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Originally published In Press as doi:10.1074/jbc.M206780200 on November 20, 2002

J. Biol. Chem., Vol. 278, Issue 9, 7500-7509, February 28, 2003
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Transcription Factor Decoy Molecules Based on a Peptide Nucleic Acid (PNA)-DNA Chimera Mimicking Sp1 Binding Sites*

Monica BorgattiDagger , Ilaria LamprontiDagger , Alessandra Romanelli§, Carlo Pedone§, Michele Saviano§, Nicoletta BianchiDagger , Carlo MischiatiDagger , and Roberto GambariDagger ||

From the Dagger  Department of Biochemistry and Molecular Biology, Ferrara University, Via L.Borsari n.46, 44100 Ferrara, Italy, § Institute of Biostructure and Bioimaging, CNR, 80134 Napoli, Italy, and  Biotechnology Centre, Ferrara University, Via Fossato di Mortara 8/A, 44100 Ferrara, Italy

Peptide nucleic acids (PNAs) are DNA-mimicking molecules in which the sugar-phosphate backbone is replaced by a pseudopeptide backbone composed of N-(2-aminoethyl)glycine units. We determined whether double-stranded molecules based on PNAs and PNA-DNA-PNA (PDP) chimeras could be capable of stable interactions with nuclear proteins belonging to the Sp1 transcription factor family and, therefore, could act as decoy reagents able to inhibit molecular interactions between Sp1 and DNA. Since the structure of PNA/PNA hybrids is very different from that of the DNA/DNA double helix, they could theoretically alter the molecular structure of the double-stranded PNA-DNA-PNA chimeras, perturbing interactions with specific transcription factors. We found that PNA-based hybrids do not inhibit Sp1/DNA interactions. In contrast, hybrid molecules based on PNA-DNA-PNA chimeras are very effective decoy molecules, encouraging further experiments focused on the possible use of these molecules for the development of potential agents for a decoy approach in gene therapy. In this respect, the finding that PDP-based decoy molecules are more resistant than DNA/DNA hybrids to enzymatic degradation appears to be of great interest. Furthermore, their resistance can even be improved after complexation with cationic liposomes to which PDP/PDP chimeras are able to bind by virtue of their internal DNA structure.

* This work was supported by CNR-P.F. Biotecnologie, Ministero dell'Università e della Ricerca Scientifica e Tecnologica-PRIN-2002, CNR Agenzia 2000, Finalized Research funds (year 2001) from the Italian Ministry of Health, and Ministero dell'Istruzione, Università e Ricerca-Contributo Straordinario Decreto 4-10-2001.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

|| To whom correspondence should be addressed. Tel.: 39-532-291448; Fax: 39-532-202723; E-mail: gam@unife.it.

Copyright © 2003 by The American Society for Biochemistry and Molecular Biology, Inc.
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