ISSN:
0947-6539
Keywords:
DNA recognition
;
hydrogen bonds
;
ligand design
;
molecular recognition
;
sequence-specificity
;
Chemistry
;
General Chemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
Notes:
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.
Additional Material:
10 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/chem.19970031009
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