DNA Translocation Through Protein Channels and Synthetic Nanopores

How DNA/RNA worms through protein channels and nuclear pores is a fundamental process in life. When a polymer is forced to translocate through a narrow path, its configurational entropy is reduced, resulting in a free energy barrier. This free energy barrier is additionally modulated by potential interactions between the polymer and the pore. We use polymer physics ideas (entropic barrier model), polymer theory, Molecular Dynamics, and Brownian Dynamics to understand the molecular mechanisms of DNA/RNA transport in terms of polymer length and sequence specificity. We compute the translocation time and its distribution, and the ionic current by the Poisson-Nernst-Planck methodology (generalized to polyelctrolytes). The specific systems are DNA/RNA through heptameric alpha-hemolysine protein channel embedded in a phospholipid bilayer, DNA/RNA through synthetic nanopores, and mRNP through nuclear pores.

Animated Description of Polymer Translocation:

figure 1 How ssDNA worms through a-hemolysin channel.

(click on the image to see animation)
figure 1 Simultaneous calculation of polymer conformations and ionic current through a-hemolysin channel.

(click on the image to see animation)
figure 1 Fluctuations of PEG tether inside a-hemolysin channel.

(click on the image to see animation)
figure 1 Stochastic sensing of streptavidin by biotinated PEG tether.

(click on the image to see animation)

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