Stacking-induced fluorescence increase reveals allosteric interactions through DNA

Morten, M. J., Lopez, S. G., Steinmark, I. E., Rafferty, A. and Magennis, S. W. (2018) Stacking-induced fluorescence increase reveals allosteric interactions through DNA. Nucleic Acids Research, 46(21), pp. 11618-11626. (doi: 10.1093/nar/gky887) (PMID:30277520) (PMCID:PMC6265455)

Abstract

From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye–DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids.

• Item Type: Articles
• Additional Information: Funding: EPSRC [EP/L027003/1 to M.J.M.]; BBSRC [BB/P001610/1 to S.G.L.]. Funding for open access charge: BBSRC [BB/P001610/1]
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Magennis, Dr Steven and Lopez, Dr Sergio and Morten, Dr Michael
• Authors: Morten, M. J., Lopez, S. G., Steinmark, I. E., Rafferty, A., and Magennis, S. W.
• College/School: College of Science and Engineering > School of Chemistry
• Journal Name: Nucleic Acids Research
• Publisher: Oxford University Press
• ISSN: 0305-1048
• ISSN (Online): 1362-4962
• Published Online: 02 October 2018
• Copyright Holders: Copyright © 2018 The Authors
• First Published: First published in Nucleic Acids Research 46(21):11618-11626
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
65718	1	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	SCHOOL OF CHEMISTRY
72720	1	Pushing proteins off DNA - how do helicases unwind protein-coated DNA?	Steven Magennis	Biotechnology and Biological Sciences Research Council (BBSRC)	BB/P001610/1	SCHOOL OF CHEMISTRY