Polyamides containing N-methylimidazole (Im) and
N-methylpyrrole (Py) amino acids can be
combined
in antiparallel side-by-side dimeric complexes for sequence-specific
recognition in the minor groove of DNA.
Covalently linking polyamide subunits has led to designed ligands
with both increased affinity and specificity. Simple
aliphatic amino acid linkers serve as internal guide residues for turn
vs extended binding in a head-to-tail-linked
polyamide motif. Polyamides of sequence composition
ImPyPy-X-PyPyPy containing linkers of incremental length
(X = 3-aminopropionic acid (β), 4-aminobutyric acid (γ), or
5-aminovaleric acid (δ)) in complex with an undecamer
DNA duplex containing a 5‘-(A,T)G(A,T)3-3‘ target site
were structurally characterized using NMR spectroscopy.
Previous quantitative DNase I footprinting studies identified γ
as the highest affinity of these “turn” linkers.
NMR
titrations and 2D NOESY data combined with restrained molecular
modeling reveal that polyamides with β, γ, and
δ linkers all may adopt a hairpin structure. Modeling supports
the idea that the linkers in the β and δ complexes
adopt an energetically less favorable turn geometry than the γ linker
and confirms that the three-carbon γ linker is
sufficient and optimal for the hairpin conformation.
Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids can be
combined in antiparallel side-by-side dimeric complexes for sequence-specific recognition in the minor groove
of DNA. Because the curvature of four or five contiguous Im−Py rings does not perfectly match the canonical
B-helix, β-alanine (β) residues have been inserted to reset the register. Complexes of three pyrrole−imidazole
polyamides of sequence composition ImPyPy-X-PyPyPy-Dp, where X = Py, β, or glycine (G), bound to a 13
base pair DNA duplex containing a 9 base pair 5‘-TGTATATCA-3‘ match site were characterized by NMR.
NMR titrations and NOESY data combined with restrained molecular modeling show that each polyamide
adopts an extended antiparallel dimeric conformation with the ligands fully overlapped around a central Py/Py, G/G, or β/β pair. Conformational exchange is seen near the linker for the G-linked complex, but not with
the β or Py linkers. In addition to providing the first direct structural evidence for formation of the aliphatic
β/β pairing in the minor groove, models support the idea that the β linker of ImPyPy-β-PyPyPy-Dp provides
an optimal combination of size, flexibility, and alignment of the polyamide-paired aromatic subunits in extended,
dimeric 2:1 complexes.
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