Template-Directed Interference Footprinting of Protein−Adenine Contacts

Abstract

Noncovalent contacts between amino acid residues and DNA bases are the principal contributors to sequence-specific recognition in most protein−DNA complexes. We have developed a method, template-directed interference (TDI) footprinting, which not only identifies DNA bases that are contacted by a protein upon formation of a specific complex but also reveals the groove location of the contacts and provides a rough gauge of their energetics. Previously, we demonstrated TDI footprinting of guanine (TDI-G), cytosine (TDI-C), and thymine (TDI-T) residues in the major groove of DNA. Here we report the development of a procedure for TDI footprinting of the fourth and final DNA base, adenine (TDI-A). The base-analog 7-deaza-7-nitroadenine (A*), present as the corresponding 2‘-deoxynucleoside 5‘-triphosphate, was found to undergo efficient incorporation into DNA during template-directed enzymatic polymerization. The analog exhibits the same base-pairing preference as its native counterpart (A), and could be selectively degraded, leading to DNA strand scission upon treatment with aqueous piperidine. To validate the use of A* as a probe of specific protein−DNA contacts, we carried out TDI-A footprinting of the bacteriophage 434 repressor/OR1 operator interaction. The observed interference by A* only at position-1 of the operator is consistent with the results of X-ray crystallographic analysis. Together with TDI-G, -C, and -T footprinting, the present TDI-A footprinting procedure now completes the series of four experiments required for the analysis of major groove contacts to all four DNA bases in solution.