Kuduvalli P N, Townsend C A, Tullius T D
Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218.
Biochemistry. 1995 Mar 28;34(12):3899-906. doi: 10.1021/bi00012a005.
The cleavage by calicheamicin gamma 1I (CLM gamma 1I) of a nucleosome formed on the 5S RNA gene of Xenopus borealis was studied in vitro as a first step toward the understanding of CLM gamma 1I-chromatin interactions within the cell. The drug does not cleave in the region of the dyad axis of the nucleosome. Outside of this region, double-stranded cleavage occurs with a periodicity of 10-11 bp. The sites of cleavage correspond to DNA sequences facing outward in the nucleosome. The drug shows some sequence preference of cleavage within these accessible sites. The predominant cleavage event within this nucleosome occurs at -1 helical turn from the dyad axis. This site constitutes a "hot spot" for CLM gamma 1I cleavage within the 5S nucleosome. We observe an overall footprinting effect whereby the drug preferentially cleaves DNA located outside the nucleosome core (analogous to the linker DNA of chromatin) as compared to cleavage within the nucleosome core. We discuss the importance of accessibility, structural deformations of DNA within the nucleosome, and steric constraints posed by sequence, in the recognition and cleavage of nucleosomal DNA by calicheamicin.
为了初步了解细胞内刺孢霉素γ1I（CLMγ1I）与染色质的相互作用，对非洲爪蟾5S RNA基因上形成的核小体进行了体外刺孢霉素γ1I（CLMγ1I）切割研究。该药物不会在核小体二分体轴区域进行切割。在该区域之外，双链切割以10 - 11 bp的周期发生。切割位点对应于核小体中向外的DNA序列。该药物在这些可及位点内表现出一定的切割序列偏好性。在这个核小体内，主要的切割事件发生在距离二分体轴-1个螺旋圈处。该位点构成了5S核小体内CLMγ1I切割的“热点”。我们观察到一种整体的足迹效应，即与核小体核心内的切割相比，该药物优先切割位于核小体核心外的DNA（类似于染色质的连接DNA）。我们讨论了可及性、核小体内DNA的结构变形以及序列造成的空间限制在刺孢霉素识别和切割核小体DNA中的重要性。
