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Nucleic Acids Research, 2000, Vol. 28, No. 18 3511-3516
© 2000 Oxford University Press

Parallel intramolecular DNA triple helix with G and T bases in the third strand stabilized by Zn2+ ions

E. B. Khomyakova1, H. Gousset, J. Liquier, T. Huynh-Dinh2, C. Gouyette2, M. Takahashi3, V. L. Florentiev1 and E. Taillandier*

Laboratoire de Spectroscopie Biomoléculaire, URA CNRS 1430, Université Paris Nord, 74 rue Marcel Cachin, F-93017 Bobigny Cedex, France, 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 117984 Moscow, Russia, 2Laboratoire de Chimie Organique, URA CNRS 487, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France and 3Groupe d’Etude Mutagénèse et Cancerogénèse, URA CNRS 1342, Institut Curie, Université Paris Sud, F-91405 Orsay, France

We present evidence of formation of an intramolecular parallel triple helix with T•A.T and G•G.C base triplets (where • represents the hydrogen bonding interaction between the third strand and the duplex while . represents the Watson–Crick interactions which stabilize the duplex). The third GT strand, containing seven GpT/TpG steps, targets the polypurine sequence 5'-AGG-AGG-GAG-GAG-3'. The triple helix is obtained by the folding back twice of a 36mer, formed by three dodecamers tethered by hydroxyalkyl linkers (-L-). Due to the design of the oligonucleotide, the third strand orientation is parallel with respect to the polypurine strand. Triple helical formation has been studied in concentration conditions in which native gel electrophoresis experiments showed the absence of intermolecular structures. Circular dichroism (CD) and UV spectroscopy have been used to evidence the triplex structure. A CD spectrum characteristic of triple helical formation as well as biphasic UV and CD melting curves have been obtained in high ionic strength NaCl solutions in the presence of Zn2+ ions. Specific interactions with Zn2+ ions in low water activity conditions are necessary to stabilize the parallel triplex.

* To whom correspondence should be addressed. Tel: +33 1 4838 7690; Fax: +33 1 4837 7443; Email: eliane.taillandier@smbh.univ-paris13.fr


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