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Nucleic Acids Research, Vol 25, Issue 16 3269-3274, Copyright © 1997 by Oxford University Press

ARTICLES

Kinetic studies on the formation of intermolecular triple helices

HM Paes and KR Fox
Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.

We have used DNase I footprinting to examine the association kinetics of GA-, GT- and CT-containing oligonucleotides with the target sequence (GGA)5GG. (CCT)5CC. These reactions are slow yielding bimolecular association rate constants between 50 and 2000 M-1s-1. We find that GT- containing oligonucleotides bind much faster than GA- or CT-containing third strands. In each case the observed rate constants are faster at the centre than at the edges of the target site. Although several explanations can be offered for this observation, it is consistent with a model in which triplex formation at this repetitive site is achieved via intermediate complexes in which the third strand is not properly aligned with its target and which subsequently migrate to the correct position.
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P. L. James, T. Brown, and K. R. Fox
Thermodynamic and kinetic stability of intermolecular triple helices containing different proportions of C+{middle dot}GC and T{middle dot}AT triplets
Nucleic Acids Res., October 1, 2003; 31(19): 5598 - 5606.
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