Probing Nucleosome Stability with a DNA Origami Nanocaliper

Area of Science:

• Molecular Biology
• Biophysics
• Nanotechnology

Background:

• Eukaryotic DNA is organized into nucleosomes and chromatin, undergoing dynamic structural changes essential for genome processing.
• Chromatin rearrangements occur across various length scales, including mesoscopic scales (tens of nanometers), but probing these is challenging.
• Existing methodologies lack the resolution to investigate mesoscopic chromatin dynamics.

Purpose of the Study:

• To develop and implement a novel DNA-based nanocaliper for probing mesoscopic length scales within chromatin.
• To investigate the dynamic structural changes of nucleosomes and their interaction with transcription factors.
• To explore the potential of DNA nanotechnology in detecting and manipulating nucleosome structure.

Main Methods:

• Design, construction, and implementation of a DNA-based nanocaliper.
• Integration of nucleosomes into the nanocaliper at two attachment points with high efficiency.
• Utilizing the nanocaliper's hinge angle as a readout for nucleosome end-to-end distance and structural transitions.

Main Results:

• The nanocaliper successfully probed mesoscopic length scales, demonstrating sensitivity to nucleosome unwrapping based on linker DNA length.
• Nucleosomes with shorter linker DNA (6-51 bp) showed partial unwrapping, while those with 75 bp linker DNA remained fully wrapped.
• The nanocaliper detected transcription factor binding and enhanced TF occupancy by partially unwrapping the nucleosome.

Conclusions:

• The DNA nanocaliper is a feasible tool for detecting and manipulating nucleosome structure at the mesoscopic level.
• This technology provides a foundation for future studies on the structural dynamics of nucleosomes and chromatin.
• The nanocaliper's ability to influence TF binding opens new avenues for understanding gene regulation.