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J Biol Chem, Vol. 274, Issue 46, 33114-33122, November 12, 1999

Interaction of the Human NF-B p52 Transcription Factor with DNA-PNA Hybrids Mimicking the NF-B Binding Sites of the Human Immunodeficiency Virus Type 1 Promoter

Carlo Mischiati, Monica Borgatti, Nicoletta Bianchi, Cristina Rutigliano, Marina Tomassetti, Giordana Feriotto, and Roberto Gambari

From the  Department of Biochemistry and Molecular Biology and the  Biotechnology Center, Ferrara University, 44100 Ferrara, Italy

We determined whether peptide nucleic acids (PNAs) are able to interact with NF-B p52 transcription factor. The binding of NF-B p52 to DNA-DNA, DNA-PNA, PNA-DNA, and PNA-PNA hybrid molecules carrying the NF-B binding sites of human immunodeficiency type 1 long terminal repeat was studied by (i) biospecific interaction analysis (BIA) using surface plasmon resonance technology, (ii) electrophoretic mobility shift, (iii) DNase I footprinting, and (iv) UV cross-linking assays. Our results demonstrate that NF-B p52 does not efficiently bind to PNA-PNA hybrids. However, a DNA-PNA hybrid molecule was found to be recognized by NF-B p52, although the molecular complexes generated exhibited low stability. From the theoretical point of view, our results suggest that binding of NF-B p52 protein to target DNA motifs is mainly due to contacts with bases; interactions with the DNA backbone are, however, important for stabilization of the protein-DNA complex. From the practical point of view, our results suggest that DNA-PNA hybrid can be recognized by NF-B p52 protein, although with an efficiency lower than DNA-DNA NF-B target molecules; therefore, our results should encourage studies on modified PNAs in order to develop potential agents for the decoy approach in gene therapy.

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