title: Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair.
abstract: 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.
authors.affiliation: Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden.
authors.forename: Blaise
authors.initials: B
authors.lastname: Dumat
authors.affiliation: Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden.
authors.forename: Anders Foller
authors.initials: AF
authors.lastname: Larsen
authors.affiliation: Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden marcus.wilhelmsson@chalmers.se.
authors.forename: L Marcus
authors.initials: LM
authors.lastname: Wilhelmsson
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D002942:Circular Dichroism; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D043542:DNA, Z-Form / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D008958:Models, Molecular; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry
chemical_list: D043542:DNA, Z-Form; D009841:Oligonucleotides; D003596:Cytosine; D004247:DNA