Low C M, Drew H R, Waring M J
Nucleic Acids Res. 1984 Jun 25;12(12):4865-79. doi: 10.1093/nar/12.12.4865.
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.
脱氧核糖核酸酶I足迹法技术已用于研究放线菌素对来自大肠杆菌的一段含tyr T启动子序列的160个碱基对的DNA片段的优先结合位点。已在该序列中精确确定了六个结合位点；第七个已部分鉴定。最小位点大小为六个碱基对。所有结合位点都含有二核苷酸序列CpG，但未发现其他规律。当比较每条互补链上的受保护区域时，很明显它们在每个位点向3'端错开2-3个碱基对。用脱氧核糖核酸酶II进行足迹分析报告了类似但不太精确的保护模式。在抗生素结合位点两侧富含AT的区域，两种酶的切割都明显增强。这种对核酸酶攻击的敏感性增加可归因于双插入放线菌素分子附近螺旋构象的改变。似乎某些序列，主要是A串或T串，在放线菌素在附近结合时从抗核酸酶形式转变为核酸酶敏感形式。
