Dynamics of an anti-VEGF DNA aptamer: A single-molecule study

J. Nick Taylor, Qusai Darugar, Katerina Kourentzi, Richard C. Willson, Christy F. Landes

Research output: Contribution to journalArticle

34 Scopus citations

Abstract

Single-molecule fluorescence resonance energy transfer (SMFRET) was used to study the interaction of a 25-nucleotide (nt) DNA aptamer with its binding target, vascular endothelial growth factor (VEGF). Conformational dynamics of the aptamer were studied in the absence of VEGF in order to characterize fluctuations in the unbound nucleic acid. SMFRET efficiency distributions showed that, while the aptamer favors a base-paired conformation, there are frequent conversions to higher energy conformations. Conversions to higher energy structures were also demonstrated to be dependent on the concentration of Mg2+-counterion by an overall broadening of the SMFRET efficiency distribution at lower Mg2+ concentration. Introduction of VEGF caused a distinct increase in the frequency of lower SMFRET efficiencies, indicating that favorable interaction of the DNA aptamer with its VEGF target directs aptamer structure towards a more open conformation.

Original languageEnglish (US)
Pages (from-to)213-218
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume373
Issue number2
DOIs
StatePublished - Aug 22 2008

Keywords

  • Angiogenesis
  • Aptamers
  • Dynamics
  • FRET
  • Hidden-Markov modeling
  • Nucleic acids
  • Single-molecule spectroscopy
  • VEGF

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

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