I have a DNA binding protein(mw 6100), presumed to be a dimer and not to need any cofactors. It suppresses the replication of a certain gene by binding to its binding sequence overlaped by the promoter site of the gene.
Its binding DNA sequence is much highly AT-rich and has two palindromic sites, each consisting of 9 base pairs. 12 base pairs exist between the palindromic sites.
I have some questions in studying its protein-induced DNA defomation:
1. Does it have any possiblity of inducing DNA deformaiton?
2. What a handy method can elucidate whether it induces DNA deformation or not?
Gel retardation assay is under consideration although I think it is suitable for only indentification of DNA bending.
Could you advise me on this matter?
email : newera at plaza.snu.ac.kr
Lee, Ji Hyun
Laboratory of Physical Pharmacy(Prof. Lee, Bong Jin)
Seoul National University
College of Pharmacy
Seoul 151-742, Korea.