Dear All, Thank you very much for your valuable suggestions.
Venkat On Sat, Jan 4, 2014 at 9:53 AM, Acoot Brett <[email protected]> wrote: > Dear All, > > For the question, I think for a protein-DNA interaction, the protein may > interact with any sequences of DNA, which will give a lot of combination of > protein-DNA sequence for crystallization screening. Or do anyone regard to > just try the crystallization of the protein-one specific sequence DNA > fragment for the trial (for example the DNA sequence with the highest > binding affinity)? In another word, does the easiness of the > crystallization has relation with how strong the protein interacts with the > DNA sequence? > > Acoot > > > On Saturday, 4 January 2014 11:02 AM, rajakumara eerappa < > [email protected]> wrote: > My suggestions are > 1 try complementary and non-complementary overhangs which can form > Watson-crick and/ or Hoogstein base pairing. > 2. If it binds self-complementary duplexes then try them also. > 3. Peg conditions with slight acidic pH are more suitable. > 4. Divalent cation salts (Ca, Mg, Mn) in crystallization. > > Wish you good luck > Raj > > > On Friday, January 3, 2014, venkatareddy dadireddy wrote: > > Hi, > > I'm working on DNA binding protein, looking to co-crystallize protein- DNA > complex and have no previous experience. Your suggestion would be very > precious on the following queries. > 1. My protein is 646 amino acid long and it exists as homodimer. It is > also having around 20 amino acid extra sequence from vector. Will > vector sequence affect crystallization? > 2. Its homologous protein shows good affinity for 31-mer. Shall I use same > length of DNA for co- crystallization. > 3. What is the length of DNA to be used? > 4. What is purity of oligos to be used? Is it HPLC pure or normal desalted > ones. I have read on CCP4 mails for screening purpose normal oligos > are fine. Please comment on that. > 3. Any other suggestions on Protein DNA co- crystallization. > > Thanks > venkat > > > > -- *Venkatareddy Dadireddy, B1-10,Prof. S. Ramakumar's Lab, Dept. of Physics,IISc, Banglore. Cell: 07259492227*
