A “master” in base unpairing during isomerization of a promoter upon RNA polymerase binding

Isomerization of a closed to open complex of a promoter upon RNA polymerase binding involves base unpairing at the −10 region. After potassium permanganate sensitivity of unpaired thymine residues, we studied base unpairing at the −10 region during isomerization upon RNA polymerase binding at the P1 and P3 promoters of the gal operon. Substitution of adenine by 2-amino purine (2-AP) at the invariable A⋅T base pair at the −11 position of P1 and P3 prevented unpairing not only at that position but also at the other downstream positions, suggesting a “master” role of the adenine base at −11 of the template strand in overall base unpairing. 2-AP at −11 did not inhibit the formation of RNA polymerase⋅promoter complex and subsequent isomerization of the polymerase. Substitution of adenine by 2-AP at several other positions did not affect thymine unpairing. Changing the position of the amino group from C6 in adenine to C2 in 2-AP is mutational only at the master switch position, −11.