Investigating Nucleosome Accessibility for MNase, FeII Peplomycin, and Duocarmycin B2 by Using Capillary Electrophoresis

Capillary electrophoresis, coupled with DNA 5′ Texas Red labeling, was used to investigate the ability of MNase, FeII peplomycin, and duocarmycin B2 to access the nucleosome. Distinct accessibility patterns of these species to the nucleosome were observed. MNase was completely prevented from approac...

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Bibliographic Details
Published in:Chembiochem : a European journal of chemical biology 2018-04, Vol.19 (7), p.664-668
Main Authors: Zou, Tingting, Kizaki, Seiichiro, Sugiyama, Hiroshi
Format: Article
Language:English
Subjects:
Accessibility
Alkylation
Capillary electrophoresis
Deoxyribonucleic acid
DNA
Electrophoresis
MNase
nucleosome
peplomycin
Stratosphere
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Summary:Capillary electrophoresis, coupled with DNA 5′ Texas Red labeling, was used to investigate the ability of MNase, FeII peplomycin, and duocarmycin B2 to access the nucleosome. Distinct accessibility patterns of these species to the nucleosome were observed. MNase was completely prevented from approaching the nucleosome core and exhibited a higher site specificity for targeting DNA sites located close to the core region. Intercalation of peplomycin in the nucleosomal core region was highly suppressed, but reaction sites located at the ends of the nucleosomal core remained accessible, which implied flexibility of the core DNA end. Duocarmycin B2 was able to enter and react in the core region, although its alkylating efficiency decreased significantly. Accessibility for all: MNase exhibited enhanced reactivity in the nucleosome and selectively cleaved DNA sites near the core region, whereas FeII‐peplomycin was highly suppressed for approaching the nucleosomal core region but was still able to react with the flexible core DNA end.
ISSN:1439-4227
1439-7633
DOI:10.1002/cbic.201700643