Aarhus University Seal

Molecular recognition with DNA nanoswitches: effects of single base mutations on structure

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • C P Mountford, Denmark
  • A H Buck, Denmark
  • C J Campbell, Denmark
  • P Dickinson, Denmark
  • E E Ferapontova
  • J G Terry, Denmark
  • J S Beattie, Denmark
  • A J Walton, Denmark
  • P Ghazal, Denmark
  • A R Mount, Denmark
  • J Crain, Denmark
  • Interdisciplinary Nanoscience Center
This paper investigates the properties of a simple DNA-based nanodevice capable of detecting single base mutations in unlabeled nucleic acid target sequences. Detection is achieved by a two-stage process combining first complementary-base hybridization of a target and then a conformational change 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 cruciform construct (similar to a Holliday junction) is formed which can adopt open and closed junction conformations. Switching between these forms occurs by junction folding in the presence of divalent ions. It has been shown from the steady-state fluorescence of judiciously labeled constructs that there are differences between the fluorescence resonance energy transfer (FRET) efficiencies of closed forms, dependent on the target sequence near the branch point, where the arms of the cruciform cross. This difference in FRET efficiency is attributed to structural variations between these folded junctions with their different branch point sequences arising from the single base mutations. This provides a robust means for the discrimination of single nucleotide mismatches in a specific region of the target. In this paper, these structural differences are analyzed by fitting observed time-resolved donor fluorescence decay data to a Gaussian distribution of donor-acceptor separations. This shows the closest mean separation (approximately 40 A) for the perfectly matched case, whereas larger separations (up to 50 A) are found for the single point mutations. These differences therefore indicate a structural basis for the observed FRET differences in the closed configuration which underpins the operation of these devices as biosensors capable of resolving single base mutations.
Original languageEnglish
JournalJournal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical
Pages (from-to)2439-44
Number of pages5
Publication statusPublished - 2008

    Research areas

  • Base Pair Mismatch, Base Sequence, DNA, Fluorescence Resonance Energy Transfer, Nanotechnology, Nucleic Acid Conformation, Staining and Labeling

See relations at Aarhus University Citationformats

ID: 15068238