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Updated: Aug 25, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Construction, analysis, and transcription of model nucleosomal templates
Wendy Walter1, Vasily M Studitsky
1Department of Biochemistry and Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
Abstract:
Transcription through the nucleosome by Saccharomyces cerevisiae RNA polymerase II (Pol II) is characterized by an almost absolute block to transcription at physiological ionic strength and displacement of one H2A/H2B dimer to form a hexasome [Mol. Cell 9 (2002) 541]. In previous studies of Pol II transcription through chromatin, templates containing nucleosomes in multiple positions were used. These templates do not allow detailed analysis of the mechanism of transcription through chromatin. Here, we describe the development of a new template that is only long enough to accommodate a single nucleosome position along the DNA so that all of the templates are identical and allow for more in-depth analysis. After ligation of the nucleosome to promoter DNA or assembled elongation complexes, the mechanism of transcription through this uniquely positioned nucleosome by various RNA polymerases can be analyzed.
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