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Nucleic Acids Research, Vol 27, Issue 15 3029-3034, Copyright © 1999 by Oxford University Press

ARTICLES

Optimization of alternate-strand triple helix formation at the 5"-TpA- 3" and 5"-ApT-3" junctions

P Brodin, JS Sun, JF Mouscadet and C Auclair
Laboratoire de Physicochimie et de Pharmacologie des Macromolecules Biologiques, CNRS UMR 8532, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif Cedex, France.

Alternate-strand triple helix formation was optimized at the two junction steps, the 5"-TpA-3" and 5"-ApT-3" junctions. Footprint experiments, gel retardation assays and thermal denaturation measures on a sequence appropriately designed with two adjacent alternate-strand polypurine tracts points out that the addition of an adenine residue and the removal of one nucleotide should facilitate the crossing strands at the 5"-TpA-3" junction and at the 5"-ApT-3" junction, respectively. These results provide a 'switch code' for the construction of alternate-strand triple helix forming oligonucleotides which open new possibilities for extending the range of applications of antigene strategy.
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