Design of new reagents on the base of DNA duplexes for irreversible inhibition of transcription factor NF-kappa B

• Published in: Antisense & nucleic acid drug development Vol. 7; no. 4; p. 279
• Main Authors: Kozlov, I A, Kubareva, E A, Ivanovskaya, M G, Shabarova, Z A
• Format: Journal Article
• Language: English
• Published: United States 01.08.1997
• Subjects: Animals; Base Sequence; Binding Sites; Cloning, Molecular; Cross-Linking Reagents; Crystallography, X-Ray; Diphosphates; DNA - metabolism; Drug Design; Escherichia coli; Humans; Macromolecular Substances; Mice; NF-kappa B - antagonists & inhibitors; NF-kappa B - chemistry; Oligonucleotides, Antisense - chemical synthesis; Oligonucleotides, Antisense - chemistry; Oligonucleotides, Antisense - pharmacology; Recombinant Proteins - antagonists & inhibitors; Recombinant Proteins - chemistry
• ISSN: 1087-2906
• DOI: 10.1089/oli.1.1997.7.279

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.