Active Nanofluidics for Analysis of Chromatin and Genomic DNA Structures A.
Specific Aims This project will develop nanotechnology to fill an unmet need in genome-wide analysis of DNA and chromatin structures. This capability will greatly enhance our understanding of how genetics and epigenetics translate the DNA-encoded information of the nucleus into cellular functions and phenotypes. The approach will use parallel nanochannels whose cross-sectional profiles can be reversibly regulated to be narrow (nanometers) or wide (micrometers). The tunable channels will be widened to enable efficient loading of the relatively large chromatin or genomic DNA molecules in their folded states. Then the channels will be gradually narrowed, under the precise control of the operator. Simultaneous application of an electric field within the nanochannel will allow controlled linearization of the chromatin or DNA inside the channels. The stretched out chromatin or DNA will be analyzed optically to map and observe genomic structures, such as replication forks, and epigenetic structures, as well as the distribution of nucleosomes, and organized chromatin regions. These capabilities will be used for comparative genomics and epigenomics of healthy and diseased/stressed cells.
Aim 1. Construction of Tunable Nanochannel Arrays: Material properties and processing methods will be tested and optimized to construct parallel arrays of nanochannels. The nanochannels provide reproducible control of channel cross-sectional profile, microfluidic flow, and surface chemistry.
Aim 2. DNA Linearization and Stabilization: Mechanisms and software will be developed to coordinate and control channel cross-sectional shape adjustments with electrical field application. Both direct current and pulsed-field current regimes will be tested. The nanochannel profile and electric fields will be optimized to allow linearization and stable molecular control using lambda bacteriophage DNA (48 kb) as an initial test.
Aim 3. Image-based Analysis of Linearized DNA: Computerized image capture and analysis programs will be developed. As an initial biological test, we will examine replication forks on linearized genomic DNA samples from cultured mammalian cells exposed or not exposed to pharmacologic replication stress.
Aim 4. Analysis of Histone-Associated DNA: Procedures for the gentle dissociation of live cells within the devices will be developed. Dynamic changes in chromatin structures, including nucleosomes, will be observed within the channels using controlled currents, temperatures, and channel morphologies. Public Health Relevance Statement: This project will develop broadly useful nanotechnology to fill an important unmet need in genome-wide analysis of DNA and chromatin structures. The specific initial biological application of the nanotechnology in this proposal will be to analyze genomic and epigenomic structures related to DNA replication. Despite intense efforts, the orderly activation of replication sites in genomes of higher organisms remains largely unexplained. This is due, at least in part, to the complexity of the process which orchestrates activation of an estimated 10,000 to million replication sites, where the sites are determined not only by sequence but by epigenetic factors as well. This type of analysis is important clinically because faulty replication is involved in a variety of diseases such as Werner syndrome, Seckel syndrome, Fanconi anemia and cancer.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
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Study Section
Special Emphasis Panel (ZRG1-NANO-M (01))
Program Officer
Schloss, Jeffery
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University of Michigan Ann Arbor
Biomedical Engineering
Schools of Engineering
Ann Arbor
United States
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Kim, Byoung Choul; Weerappuli, Priyan; Thouless, M D et al. (2015) Fracture fabrication of a multi-scale channel device that efficiently captures and linearizes DNA from dilute solutions. Lab Chip 15:1329-34
Meng, Fanbo; Huang, Jiexi; Thouless, M D (2015) The Collapse and Expansion of Liquid-Filled Elastic Channels and Cracks. J Appl Mech 82:1010091-10100911
Moraes, Christopher; Kim, Byoung Choul; Zhu, Xiaoyue et al. (2014) Defined topologically-complex protein matrices to manipulate cell shape via three-dimensional fiber-like patterns. Lab Chip 14:2191-201
Labuz, Joseph M; Takayama, Shuichi (2014) Elevating sampling. Lab Chip 14:3165-71
Kim, Byoung Choul; Moraes, Christopher; Huang, Jiexi et al. (2014) Fracture-based fabrication of normally closed, adjustable, and fully reversible microscale fluidic channels. Small 10:4020-4029
Dixon, Angela R; Moraes, Christopher; Csete, Marie E et al. (2014) One-dimensional patterning of cells in silicone wells via compression-induced fracture. J Biomed Mater Res A 102:1361-9
Kim, Byoung Choul; Moraes, Christopher; Huang, Jiexi et al. (2014) Fracture-based micro- and nanofabrication for biological applications. Biomater Sci 2:288-296
Kim, Byoung Choul; Matsuoka, Toshiki; Moraes, Christopher et al. (2013) Guided fracture of films on soft substrates to create micro/nano-feature arrays with controlled periodicity. Sci Rep 3:3027
Cheng, Mou-Chi; Leske, Austin T; Matsuoka, Toshiki et al. (2013) Super-resolution imaging of PDMS nanochannels by single-molecule micelle-assisted blink microscopy. J Phys Chem B 117:4406-11
Matsuoka, Toshiki; Kim, Byoung Choul; Huang, Jiexi et al. (2012) Nanoscale squeezing in elastomeric nanochannels for single chromatin linearization. Nano Lett 12:6480-4

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