Interaction of the human NF-kappa B p52 transcription factor with DNA-PNA hybrids mimicking the NF-kappa B binding sites of the human immunodeficiency virus type 1 promoter

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