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Nucleic Acids Res. 2005 Jan 7;33(1):81-94. Print 2005.

Kinetics of tetramolecular quadruplexes.

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1
Laboratoire de Biophysique, Muséum National d'Histoire Naturelle USM503 INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris Cedex 05, France. mergny@vnumail.com

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.

PMID:
15642696
PMCID:
PMC546136
DOI:
10.1093/nar/gki148
[Indexed for MEDLINE]
Free PMC Article
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