What is the SMALLEST DNA BINDING DOMAIN?

Dima Klenchin klenchin at facstaff.wisc.edu
Sun Jan 12 02:45:45 EST 1997


In article <slrn5dg185.1n1.aiyar at ebv.oncology.wisc.edu>, aiyar at ebv.oncology.wisc.edu wrote:
#On Sat, 11 Jan 1997 11:52:26 EST, jstrassw at OPAL.TUFTS.EDU
# <jstrassw at OPAL.TUFTS.EDU> wrote:
#
#>Well, the Bovine Papillomavirus DNA binding domain (minimal) iosonlt 85 AA
#>although tit forms a dimer.  It has the aadvantage of many characterized
#>mutations, and an excellent crystal structure (1.2A) and  binds
#>sequence-specific to a palindropme at 10 -12 M.
#>
#>I also study it!
#
#The Kd value that you have listed for the minimal portion of "BPV-E2 
#DNA binding domain" binding it's cognate site is very different from 
#that which has been published.
#
#For instance, from J. Virol. 71:828-831 (1997) (a publication from
#the Androphy lab), the Kd of the 87 a.a minimal DNA binding domain 
#for it's cognate site is listed as approximately 7.0 nM (i.e. 7 x 10e-9 M), 
#while a larger fragment, containing 127 a.a has a Kd of about 0.9 nM, 
#and even this is quite far from the picomolar affinity you have listed ....

Umm, I know nothing about DNA binding, but biology is not a quantitative 
science, so 3 orders of magnitude makes no difference (since nobody knows 
how to apply those numbers anyway). 

Couldn't resist, 

- Dima
 



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