DNA conformations and dynamics squeezed inside a nano-channel with a sliding gasket

Monday, May 1, 20173:00pm - 4:30pm

ABSTRACT

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 replication [1,2].

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 width [3,4]. I will then show the transients and the steady states of an initially straightened DNA inside a nanochannel squeezed by a nano-dozer assay [5].

Finally, I will compare the time dependent density profiles from the BD simulation with those obtained from a Nonlinear Partial Differential Equation (NPDE) approach [5] 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 nanochannel [3].

*Work done in collaboration with Aiqun Huang, Walter Reisner, H.-P. Hsu and Kurt Binder

1. A. Khorshid, P. Zimmy, D. Tetreault-La Roche, G. Massarelli, T. Sakaue, and W. Reisner, Dynamic Compression of Single Nanochannel Confined DNA via a Nanodozer Assay, Phys. Rev. Lett, 113, 268104 (2014).2. A. Khorshid, S. Amin, Z. Zhang, T. Sakaue, and W. Reisner, Nonequilibrim Dynamics of Nanochannel Confined DNA, Macromolecules 49, 1933 (2016).3. Aiqun Huang, H.-P Hsu, Aniket Bhattacharya, and Kurt Binder, Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles, J. Chem. Phys. 143, 243102 (2015).4. Aiqun Huang and Aniket Bhattacharya, DNA confined in a two-dimensional strip geometry, Euro Phys. Lett. 106, 18004 (2014).5. A. Huang, W. Reisner, and A. Bhattacharya, Dynamics of DNA Squeezed inside a Nanochannel via a Sliding Gasket, Polymers 8, 352 (2016).

BIOGRAPHY

BS (Hons) Physics from Presidency College, Kolkata, India l MS (Physics) from University College of Science, Kolkata, India l PhD in Condensed Matter Physics, University of Maryland, College Park l Research Associate at Penn State University l Research Asst. Professor at Michigan State University l UCF Physics - since 2000Research Interest: Theoretical and Computational Soft Matter and Biological Physics