SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR-GROOVE BINDER

The tripeptide ,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDP l(3)) binds to the minor groove of DNA with high affinity. When this m inor groove binder is conjugated to the 5'-end of short oligonucleotid es the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions betwe en the CDPl(3) minor groove binding moiety and the DNA, we have determ ined and compared the solution structure of a duplex consisting of oli godeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDP l(3) and its complementary strand to an unmodified control duplex of t he same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restr ained molecular dynamics and relaxation matrix refinement, the solutio n structure of the CDPl(3)-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and t hat the CDPl(3) moiety was bound snugly in the minor groove,where it w as stabilized by extensive van der Waal's interactions.