We propose to develop the macromolecular modeling needed for a fundamental molecular understanding of how electrically charged polymer molecules move through protein channels and solid-state nanopores. Such a molecular understanding is crucial for probing the fundamental process of polymer translocation and for a successful development of high-speed detection of DNA sequences. Stimulated by the need to sequence enormous number of genomes immediately and inexpensively, very exciting single-molecule electrophysiology experiments have recently been reported. Although couched in the technology of sequencing, these experiments are the in vitro analogs of the more complex biological translocation processes. Even under such simpler conditions, the results of these experiments are very puzzling and require an understanding of polymer physics, in combination with chemical specificities. We propose to implement polymer physics concepts valid at large length and time scales, in conjunction with Brownian Dynamics simulations accounting for details at smaller length and time scales. The present proposal addresses a fundamental understanding of (1) effects of secondary structures on the mechanism of movement of single stranded DNA/RNA through alpha-hemolysin pores and on the ionic current signatures, (2) enzyme-modulated DNA translocation through pores to optimize the speed of the polymer in the pore to enable simultaneous interrogation at a single-base level, and (3) conformations of dsDNA inside solid-state nanopores to enable a steady movement required for sequencing strategies and to understand the electrodynamical behavior of semiflexible dsDNA molecules under spatial constraints. Our unique combination of theory, simulations, and collaborations with active experimentalists, will have a direct and profound impact on understanding of polymer translocation, high-speed sequencing of DNA/RNA and proteins, signal transduction, screening of biological warfare agents, pharmaceutical diagnostics, and macromolecular aspects of diseases and their control.
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