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Center for Nonlinear Studies |
DNA is one of the most important biomolecules in living organism, forms a helix from two intertwined strands with complementary base pairs. Biological functions of a DNA depend on its mechanical properties, which in turn depend on its sequence specificity. Under physiological condition a double stranded DNA (dsDNA) is described as a semi-flexible biopolymer with persistence length of 50 nm, while a single-stranded DNA (ssDNA) is quite flexible. Recently straightening a dsDNA inside a nanochannel is being explored as an alternate method to determine DNA sequences at a single molecule level without replication1;2. First, I will present coarse grained (CG) models for fast computations of DNA conformations and dynamics. I will use scaling arguments validated by Brownian dynamics (BD) simulation results performed on the CG models to demonstrate how the equilibrium DNA conformations change inside a nanochannel as one varies the persistence length (stiffness) and the channel width3;4. I will then show the transients and the steady states of an initially straightened DNA inside a nanochannel squeezed by a nano-dozer assay5. I will compare the time dependent density profiles from the BD simulation with those obtained from a Nonlinear Partial Differential Equation (NPDE) approach5 recently introduced by Khorshid et al.1;2, and demonstrate how this combined approach can be effectively used to study nonequilibrium dynamics of very long dsDNA segments inside a nanochannel3. For stiff chains in nanopores, we further show that chain compression proceeds through a unique folding kinetics driven by repeated double fold nucleation events and growth of nested folds. We show that the folding kinetics can be understood by coupling a theory for deterministic contour spooling across the folds with a dynamically varying energy landscape for fold nucleation. These findings are critical for understanding compression of nanochannel confined DNA in the sub-persistence length (Odijk) regime6.
Host: Angel Garcia