Stacking-induced fluorescence increase reveals allosteric interactions through DNA.

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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Morten MJ,Lopez SG,Steinmark IE,Rafferty A,Magennis SW

doi

10.1093/nar/gky887

subject

Has Abstract

pub_date

2018-11-30 00:00:00

pages

11618-11626

issue

21

eissn

0305-1048

issn

1362-4962

pii

5114258

journal_volume

46

pub_type

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