title: Hoogsteen base pairs proximal and distal to echinomycin binding sites on DNA.
abstract: Forms of the DNA double helix containing non-Watson-Crick base-pairing have been discovered recently based on x-ray diffraction analysis of quinoxaline antibiotic-oligonucleotide complexes. In an effort to find evidence for Hoogsteen base-pairing at quinoxaline-binding sites in solution, chemical "footprinting" (differential cleavage reactivity) of echinomycin bound to DNA restriction fragments was examined. We report that purines (A greater than G) in the first and/or fourth base-pair positions of occupied echinomycin-binding sites are hyperreactive to diethyl pyrocarbonate. The correspondence of the solid-state data and the sites of diethyl pyrocarbonate hyperreactivity suggests that diethyl pyrocarbonate may be a sensitive reagent for the detection of Hoogsteen base-pairing in solution. Moreover, a 12-base-pair segment of alternating A-T DNA, which is 6 base pairs away from the nearest strong echinomycin-binding site, is also hyperreactive to diethyl pyrocarbonate in the presence of echinomycin. This hyperreactive segment may be an altered form of right-handed DNA that is entirely Hoogsteen base-paired.
mesh_terms: D001482:Base Composition; D001665:Binding Sites; D004247:DNA / Q000235:genetics* / Q000378:metabolism; D003850:Deoxyribonuclease I / Q000494:pharmacology; D004047:Diethyl Pyrocarbonate; D004448:Echinomycin / Q000378:metabolism*; D004492:Edetic Acid / Q000031:analogs & derivatives / Q000494:pharmacology; D011687:Purines / Q000502:physiology; D011810:Quinoxalines / Q000378:metabolism*
chemical_list: D011687:Purines; D011810:Quinoxalines; C038200:methidiumpropyl-EDTA-iron(II); D004448:Echinomycin; D004247:DNA; D004492:Edetic Acid; D003850:Deoxyribonuclease I; D004047:Diethyl Pyrocarbonate