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Sequence specific recognition of DNA by tailor-made hairpin conjugates of achiral seco -cyclopropaneindoline-2-benzofurancarboxamide and pyrrole–imidazole polyamides

Bioorganic & Medicinal Chemistry Letters, ISSN: 0960-894X, Vol: 15, Issue: 12, Page: 3151-3156
2005
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Article Description

Hairpin conjugates of achiral seco -cyclopropaneindoline-2-benzofurancarboxamide (achiral seco -CI-Bf) and three diamides (ImPy 1, PyIm 2, and PyPy 3, where Py is pyrrole, and Im is imidazole), linked by a γ-aminobutyrate group, were synthesized. The sequence-specific covalent alkylation of the achiral CI moiety with adenine-N3 in the minor groove was ascertained by thermally induced DNA cleavage experiments. The results provide evidence that hairpin conjugates of achiral seco -CI-Bf-γ-polyamides could be tailored to target specific DNA sequences according to a set of general rules: the achiral CI moiety selectively reacts with adenine-N3, a stacked pair of imidazole/benzofuran prefers a G/C base pair, and a pyrrole/benzofuran prefers an A/T or T/A base pair. Models for the binding of hairpin conjugates 1 – 3 with sequences 5′-TC A (888)G-3′, 5′-CA A (857)C-3′, and 5′-TT A (843)C-3′ are proposed.

Bibliographic Details

Price, Carly A.; Lingerfelt, Brian M.; Handl, Heather L.; Kiakos, Konstantinos; Hartley, John A.; Lee, Moses

Elsevier BV

Biochemistry, Genetics and Molecular Biology; Pharmacology, Toxicology and Pharmaceutics; Chemistry; AT Rich Sequence; physiology; Amides; chemistry; metabolism; Antigens; Benzofurans; Binding Sites; DNA; DNA Topoisomerases; DNA-Binding Proteins; genetics; radiation effects; GC Rich Sequence; Genetic; Hot Temperature; Imidazoles; Molecular Conformation; Neoplasm; Nucleic Acid Conformation; Promoter Regions; Pyrroles; Substrate Specificity; Thermodynamics; Type II

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