Energetics and kinetics of a conformational switch in G-quadruplex DNA

J Phys Chem B. 2009 Mar 5;113(9):2676-83. doi: 10.1021/jp809578f.

Abstract

Circular dichroism and differential scanning calorimetry were used to determine the energetics of the conformational switch of the human telomere quadruplex formed by the sequence d[AGGG(TTAGGG)3] between the sodium basket form and the potassium hybrid form. The energy barrier separating the two conformations was found to be modest, only 1.4-2.4 kcal mol(-1). The kinetics of exchange of bound K+ for Na+ cations and the concomitant conformational switch was assessed by measuring time-dependent changes in the circular dichroism spectrum accompanying the cation exchange reaction. The time course of these changes was found to consist of three distinct kinetic processes: a rapid phase that was complete in less than 5 ms followed by two slower phases with relaxation times of 40-50 s and 600-800 s at 25 degrees C and pH 7.0. We interpret these kinetics in terms of a model in which the bound Na+ cations are rapidly replaced by K+ followed by relatively slow structural rearrangements to generate the final K(+)-bound product(s). Circular dichroism studies showed that addition of the porphyrin TmPyP4 promoted conversion of the basket to the hybrid form. The kinetics of the TmPyP4-induced conformational change were the same as those observed for the cation exchange reaction.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biophysics / methods*
  • Calorimetry, Differential Scanning / methods
  • Cations
  • Circular Dichroism
  • DNA / chemistry*
  • G-Quadruplexes*
  • Kinetics
  • Models, Statistical
  • Molecular Conformation
  • Potassium / chemistry
  • Sodium / chemistry
  • Telomere / chemistry
  • Temperature
  • Thermodynamics

Substances

  • Cations
  • DNA
  • Sodium
  • Potassium