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 Resjournal_title
Nucleic acids researchauthors
Morten MJ,Lopez SG,Steinmark IE,Rafferty A,Magennis SWdoi
10.1093/nar/gky887subject
Has Abstractpub_date
2018-11-30 00:00:00pages
11618-11626issue
21eissn
0305-1048issn
1362-4962pii
5114258journal_volume
46pub_type
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