Science, Vol.266, No.5185, 646-650, 1994
Design of a G-Center-Dot-C-Specific DNA Minor Groove-Binding Peptide
A four-ring tripeptide containing alternating imidazole and pyrrole carboxamides specifically binds six-base pair 5’-(A,T)GCGC(A,T)-3’ sites in the minor groove of DNA. The designed peptide has a specificity completely reversed from that of the tripyrrole distamycin, which binds A,T sequences. Structural studies with nuclear magnetic resonance revealed that two peptides bound side-by-side and in an antiparallel orientation in the minor groove. Each of the four imidazoles in the 2:1 ligand-DNA complex recognized a specific guanine amino group in the GCGC core through a hydrogen bond. Targeting a designated four- base pair G-C tract by this synthetic ligand supports the generality of the 2:1 peptide-DNA motif for sequence-specific minor groove recognition of DNA.
Keywords:SEQUENCE-SPECIFIC RECOGNITION;TWO-DIMENSIONAL NMR;MOLECULAR RECOGNITION;DISTAMYCIN-A;N-METHYLPYRROLECARBOXAMIDE;2-DIMENSIONAL NMR;DYNAMIC ASPECTS;NUCLEIC-ACIDS;NETROPSIN;COMPLEX