue
37
Copyright Statement
© 2025 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY 4.0 .
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Publication Status
Published
Date Publish Online
2025-09-04