The Statistics of DNA Capture and Re-Capture by a Solid-State Nanopore

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The Statistics of DNA Capture and Re-Capture by a Solid-State Nanopore
Mihovilovic, Mirna (creator)
Stein, Derek (Director)
Valles, James (Reader)
Ying, See-Chen (Reader)
Brown University. Physics (sponsor)
Copyright Date
A nanopore detector is a voltage-biased nanometer-scale hole in a thin insulating membrane that can sense the threading of individual charged biopolymers, such as DNA, via partial blockages of the ionic current through the nanopore. Besides having the ability to detect a single DNA molecule, its size also compels a naturally coiled DNA molecule to go linearly through, end-to-end. Previous studies have found that the end-to-end translocation time of DNA through nanopores scales super-linearly with its length, which indicates that nanopores are sensitive to the DNA coil outside the nanopore. Here we describe studies that probe the configuration and size of DNA coils, performed using 10 nm-wide solid state nanopores. In the first, we study the statistics of 16.5 um-long lambda DNA threading through a nanopore which allows a DNA molecule to go through in a straight as well as a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. We find a strong bias favoring the capture of molecules near their ends. A theoretical model shows that bias to be a consequence of configurational entropy, rather than a search by the polymer for an energetically favorable configuration. In this study we also quantified the fluctuations and length-dependence of the speed of simultaneously translocating polymer segments from our study of folded DNA configurations. In the second, we characterize the relaxation of lambda DNA following a translocation through a solid-state nanopore using the delayed capture and re-capture technique, also called molecular ping-pong. In DNA ping-pong, a single molecule is shuffled back and forth through the nanopore by reversing the applied voltage after each translocation. The fast translocation process drives DNA into a compressed, out-of-equilibrium state and subsequent recapture enables a quantification of its relaxation via the current blockade signal. The recaptured molecules are observed to translocate faster, which is explained by the reduced viscous drag on a compact coil. Experimental evidence supports a simple relaxation model of DNA which is also consistent with our translocation speed measurements.
solid-state nanopore
DNA translocation
DNA dynamics
Polymer networks
Thesis (Ph.D. -- Brown University (2014)
13, 119 p.


Mihovilovic, Mirna, "The Statistics of DNA Capture and Re-Capture by a Solid-State Nanopore" (2014). Physics Theses and Dissertations. Brown Digital Repository. Brown University Library.