Bait-and-Switch Molecular Recognition in Nucleic Acid Sensors

Mira K. Y. Nishimura, Colin D. McGuinness, David Keszenman-Pereyra, Paul Dickinson, Cohn J. Campbell, Till T. Bachmann, Peter Ghazal, Jason Crain, Colin Campbell

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

Abstract

We investigate the properties of a simple DNA-based nanodevice capable of detecting single nucleotide polymorphisms (SNPs) in unlabelled nucleic acid target sequences. Detection is achieved by a two-stage bait-and-switch process combining complementary-base hybridization and switching as molecular recognition criteria. A probe molecule is constructed from a single DNA strand designed to adopt a partial cruciform structure with a pair of exposed (unhybridized) strands. Upon target binding, a switchable cloverleaf construct (similar to a Holliday junction) is formed where the states are the open and closed junction conformations. Switching between these occurs by junction folding in the presence of divalent ions. A combination of steady-state and time-resolved fluorescence spectroscopy is used to measure Forster resonance energy transfer.

Original languageEnglish
Title of host publication2009 SYMPOSIUM ON PHOTONICS AND OPTOELECTRONICS (SOPO 2009)
Place of PublicationNEW YORK
PublisherInstitute of Electrical and Electronics Engineers (IEEE)
Pages915-920
Number of pages6
ISBN (Print)978-1-4244-4411-3
Publication statusPublished - 2009

Keywords

  • Biosensor
  • FRET
  • single nucleotide polymorphisms
  • fluorescence lifetime
  • DNA
  • JUNCTION

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