Molecular interactions between nuclear factor kappa B (NF-kappa B) transcription factors and a PNA-DNA chimera mimicking NF-kappa B binding sites

The decoy approach against nuclear factor kappaB (NF-kappaB) is a useful to ol to alter NF-kappaB dependent gene expression using synthetic oligonucleo tides (ODNs) carrying NF-kappaB specific cis-elements. Unfortunately, ODNs are not stable and need to be extensively modified to be used in vivo or ex vivo. We have previously evaluated the possible use of peptide nucleic aci ds (PNAs) as decoy molecules. The backbone of PNAs is composed of N-(2-amin oethyl)glycine units, rendering these molecules resistant to both nucleases and proteases. We found that the binding of NF-kappaB transcription factor s to PNAs was either very low (binding to PNA-PNA hybrids) or exhibited low stability (binding to PNA-DNA hybrids). The main consideration of the pres ent paper was to determine whether PNA-DNA chimeras mimicking NF-kappaB bin ding sites are capable of stable interactions with proteins belonging to th e NF-kappaB family. Molecular modeling was employed for the design of PNA-D NA chimeras; prediction of molecular interactions between chimeras and NF-k appaB nuclear proteins were investigated by molecular dynamics simulations, and interactions between PNA-DNA chimeras and NF-kappaB proteins were stud ied by gel shifts. We found significant differences between the structure o f duplex NF-kappaB PNA-DNA chimera and duplex NF-kappaB DNA-DNA. However, i t was found that these differences do not prevent the duplex PNA-DNA chimer a from binding to NF-kappaB transcription factors, being able to suppress t he molecular interactions between HIV-1 LTR and p50, p52 and nuclear factor s from B-lymphoid cells. Therefore, these results demonstrate that the desi gned NF-kappaB DNA-PNA chimeras could be used for a decoy approach in gene therapy.