Journal Article

Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair

Blaise Dumat, Anders Foller Larsen and L. Marcus Wilhelmsson

in Nucleic Acids Research

Volume 44, issue 11, pages e101-e101
Published in print June 2016 | ISSN: 0305-1048
Published online February 2016 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gkw114

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Herein, we report on the use of a tricyclic cytosine FRET pair, incorporated into DNA with different base pair separations, to study Z-DNA and B-Z DNA junctions. With its position inside the DNA structure, the FRET pair responds to a B- to Z-DNA transition with a distinct change in FRET efficiency for each donor/acceptor configuration allowing reliable structural probing. Moreover, we show how fluorescence spectroscopy and our cytosine analogues can be used to determine rate constants for the B- to Z-DNA transition mechanism. The modified cytosines have little influence on the transition and the FRET pair is thus an easily implemented and virtually non-perturbing fluorescence tool to study Z-DNA. This nucleobase analogue FRET pair represents a valuable addition to the limited number of fluorescence methods available to study Z-DNA and we suggest it will facilitate, for example, deciphering the B- to Z-DNA transition mechanism and investigating the interaction of DNA with Z-DNA binding proteins.

Journal Article.  7768 words.  Illustrated.

Subjects: Molecular and Cell Biology

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