Schultz P G, Dervan P B
Laboratories of Chemistry, California Institute of Technology, Pasadena 91125.
J Biomol Struct Dyn. 1984 Mar;1(5):1133-47. doi: 10.1080/07391102.1984.10507508.
Using two direct methods we have studied the binding locations and site sizes of distamycin and penta-N-methylpyrrolecarboxamide on three DNA restriction fragments from pBR322 plasmid. We find that methidiumpropyl-EDTA.Fe(II) footprinting and DNA affinity cleaving methods report common binding locations and site sizes for the tri- and pentapeptides bound to heterogeneous DNA. The tripeptide distamycin binds 5-base-pair sites with a preference for poly(dA).poly(dT) regions. The pentapeptide binds 6-7-base-pair sites with a preference for poly(dA).poly(dT) regions. These results are consistent with distamycin binding as an isogeometric helix to the minor groove of DNA with the four carboxamide N-H's hydrogen bonding five A + T base pairs. The data supports a model where each of the carboxamide N-H's can hydrogen bond to two bases, either O(2) of thymine or N(3) of adenine, located on adjacent base pairs on opposite strands of the helix. In most (but not all) cases the tri- and pentapeptide can adopt two orientations at each A + T rich binding site.
我们使用两种直接方法研究了偏端霉素和五-N-甲基吡咯甲酰胺在来自pBR322质粒的三个DNA限制片段上的结合位置和位点大小。我们发现，甲基丙基乙二胺铁（II）足迹法和DNA亲和切割法报告了与异质DNA结合的三肽和五肽的共同结合位置和位点大小。三肽偏端霉素结合5个碱基对的位点，偏好于聚（dA）·聚（dT）区域。五肽结合6-7个碱基对的位点，偏好于聚（dA）·聚（dT）区域。这些结果与偏端霉素作为等几何螺旋与DNA小沟结合一致，其中四个羧酰胺N-H与五个A+T碱基对形成氢键。数据支持一个模型，其中每个羧酰胺N-H可以与位于螺旋相反链上相邻碱基对的两个碱基形成氢键，即胸腺嘧啶的O(2)或腺嘌呤的N(3)。在大多数（但不是所有）情况下，三肽和五肽在每个富含A+T的结合位点可以采取两种取向。
