Hi all,
I am performing a protein (15 kDa)-DNA (41 bp ds DNA) co-crystallization and have some questions:
1. The DNA has a mid-micromolar affinity for the protein. So, what should be the effective DNA concentration while forming protein-DNA complexes?
2. The DNA sequence is 41 bp long which might be a problem. If I truncate the sequence, there is a loss in affinity as this is nonsequence-specific interaction. Should I still try smaller DNA sequences?
Thanks,
Prakriti