Tunable Nano-Channels for Chromatin Fiber Linearization and Imaging

Tunable channels in the nanoscale resulting from crack formations are presented here for the imaging of linearized chromatin/DNA fibers. The linearization of biopolymers can eventually provide information on epigenetic modifications. Generations of periodical nano-cracks patterns are achieved by subjecting oxidized polydimethylsiloxane(PDMS)/bulk PDMS (Kim et al. Small 2014) or a nanoscale thin hPDMS film/bulk PDMS system to an applied strain. The cracks can be used as nano-channels with adjustable channel widths and the ability to completely collapse and immobilize a single fiber. The detailed crack profiles are studied by use of atomic force microscopy. In small conduits with channel diameters falling below the persistence length, local thermodynamics are such that nanoconfinement restricts the conformational degrees of freedom, favoring the stretched conformation that reduces bending energy. The device’s abilities to confine and stretch chromatin/DNA fibers are demonstrated by inducing stretching with repeated straining/relaxation cycles. The system can be used to study histone modifications using chromatin fibers extracted from Tetrahymena as a model system.