Design of New Reagents on the Base of DNA Duplexes for Irreversible Inhibition of Transcription Factor NF-κB

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Abstract
The main purpose of the present work is to search for the optimal design of a DNA duplex containing an active group for crosslinking and irreversible inhibition of the transcription factor NF-kappa B. Modified DNA duplexes with an identical nucleotide sequence but different internucleotide phosphates replaced by the trisubstituted pyrophosphate internucleotide group were synthesized. Crosslinking of the human NF-kappa B p50 subunit with the modified DNA duplexes was carried out. It was shown that only four modified duplexes crosslinked with the NF-kappa B p50 subunit. The specificity of these reactions was confirmed. A position of the phosphate in the NF-kappa B recognition site was found where replacement on the active trisubstituted pyrophosphate group resulted in a 50% yield of crosslinking. The fact that DNA duplexes containing the trisubstituted pyrophosphate group specifically react with the NF-kappa B p50 subunit in the Escherichia coli total lysate supports the idea that such modified DNA can be used as high specific inhibitors for DNA-recognizing proteins.