Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions

Biochem Biophys Res Commun. 2007 Jan 19;352(3):812-7. doi: 10.1016/j.bbrc.2006.11.088. Epub 2006 Nov 27.

Abstract

It is noteworthy that the formation of the DNA G-quadruplex is induced by factors other than stabilizing cations because this event probably occurs in living cells. Previous studies have shown that thrombin-binding DNA aptamer (TBA) forms a chair-type intramolecular G-quadruplex structure that binds with thrombin protein in the absence of stabilizing cations. Here, we used circular dichroism (CD) spectroscopy to confirm G-quadruplex formation in the presence of thrombin without stabilizing cations. We obtained characteristic CD spectra that demonstrated that TBA forms the distinctive G-quadruplex structure. Additionally, we investigated G-quadruplex formation induced by change of solvent environment: the influence of low-temperature conditions and molecular crowding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aptamers, Nucleotide / chemistry*
  • Binding Sites
  • Cations
  • Circular Dichroism
  • Guanine / chemistry*
  • Macromolecular Substances / chemistry
  • Protein Binding
  • Thrombin / chemistry*

Substances

  • Aptamers, Nucleotide
  • Cations
  • Macromolecular Substances
  • Guanine
  • Thrombin