Wakelin S P, Waring M J
Biochem J. 1976 Sep 1;157(3):721-40. doi: 10.1042/bj1570721.
Echinomycin is a peptide antibiotic which binds strongly to double-helical DNA up to a limit of approximately one molecule per five base-pairs. There is no detectable interaction with rRNA and only extremely feeble non-specific interaction with poly(rA)-poly(rU). Heat denaturation of DNA greatly decreases the binding, and similarly limited interaction is observed with naturally occurring single-stranded DNA. Association constants for binding to nine double-helical DNA species from different sources are presented; they vary by a factor of approximately 10, but are not simply related to the gross base composition. The interaction with DNA is ionic-strength-dependent, the binding constant falling by a factor of 4 when the ionic strength is raised from 0.01 to 0.10mol/litre. From the effect of temperature on the association constant for calf thymus DNA, the enthalpy of interaction is calculated to be about -13kJ/mol (-3kcal/mol). Binding of echinomycin persists in CsCl gradients and the buoyant density of nicked bacteriophage PM2 DNA is decreased by 25 mg/ml. Echinomycin interacts strongly with certain synthetic poly-deoxynucleotides, the binding constant decreasing in the order poly(dG)-poly(dC) greater than poly(dG-dC) greater than poly(dA-dT). For the latter two polymers the number of base-pairs occluded per bound antibiotic molecule is calculated to be three, whereas for poly(dG)-poly(dC) it is estimated to be four to five. Poly(dA)-poly(dT) and poly(dI)-poly(dC) interact only very weakly with the antibiotic. Poly(dI-dC) interacts to a slightly greater extent, but the binding curve is quite unlike that seen with the three strongly binding synthetic polynucleotides. Echinomycin affects the supercoiling of closed circular duplex bacteriophage PM2 DNA in the characteristic fashion of intercalating drugs. At low ionic strength the unwinding angle is almost twice that of ethidium. Likewise the extension of the helix, determined from changes in the viscosity of rod-like sonicated DNA fragments, is nearly double that expected for a simple (monofunctional) intercalation process. On this basis the interaction process is characterized as bifunctional intercalation. At higher ionic strength the unwinding angle relative to that of ethidium and the helix extension per bound echinomycin molecule fall, indicating a smooth progression towards more nearly monofunctional intercalation. Two simpler compounds which act as analogues of the quinoxaline chromophores of echinomycin, quinoxaline-2-carboxamide and the trypanocidal drug Bayer 7602, interact with DNA very much more weakly than does echinomycin, showing that the peptide portion of the antibiotic plays an essential role in determining the strength and specificity of the interaction.
棘霉素是一种肽类抗生素，它能与双螺旋DNA紧密结合，每五个碱基对最多结合一个分子。未检测到它与rRNA有相互作用，与聚（rA）-聚（rU）只有极其微弱的非特异性相互作用。DNA的热变性会大大降低其结合能力，与天然存在的单链DNA也观察到类似的有限相互作用。给出了与来自不同来源的九种双螺旋DNA结合的缔合常数；它们相差约10倍，但与总体碱基组成并无简单关联。与DNA的相互作用依赖于离子强度，当离子强度从0.01mol/L提高到0.10mol/L时，结合常数下降4倍。根据温度对小牛胸腺DNA缔合常数的影响，计算出相互作用的焓约为-13kJ/mol（-3kcal/mol）。棘霉素在CsCl梯度中仍能保持结合，切口噬菌体PM2 DNA的浮力密度降低了25mg/ml。棘霉素与某些合成多脱氧核苷酸强烈相互作用，结合常数按聚（dG）-聚（dC）＞聚（dG-dC）＞聚（dA-dT）的顺序降低。对于后两种聚合物，计算出每个结合的抗生素分子封闭的碱基对数为3，而对于聚（dG）-聚（dC），估计为4至5。聚（dA）-聚（dT）和聚（dI）-聚（dC）与该抗生素的相互作用非常微弱。聚（dI-dC）的相互作用程度稍大，但结合曲线与三种强结合合成多核苷酸的不同。棘霉素以嵌入药物的典型方式影响闭环双链噬菌体PM2 DNA的超螺旋。在低离子强度下，解旋角几乎是溴化乙锭的两倍。同样，根据棒状超声处理的DNA片段粘度变化确定的螺旋伸长几乎是简单（单功能）嵌入过程预期值的两倍。在此基础上，将相互作用过程表征为双功能嵌入。在较高离子强度下，相对于溴化乙锭的解旋角和每个结合的棘霉素分子的螺旋伸长减小，表明向更接近单功能嵌入的方向平稳发展。两种作为棘霉素喹喔啉发色团类似物的较简单化合物，喹喔啉-2-甲酰胺和杀锥虫药物拜耳7602，与DNA的相互作用比棘霉素弱得多，这表明抗生素的肽部分在决定相互作用的强度和特异性方面起着至关重要的作用。
