Detection of Nucleosomal Substructures using Solid-State Nanopores

Histone proteins assemble onto DNA into nucleosomes that control the structure and function of eukaryotic chromatin. More specifically, the structural integrity of nucleosomes regulates gene expression rates and serves as an important early marker for cell apoptosis. Nucleosomal (sub)structures are...

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Bibliographic Details
Published in:Nano letters 2012-06, Vol.12 (6), p.3180-3186
Main Authors: Soni, Gautam V, Dekker, Cees
Format: Article
Language:English
Subjects:
Arrays
Blocking
Condensed matter: structure, mechanical and thermal properties
Conductance
Conductometry - methods
Exact sciences and technology
Histones
Low-dimensional structures (superlattices, quantum well structures, multilayers): structure, and nonelectronic properties
Markers
Molecular weight
Nanostructures - chemistry
Nucleosomes - chemistry
Physics
Porosity
Proteins
Substructures
Surfaces and interfaces
thin films and whiskers (structure and nonelectronic properties)
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Summary:Histone proteins assemble onto DNA into nucleosomes that control the structure and function of eukaryotic chromatin. More specifically, the structural integrity of nucleosomes regulates gene expression rates and serves as an important early marker for cell apoptosis. Nucleosomal (sub)structures are however hard to detect and characterize. Here, we show that solid-state nanopores are well suited for fast and label-free detection of nucleosomes and its histone subcomplexes. (Nucleo-)protein complexes are individually driven through the nanopore by an applied electric field, which results in characteristic conductance blockades that provide quantitative information on the molecular size of the translocating complex. We observe a systematic dependence of the conductance blockade and translocation time on the molecular weight of the nucleosomal substructures. This allows discriminating and characterizing these protein and DNA–protein complexes at the single-complex level. Finally, we demonstrate the ability to distinguish nucleosomes and dinucleosomes as a first step toward using the nanopore platform to study chromatin arrays.
ISSN:1530-6984
1530-6992
DOI:10.1021/nl301163m