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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
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DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications
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Exploring Nucleosome Unwrapping Using DNA Origami.

Jonas J Funke, Philip Ketterer, Corinna Lieleg1

  • 1Biomedical Center, Molecular Biology, LMU Munich , 82152 Martinsried near Munich, Germany.

Nano Letters
|December 15, 2016
PubMed
Summary
This summary is machine-generated.

We developed a DNA origami tool to measure how biomolecular assemblies change shape with their environment. This tool quanties nucleosome core particle disassembly, revealing salt-dependent dissociation constants.

Keywords:
DNA origamiFRETTEMforce spectroscopynucleosome

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Structural Biology

Background:

  • Understanding biomolecular assembly conformation is crucial for molecular mechanisms.
  • Environmental factors significantly influence biomolecular structure and function.
  • Existing methods for quantifying conformational equilibria can be limited.

Purpose of the Study:

  • To develop a novel DNA origami-based tool for quantifying conformational equilibria of biomolecular assemblies.
  • To apply this tool to study the salt-induced disassembly of nucleosome core particles.
  • To extract binding constants and energetic penalties associated with nucleosome disassembly.

Main Methods:

  • DNA origami construction for a custom spectrometer.
  • Integration of nucleosomes with the spectrometer for direct conformation imaging.
  • Utilizing negative staining transmission electron microscopy (TEM) and Förster resonance energy transfer (FRET) for readout.
  • Inducing nucleosome unwrapping by increasing ionic strength (MgCl2 and NaCl).

Main Results:

  • Quantified nucleosome dissociation constants across a range of ionic strengths: picomolar (low), nanomolar (intermediate), and micromolar (high).
  • Demonstrated that stacking of up to four nucleosomes does not affect salt-induced unwrapping.
  • Showcased the spectrometer's modularity for studying diverse biomolecular assemblies.

Conclusions:

  • The DNA origami spectrometer is an effective tool for studying conformational equilibria.
  • Ionic strength plays a critical role in nucleosome core particle disassembly.
  • The platform is adaptable for a wide range of biomolecular targets, from small molecules to large assemblies.