Positional characteristics of fluorophores influencing signal output of a DNA nanoswitch

Paul Dickinson, Colin J. Campbell, Stuart Evans, Amy H. Buck, Christopher P. Mountford, Lorraine M. Keane, Jonathan G. Terry, Tsueu-Ju Su, Andrew R. Mount, John S. Beattie, Anthony J. Walton, Jason Crain, Peter Ghazal

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The Holliday junction (HJ) structure, consisting of four DNA double helices with a central branch point, is capable of switching between conformational states upon ion binding. The HJ nanoswitch described here comprises a long, dual labeled cloverleaf oligonucleotide and a short, unlabeled oligonucleotide. Fluorescent labeling with donor and acceptor dyes placed on the HJ arms of the cloverleaf strand allows the ion induced conformational switch to be detected optically using fluorescence resonance energy transfer (FRET). The influence of donor and acceptor dye location on the detection of conformational switching has been investigated using two distinct HJ structures. In addition, the effect of increasing HJ arm length in order to increase donor and acceptor dye separation has been evaluated. We report that a preferential HJ nanoswitch structure can be determined, capable of efficient detection of ion induced conformational switching.

Original languageEnglish
Title of host publication2006 Bio- Micro- and Nanosystems Conference
Place of PublicationNEW YORK
PublisherInstitute of Electrical and Electronics Engineers (IEEE)
Pages36
Number of pages4
ISBN (Print)978-1-4244-0056-0
Publication statusPublished - 2006

Keywords

  • HOLLIDAY JUNCTION
  • CRYSTAL-STRUCTURE
  • ENERGY-TRANSFER
  • 4-WAY JUNCTION
  • NANOTECHNOLOGY
  • MOLECULES
  • GEOMETRY

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