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)

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)

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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

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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
727201Pushing proteins off DNA - how do helicases unwind protein-coated DNA?Steven MagennisBiotechnology and Biological Sciences Research Council (BBSRC)BB/P001610/1SCHOOL OF CHEMISTRY