title: The stability and characteristics of a DNA Holliday junction switch.
abstract: A Holliday junction (HJ) consists of four DNA double helices, with a branch point discontinuity at the intersection of the component strands. At low ionic strength, the HJ adopts an open conformation, with four widely spaced arms, primarily due to strong electrostatic repulsion between the phosphate groups on the backbones. At high ionic strength, screening of this repulsion induces a switch to a more compact (closed) junction conformation. Fluorescent labelling with dyes placed on the HJ arms allows this conformational switch to be detected optically using fluorescence resonance energy transfer (FRET), producing a sensitive fluorescent output of the switch state. This paper presents a systematic and quantitative survey of the switch characteristics of such a labelled HJ. A short HJ (arm length 8 bp) is shown to be prone to dissociation at low switching ion concentration, whereas an HJ of arm length 12 bp is shown to be stable over all switching ion concentrations studied. The switching characteristics of this HJ have been systematically and quantitatively studied for a variety of switching ions, by measuring the required ion concentration, the sharpness of the switching transition and the fluorescent output intensity of the open and closed states. This stable HJ is shown to have favourable switch characteristics for a number of inorganic switching ions, making it a promising candidate for use in nanoscale biomolecular switch devices.
authors.affiliation: School of Chemistry, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JJ, UK. A.Mount@ed.ac.uk
authors.forename: A R
authors.initials: AR
authors.lastname: Mount
authors.forename: C P
authors.initials: CP
authors.lastname: Mountford
authors.forename: S A G
authors.initials: SA
authors.lastname: Evans
authors.forename: T-J
authors.initials: TJ
authors.lastname: Su
authors.forename: A H
authors.initials: AH
authors.lastname: Buck
authors.forename: P
authors.initials: P
authors.lastname: Dickinson
authors.forename: C J
authors.initials: CJ
authors.lastname: Campbell
authors.forename: L M
authors.initials: LM
authors.lastname: Keane
authors.forename: J G
authors.initials: JG
authors.lastname: Terry
authors.forename: J S
authors.initials: JS
authors.lastname: Beattie
authors.forename: A J
authors.initials: AJ
authors.lastname: Walton
authors.forename: P
authors.initials: P
authors.lastname: Ghazal
authors.forename: J
authors.initials: J
authors.lastname: Crain
mesh_terms: D045566:DNA, Cruciform / Q000737:chemistry* / Q000187:drug effects; D005456:Fluorescent Dyes / Q000737:chemistry; D007477:Ions / Q000494:pharmacology; D009690:Nucleic Acid Conformation / Q000187:drug effects; D013050:Spectrometry, Fluorescence; D013095:Spermidine / Q000494:pharmacology
chemical_list: D045566:DNA, Cruciform; D005456:Fluorescent Dyes; D007477:Ions; D013095:Spermidine