Lisa, there isn't unfortunately a hard and fast rule for the length of DNA used in co-crystallisation. It usually is just a case of screening different lengths, permuting the sequence, and investigating overhangs or gaps in the DNA duplex. We generally work with oligos between 8 and 21 nts in length, but there are many examples of longer DNAs being co-crystallised, the nucleosome comes to mind as an extreme example.
Do you know if the protein binds better to DNA containing secondary structure elements, such as hairpin loops? This can make a difference, especially when you don't have sequence-specificity. Tony O. --- Mobile Account --- On 15 Feb 2012, at 08:07, "LISA" <science...@gmail.com> wrote: > Hi all, > > I have a DNA binding protein. I can get crystals when I mix 8-28 nt dsDNA > with my protein. But neither of them has good diffraction. Some biochemical > data said the longer of DNA, the tigher of the binding betwwen DNA and my > protein. The binding is not sequence-specfic. Does anyone have suggestion of > the optimization? What is the good length of DNA for crystallization? > Thank you. > > Lisa
