The NF-kappa B transcription factor induces DNA bending which is modulated by its 65-kD subunit

• Published in: Nucleic acids research Vol. 18; no. 22; pp. 6497 - 6502
• Main Authors: Schreck, R, Zorbas, H, Winnacker, E L, Baeuerle, P A
• Format: Journal Article
• Language: English
• Published: England 25.11.1990
• Subjects: Animals; Base Sequence; Binding Sites; DNA - chemistry; DNA - metabolism; DNA Damage; Hydroxides; Hydroxyl Radical; Metals - pharmacology; Mice; Molecular Sequence Data; Molecular Weight; NF-kappa B - physiology; Nucleic Acid Conformation - drug effects; Nylons - pharmacology
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/18.22.6497

This study describes a novel functional property of the eukaryotic transcription factor NF-kappa B in altering the DNA structure. We observed that the binding of purified NF-kappa B to DNA was facilitated by spermine and cations which are known to promote DNA bending, and by a nick in one position at the 3'-end of the binding site. Furthermore, the position of the NF-kappa B binding sequence 5'-GGGACTTTCC-3' (kappa B motif) within circularly permutated DNA fragments had a profound influence on the mobility of NF-kappa B-DNA complexes in a gel retardation assay while the mobility of unbound DNA fragments did not depend on the position of the kappa B motif. The mobility effect was slightly reduced at increased temperature. These observations suggested that binding of NF-kappa B to DNA induces bending. The estimated bending angle induced by the 50-kD DNA binding subunit of NF-kappa B (p50) was smaller than that induced by p50 which was associated with the 65-kD non-DNA binding subunit (p65). Moreover, the presence of p65 appeared to result in a shift of the bending center from the middle towards the 3'-end of the kappa B motif. This shows a role for the p65 subunit of NF-kappa B in modulating the extent and altering the position of protein-induced DNA bending.