Sub-ensemble monitoring of DNA strand displacement using multiparameter single-molecule FRET

Baltierra Jasso, L., Morten, M. and Magennis, S. W. (2018) Sub-ensemble monitoring of DNA strand displacement using multiparameter single-molecule FRET. ChemPhysChem, 19(5), pp. 551-555. (doi:10.1002/cphc.201800012) (PMID:29316151)

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Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of ca. 10 M-1 s-1. We also followed the displacement from a DNA three-way junction (3WJ) by ssDNA. The presence of three internal mismatched bases in the middle of the invading strand did not prevent displacement from the 3WJ, but reduced the second-order rate constant by ca. 50 %. We attribute strand exchange in the dsDNA and 3WJ to a zero-toehold pathway from the blunt-ended duplex arms. The single-molecule approach demonstrated here will be useful for studying complex DNA networks.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Magennis, Dr Steven and Morten, Dr Michael and Baltierra Jasso, Dr Laura
Authors: Baltierra Jasso, L., Morten, M., and Magennis, S. W.
College/School:College of Science and Engineering > School of Chemistry
Journal Name:ChemPhysChem
ISSN (Online):1439-7641
Published Online:05 January 2018
Copyright Holders:Copyright © 2018 Wiley-VCH Verlag GmbH & Co.
First Published:First published in ChemPhysChem 19(5):551-555
Publisher Policy:Reproduced in accordance with the publisher copyright policy

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
657181From nature to nano: structure, dynamics and reactivity of DNA three-way junctionsSteven MagennisEngineering and Physical Sciences Research Council (EPSRC)EP/L027003/1SCHOOL OF CHEMISTRY