Nonamer binding protein induces a bend in the immunoglobulin gene recombinational signal sequence

DNA bending has been shown to play a critical role in conservative site-specific DNA recombination reactions such as lambda integration. V(D)J recombination, the only mammalian site directed recombination system, is directed by recombinational signal sequences composed of heptamer, nonamer and spacer elements. The nonamer element, GGTTTTTGT, is similar to the consensus sequence for bent DNA. Using the circular permutation electrophoretic mobility assay, we show that the nonamer sequence has a detectable intrinsic bend. The nonamer sequence has been shown to be the binding site for nonamer binding protein (NBP). Binding of NBP to the nonamer site increases the apparent angle of the bend from 32 degrees to 66 degrees. The identification of a protein induced DNA bend near the site of V(D)J recombination may have implications for our understanding of the mechanism of V(D)J recombination.