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  Choice of fluorophore affects dynamic DNA nanostructures

Jahnke, K., Grubmüller, H., Igaev, M., & Göpfrich, K. (2021). Choice of fluorophore affects dynamic DNA nanostructures. Nucleic Acids Research, 49(7), 4186-4195. doi:10.1093/nar/gkab201.

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Jahnke, K., Author
Grubmüller, H.1, Author              
Igaev, M.2, Author              
Göpfrich, K., Author
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1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              
2Department of Theoretical and Computational Biophysics, MPI for Biophysical Chemistry, Max Planck Society, ou_578631              

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 Abstract: The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modelling, we demonstrate for 12 different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation—without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.

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Language(s): eng - English
 Dates: 2021-03-302021-04-19
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: DOI: 10.1093/nar/gkab201
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 49 (7) Sequence Number: - Start / End Page: 4186 - 4195 Identifier: -