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A Pyrrole‐Imidazole Polyamide Motif for Recognition of Eleven Base Pair Sequences in the Minor Groove of DNA
Author(s) -
Swalley Susanne E.,
Baird Eldon E.,
Dervan Peter B.
Publication year - 1997
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.19970031009
Subject(s) - antiparallel (mathematics) , base pair , dna , imidazole , stereochemistry , dimer , chemistry , binding site , footprinting , crystallography , biochemistry , base sequence , organic chemistry , physics , quantum mechanics , magnetic field
A new upper limit of binding site size is defined for the 2:1 overlapped polyamide: DNA motif. Eight‐ring polyamides composed of four‐ring subunits containing pyrrole (Py) and imidazole (Im) amino acids linked by a central β‐alanine (β) spacer („4‐β‐4 ligands”) were designed for recognition of eleven base pair sequences as antiparallel dimer (4‐β‐4) 2 .DNA complexes in the minor groove. The DNA binding properties of three polyamides, ImPyPyPy‐β‐PyPyPyPy‐β‐Dp, ImImPyPy‐β‐PyPyPyPy‐β‐Dp, and ImImImPy‐β‐PyPyPyPy‐β‐Dp, were analyzed by footprinting experiments on DNA fragments containing the respective match sites 5'‐AGTAATTTACT‐3', 5'‐AGGTATTACCT‐3', and 5'‐AGGGATTCCCT‐3' (Dp = dimethylaminopropylamide). Quantitative footprint titrations reveal that each polyamide binds its respective target site with subnanomolar affinity and 7‐fold to over 30‐fold specificity over double‐base‐pair mismatch sites. A 20‐fold decrease in binding affinity is observed for placement of a side‐by‐side β‐β pairing opposite G.C/C.G relative to placement opposite a A.T/T.A base pair. The use of side‐by‐side antiparallel β‐alanine residues as an A.T/T.A‐specific DNA binding element provides a new pairing rule for polyamide design. Expanding the DNA binding site size targeted by pyrrole‐imidazole polyamides represents an important step in the development of cell‐permeable synthetic ligands for the control of gene‐specific regulation.