Kinds of DNA-binding protein the recognizes the DNA backbone?

As you rightly say the DNA backbone is highly negatively charged due to the phosphate groups and so any DNA binding protein must have within its active surface positively charged amino acids or in some cases positively charged ions. Positively charged amino acids include Lysine and Arginine which have amino groups at the end of long CH2 chains enabling them to extend out of tertiary structures and interact with another molecule. Other DNA binding proteins use ions, a common one is known as the zinc finger because it contains zinc!