Computational procedures to explain the different biological activity of DNA/DNA, DNA/PNA and PNA/PNA hybrid molecules mimicking NF-kappa B binding sites

Peptide nucleic acids (PNA) have recently been proposed as alternative reag ents in experiments aimed to the control of gene expression. In PNAs, the p seudopeptide backbone is composed of N-(2-aminoethyl)glycine units and ther efore is stable in human serum and cellular extracts. PNAs hybridize with h igh affinity to complementary sequences of single-stranded RNA and DNA, for ming Watson-Crick double helices and giving rise to highly stable (PNA)(2)- RNA triplexes with RNA targets. Therefore, antisense and antigene PNAs have been synthetized and characterized. The major issue of the present paper is to describe some computational proc edures useful to compare the behaviour of PNA double stranded molecules and PNA/DNA hybrids with the behaviour of regular DNA duplexes in generating c omplexes with DNA-binding proteins. The performed computational analyses cl early allow to predict that the lack of charged phosphate groups and the di fferent shape of helix play a critical role in the binding efficiency of NF -kappaB transcription factors. These computational analyses are in agreemen t with competitive gel shift and UV-cross linking experiments. These experi ments demonstrate that NF-kappaB PNA/PNA hybrids do not interact efficientl y with proteins recognizing the NF-kappaB binding sites in genomic sequence s. In addition, the data obtained indicate that the same NF-kappaB binding proteins recognize both the NF-kappaB DNA/PNA and DNA/DNA hybrids, but the molecular complexes generated with NF-kappaB DNA/PNA hybrids are less stabl e than those generated with NF-kappaB target DNA/DNA molecules.