There are quite a few things that affect protein binding to DNA. However most of that's rather off-topic for this site. While others might give you a sufficient answer (thus, I haven't closed this...though I wouldn't be surprised if someone else does), you're likely to receive a longer reply on the biology stack exchange. Please do do some research beforehand. The basics of this is are covered in undergrad genomics/molecular biology text-books (hint, look in the back index for major and minor grooves).