Quadruplex Turncoats: Cation-Dependent Folding and Stability of Quadruplex-DNA Double Switches

J Am Chem Soc. 2016 Mar 2;138(8):2780-92. doi: 10.1021/jacs.5b13130. Epub 2016 Feb 18.

Abstract

Quadruplex (G4) nucleic acids, a family of secondary structures formed by guanine-rich sequences, exhibit an important structural polymorphism. We demonstrate here that G-rich DNA sequences may function as a double switch based on different triggers, provided that their quadruplex structures and stability display a high dependence on cation nature and concentration. A first switch is based on a remarkable antiparallel-to-parallel conversion, taking place in a few seconds at room temperature by addition of low KCl amounts to a sodium-rich sample. The second switch involves the conversion of alternative antiparallel quadruplex structures binding only one cation, formed in the presence of sub-millimolar potassium or strontium concentrations, to parallel structures by increasing the cation concentration. Incidentally, extremely low K(+) or Sr(2+) concentrations (≤5 equiv) are sufficient to induce G4 formation in a buffer devoid of other G4-promoting cations, and we suggest that the alternative structures observed contain only two tetrads. Such DNA systems are biological relevant targets, can be used in nanotechnology applications, and are valuable methodological tools for understanding DNA quadruplex folding, notably at low cation concentrations. We demonstrate that this behavior is not restricted to a narrow set of sequences but can also be found for other G-quadruplex-forming motifs, arguing for widespread applications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cations / chemistry
  • Circular Dichroism
  • DNA / chemistry*
  • DNA / genetics
  • G-Quadruplexes*
  • Polymorphism, Genetic
  • Potassium / chemistry
  • Sodium / chemistry
  • Structure-Activity Relationship
  • Thermodynamics

Substances

  • Cations
  • DNA
  • Sodium
  • Potassium