Assessment of the sequence dependency for the binding of 2-aminonaphthyridine to the guanine bulge

We have studied the sequence dependent binding of 2-amino-1,8-naphthyridine derivative 1 to a single guanine bulge. The free energy changes for the binding to a guanine bulge with different sequence contexts (5'X_Y3'/3X'GY'5') were determined by a curve fitting of the thermal denaturation profile of DNA in the presence and absence of 1. The data showed that (i) the binding of I to a guanine bulge is stronger for those flanking the G-C base pair than A T base pair, (ii) the guanine 3' side to I in the complex is especially effective for the complex stabilization, and (iii) the increase of T, in the presence of I is not a good estimate for the sequence dependent binding. The most efficient 1-binding was observed for the sequence of G_G/CGC. Molecular modeling simulations suggested that stacking interaction between the 3' side guanine and I is the molecular basis for the strong binding to G_G/CGC. (C) 2003 Elsevier Science Ltd. All rights reserved.