Probing DNA dynamics: stacking-induced fluorescence increase (SIFI) versus FRET

Morten, M. J., Steinmark, E. and Magennis, S. W. (2020) Probing DNA dynamics: stacking-induced fluorescence increase (SIFI) versus FRET. ChemPhotoChem, 4(9), pp. 664-667. (doi: 10.1002/cptc.202000069)

Abstract

Stacking‐induced fluorescence increase (SIFI) was introduced recently as a method to probe DNA structure and dynamics using only a single fluorescent label. Here we show that the same DNA hairpin dynamics can be recovered, at the single‐molecule level, using either SIFI (with Cy3 as the label) or FRET (with Cy3 as donor and Cy5 as acceptor). We also measured FRET using a donor that cannot undergo SIFI, Cy3B, in the presence and absence of a molecular crowding agent (PEG). While crowding increases hybridisation to the same extent, the absolute rates are affected by the choice of donor dye. This work shows that SIFI can be used to measure single‐molecule dynamics, which could offer advantages over FRET in some cases. It also illustrates how local dye interactions can influence biomolecular dynamics, which should be considered when designing experiments.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Magennis, Dr Steven and Morten, Dr Michael
• Authors: Morten, M. J., Steinmark, E., and Magennis, S. W.
• College/School: College of Science and Engineering > School of Chemistry
• Journal Name: ChemPhotoChem
• Publisher: Wiley
• ISSN: 2367-0932
• ISSN (Online): 2367-0932
• Published Online: 17 April 2020
• Copyright Holders: Copyright © 2020 The Authors
• First Published: First published in ChemPhotoChem 4(9):664-667
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
170215		From nature to nano: structure, dynamics and reactivity of DNA three-way junctions	Steven Magennis	Engineering and Physical Sciences Research Council (EPSRC)	EP/L027003/1	Chemistry