Recognition of Nucleic Acids by Transcription Factor NF-κB

  • Gourisankar Ghosh
  • De-Bin Huang
  • Tom Huxford
Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)


NF-κB is a ubiquitous transcription factor that controls the expression of genes involved in development, inflammation, and cell survival. Since the first X-ray crystal structures revealed the DNA-binding portions of NF-κB in complex with target DNA, it has been appreciated that NF-κB exhibits a unique and complicated mechanism for DNA recognition and binding. NF-κB possesses the ability to bind to specific DNA sequences with high affinity. It accomplishes this through the action of conserved structured loops that strategically place specific DNA base-contacting amino acid side chains into register with double-stranded DNA. The bi-domain structure of the individual NF-κB subunit DNA-binding scaffolds permits degeneracy within the consensus target DNA sequence. Alternative conformations of NF-κB upon these degenerate DNA sequences directly affect target gene expression levels. The combination of ordered nucleotide base-contacting loops within a flexible domain architecture has been exploited by small folded RNA molecules that have been developed to specifically bind and inhibit NF-κB subunits.


Dime Interface Dimerization Domain Half Site 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors thank Vivien Wang for reading the manuscript and for aid in the preparation of figures. Research in the laboratory of GG is supported by the NIH (grants GM085490 and AI064326). TH is supported by American Cancer Society grant RSG-08-287-01-GMC.


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Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of CaliforniaSan DiegoUSA

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