Hi all,
I am working on a DNA binding protein (mol wt around 30 kDa), which binds
to Duplex DNA in a non-specific sequence manner. The structure has been
published with 12 base pair duplex DNA.
I am trying to understand the DBD protein DNA interaction even more by
choosing different lengths
How is the DNA packed in the crystal? Coaxially stacked pseudo-infinite
helices?
--paul
On 05/05/2013 02:21 AM, ASHOK KUMAR Patel wrote:
Hi all,
I am working on a DNA binding protein (mol wt around 30 kDa), which
binds to Duplex DNA in a non-specific sequence manner. The structure
has
Dear Ashok,
There are many questions underlying your questions. A couple of things to
check right off the bat:
(1) Do you actually know that your crystal still contains all of the DNA bp
that you started with? Did you analyze the contents of your crystal by
native PAGE, mass spec or other
Because your protein binds non-specifically, it could be an interesting case of
static disorder where the DNAs are making a pseudo-continuous helix through the
crystal regardless of sequence, and 12 bp/turn happens to fit nicely into a
generic lattice.
How does the density for the individual
Hi Ashok,
You say your DNA is palindromic - have you looked at the possibility that the
longer DNAs are actually folded on themselves rather than duplexes of two
separete oligos? Depending on the location of the centre of your palindrome and
on interactions with adjacent molecules, this
Dear all
i have a basic question regarding SPR experiment and that is: What is the
recommended glycerol concentration in the protein sample for doing SPR
experiment and getting the best possible result.? i have kept 10% Glycerol
in my protein preparation..is it O.K ?
Thanx in advance
--
Hi Faisal,
whatever makes your protein happy is good. What type of experiment were you
thinking of ? Protein-protein interaction or protein-small molecule interaction
? In the latter case add some Tween20 or Brij-35 into the mix. A decent
overview can be found under this webpage for what to
