Dear All,
First I would like to thanks
everyone who took the time to respond. It never fails to amaze me what an
awesome forum the ccp4bb board is and how willing people are to share their
expertise!
Below is a summary of the
replies I received
1. Do people routinely try different lengths of DNA?
Yes,
this seems to be the biggest variable
2. Do you start with blunt or sticky ends?
The
general consensus seems ideally to try both. Sticky ends seems the best option
to try first though with complementary ends
3. Would purification of the resultant complex by gel
filtration be a good idea as the interaction is so tight?
Most replies seem to
suggest just mixing protein and DNA together is just as likely to get good
results
4.
Which
screens would you try first?
In no particular order
Natrix, Nucleix, PEGS, Index, JCSG core, MPD
screen, Peg ion screen, home made PEG salt screen (=/- Mg++)
5.
Where
do you order the DNA from as there is a large difference in price depending on
supplier. What scale do you go for and what purification?
A wide range of suppliers were suggested.
Didn’t seem to be a great preference for one over another
Some people purify their own DNA, others
order HPLC purified and some use un-purified for screening.
6.
We
expect 1:1 binding. What ratios of protein to DNA are generally used (bearing
in mind the inaccuracies of protein estimation)?
1/1.2 seems to be the best option. People
incubate together and then dialyse prior to crystallisation
7. Any other useful tips?
Protein DNA crystals
can be very fragile so good idea to screen with cryoprotectant in the screen to
save manipulations
Test crystals with a
gel to see if DNA is present
Use of SAXS to get
molecular envelop of complex
Several papers were
suggested
Schultz, S. C., Shields, G. C. &
Steitz, T. A. (1990).
Crystallization of Escherichia coli
catabolite gene activator protein with its DNA binding site. J. Mol.
Biol. 213,
159–166.
Tan et al,
Crystallization of the Yeast MATa2/MCM1/DNA Ternary Complex: General Methods
and Principles for Protein/DNA Cocrystallization J. Mol. Biol. (2000) 297,
947±959
Cannone et al,
Crystallization of bFGF-DNA aptamer complexes using a
Sparse Matrix
designed for protein–nucleic acid complexes Journal of Crystal Growth,
2001 232 (2001) 409–417
Book chapter 8 from Crystallization of
nucleic acids and proteins: a practical approach.
Edited by A.Ducruix and R. Giege (Oxford
University Press)
Thanks again for all your replies
Best wishes
Clare
Dr. Clare E. M. Stevenson
John Innes Centre,
Department Biological
Chemistry
Colney Lane
Norwich
Norfolk
NR4 7UH