Sequence-specific binding of echinomycin to DNA: evidence for conformational changes affecting flanking sequences

摘要: The technique of DNAase I footprinting has been used to investigate preferred binding sites for echinomycin on a 160-base-pair DNA fragment from E. coli containing the tyr T promoter sequence. Six have precisely located in sequence; seventh partially identified. minimum site-size is six base pairs. All contain dinucleotide sequence CpG but no other regularities can be discerned. When protected regions each complementary strand are compared it evident that they staggered by 2-3 base-pairs towards 3' end at site. Footprinting with II reports similar, though less precise, pattern protection. Cutting both enzymes markedly enhanced AT-rich flanking antibiotic-binding sites. This increased susceptibility nuclease attack attributed an altered helix conformation vicinity bis-intercalated molecule. It seems certain sequences, mainly runs A or T, switch nuclease-resistant nuclease-sensitive form when binds nearby.