Nucleic Acids Research, Vol 27, Issue 4 1063-1069, Copyright © 1999 by Oxford University Press
DJ Hart, RE Speight, MA Cooper, JD Sutherland and JM Blackburn
The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA
duplex with no specific binding site were determined under varying
conditions of potassium chloride concentration using a surface
plasmonresonance biosensor. Association and dissociation rate constants
were measured enabling calculation of the dissociation constants. Under
previously established high affinity buffer conditions, the k a for both
sequences was in the order of 10(7) M-1s-1whilst the k d values varied
600-fold in a sequence-dependent manner between 10(-1) and 10(-4 )s-1,
suggesting that the selectivity of p50 for different sequences is mediated
primarily through sequence-dependent dissociation rates. The calculated K D
value for the Ig-kappaB sequence was 16 pM, whilst the K D for the
non-specific sequence was 9.9 nM. As the ionic strength increased to levels
which are closer to that of the cellular environment, the binding of p50 to
the non-specific sequence was abolished whilst the specific affinity
dropped to nanomolar levels. From these results, a mechanism is proposed in
which p50 binds specific sequences with high affinity whilst binding
non-specific sequences weakly enough to allow efficient searching of the
DNA.
ARTICLES
The salt dependence of DNA recognition by NF-kappaB p50: a detailed kinetic analysis of the effects on affinityand specificity
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. U. Ferreiro, I. E. Sanchez, and G. de Prat Gay Transition state for protein-DNA recognition PNAS, August 5, 2008; 105(31): 10797 - 10802. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Zhang, V. Metelev, D. Tabatadze, P. C. Zamecnik, and A. Bogdanov Jr Fluorescence resonance energy transfer in near-infrared fluorescent oligonucleotide probes for detecting protein-DNA interactions PNAS, March 18, 2008; 105(11): 4156 - 4161. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. D. Auweter, F. C. Oberstrass, and F. H.-T. Allain Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res., October 18, 2006; 34(17): 4943 - 4959. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hallier, J. Desreac, and B. Felden Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation. Nucleic Acids Res., January 1, 2006; 34(6): 1935 - 1943. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Sasuga, T. Tani, M. Hayashi, H. Yamakawa, O. Ohara, and Y. Harada Development of a microscopic platform for real-time monitoring of biomolecular interactions Genome Res., January 1, 2006; 16(1): 132 - 139. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D.-B. Huang, D. Vu, L. A. Cassiday, J. M. Zimmerman, L. J. Maher III, and G. Ghosh Crystal structure of NF-{kappa}B (p50)2 complexed to a high-affinity RNA aptamer PNAS, August 5, 2003; 100(16): 9268 - 9273. [Abstract] [Full Text] [PDF]
|
|