Kinetics of tetramolecular quadruplexes

Nucleic Acids Res. 2005 Jan 7;33(1):81-94. doi: 10.1093/nar/gki148. Print 2005.

Abstract

The melting of tetramolecular DNA or RNA quadruplexes is kinetically irreversible. However, rather than being a hindrance, this kinetic inertia allows us to study association and dissociation processes independently. From a kinetic point of view, the association reaction is fourth order in monomer and the dissociation first order in quadruplex. The association rate constant k (on), expressed in M(-3) x s(-1) decreases with increasing temperature, reflecting a negative activation energy (E (on)) for the sequences presented here. Association is favored by an increase in monocation concentration. The first-order dissociation process is temperature dependent, with a very positive activation energy E (off), but nearly ionic strength independent. General rules may be drawn up for various DNA and RNA sequence motifs, involving 3-6 consecutive guanines and 0-5 protruding bases. RNA quadruplexes are more stable than their DNA counterparts as a result of both faster association and slower dissociation. In most cases, no dissociation is found for G-tracts of 5 guanines or more in sodium, 4 guanines or more in potassium. The data collected here allow us to predict the amount of time required for 50% (or 90%) quadruplex formation as a function of strand sequence and concentration, temperature and ionic strength.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Buffers
  • DNA / chemistry*
  • G-Quadruplexes
  • Guanine / chemistry
  • Kinetics
  • Nucleic Acid Denaturation
  • Nucleic Acid Renaturation
  • Osmolar Concentration
  • RNA / chemistry*
  • Temperature
  • Thermodynamics

Substances

  • Buffers
  • Guanine
  • RNA
  • DNA