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Oxford University Press, Nucleic Acids Research, 1(33), p. 81-94, 2005

DOI: 10.1093/nar/gki148

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Kinetics of tetramolecular quadruplexes

Journal article published in 2005 by J.-L. Mergny ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.