Understanding the physical properties of the genome (which is composed of DNA) is essential to determining how processes such as gene expression, DNA replication, and DNA repair are controlled. A wide range of organisms organize their genome by repeatedly wrapping the DNA into small spools called nucleosomes. As a gene is expressed, replicated or repaired the organization of the nucleosomes is rearranged, and this project will develop a new approach to enable the study of chromatin structural dynamics over the length of a gene, thereby enabling new physical insights into how genes are turned on and off. Interdisciplinary training will be provided in a wide range of fields from molecular biology and biochemistry to nanotechnology and single molecule biophysics. The researchers will integrate this project into outreach programs including a Minority Engineering Program, Women in Engineering, and the Masters to PhD Bridge Program, all of which serve to increase the diversity of the next generation of STEM researchers.
Chromatin structural dynamics control the accessibility of DNA to complexes that regulate transcription, repair DNA damage and replicate DNA. Conversion between open euchromatin that is accessible to DNA regulatory complexes and compact heterochromatin that is inaccessible is essential for genome regulation and processing. Currently, there is a lack of tools for probing critical events during gene regulation at specific DNA sequences (i.e. promoter regions) that span 10-100nm over multiple nucleosomes. To address this challenge, the principal investigators will: (1) develop nanoscale hinge devices using DNA origami nanotechnology to quantitatively measure mesoscale conformational dynamics of chromatin; and (2) determine the 10-100nm structural dynamics of H1 compacted chromatin. The conformational changes in these nano-hinges will be detected by transmission electron microscopy and single molecule fluorescence. The development and application of these single molecule methods will provide new tools and insight into the structural events that occur within chromatin as it converts between distinct functional states.
This project is funded jointly by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Division of Materials Research in the Directorate for Mathematical and Physical Sciences.
