Nucleic Acids Research, Vol 26, Issue 21 4797-4803, Copyright © 1998 by Oxford University Press
JL Mergny and L Lacroix
At slightly acidic or even neutral pH, oligodeoxynucleotides that include a
stretch of cytidines have been shown to form a tetrameric structure in
which two parallel-stranded duplexes have their hemiprotonated C.C+base
pairs face to face and fully intercalated, in a so-called i-motif.
Cytosine-rich pyrimidine oligodeoxynucleotides can form an intramolecular
i-motif. We have studied the ability of several DNA analogs to fold into
this structure. Evidence for folding was provided by thermal denaturation.
We have shown that phosphorothioate and phosphodiester
oligodeoxynucleotides, but not methylphosphonate or PNA oligomers, may form
the i-motif. Four different PS oligodeoxynucleotides were compared with
their PO counterparts. In all cases, the melting temperature (Tm) of the
phosphorothioate oligomer was equal or slightly inferior (by 2-3 degreesC)
to the Tmof the natural oligodeoxynucleotide. For long
oligodeoxynucleotides, a small change of pH leads to a completely different
melting profile: the curves are reversible at pH 6.4 or lower, and a
hysteresis is obtained at pH 6.8 or higher; cooling and heating curves were
not superimposed, allowing us to determine the rate constants of
association (kon) and dissociation (koff) as a function of the temperature:
these rate constants give linear Arrhenius plots, in agreement with the
prediction of the two-state model of association-dissociation. The
activation energy Eonis strongly negative and, at neutral pH, the
phosphorothioate associates and dissociates nine times faster than the
phosphodiester oligodeoxynucleotide of identical sequence.
ARTICLES
Kinetics and thermodynamics of i-DNA formation: phosphodiester versus modified oligodeoxynucleotides
Laboratoire de Biophysique, Museum National d'Histoire Naturelle, INSERM U201, CNRS UA481,43 rue Cuvier 75005 Paris, France.
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