Sequence-specific recognition of B-DNA by oligo(N-methylpyrrolecarboxamide)s.
Four homologous oligopeptide-EDTA molecules, tri-, tetra, penta-, and hexa(N-methylpyrrolecarboxamide)-EDTA, in the presence of Fe(II), O2, and dithiothreitol, cleave 32P-end-labeled restriction fragments from plasmid pBR322 DNA at common locations rich in A X T base pairs that differ in the size of the binding site. From analysis of the cleavage patterns visualized by high-resolution denaturing gel electrophoresis, the oligopeptides with three, four, five, and six N-methylpyrrolecarboxamide units, containing four, five, six, and seven amide NHs, bind sites of A X T-rich DNA consisting of five, six, seven, and eight contiguous base pairs, respectively. The general rule of n amides affording binding site sizes of n + 1 base pairs is consistent with the oligopeptides binding in the minor groove of right-handed DNA, with the amide NH groups forming bridges between the adjacent N-3 and O-2 atoms of adenine or thymine on opposite strands of the DNA helix.
Youngquist
R S
RS
Dervan
P B
PB
D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA; D004214:Distamycins; D009429:Netropsin; D009690:Nucleic Acid Conformation; D011758:Pyrroles
D004214:Distamycins; D011758:Pyrroles; D009429:Netropsin; C030000:stallimycin; D004247:DNA