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Nucleic Acids Research, 1984, Vol. 12, No. 12 4865-4879
© 1984

MOLECULAR BIOLOGY

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

C.M.Loretta Low, Horace R. Drew+ and Michael J. Waring

University of Cambridge Department of Pharmacology, Medical School, Hills Road Cambridge, CB2 2QD +Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge, CB2 2QH, UK

Received April 16, 1984. Revised June 1, 1984. Accepted June 1, 1984.

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


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