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Dimensional Reduction of Duplex DNA Under Nanofluidic Slit Confinement

Published

Author(s)

Luis Fernando Vargas Lara, Jack F. Douglas, Samuel M. Stavis, Elizabeth A. Strychalski, Jon C. Geist, Brian J. Nablo

Abstract

There has been much recent interest in the dimensional properties of duplex DNA under nanoscale confinement conditions as a problem of fundamental interest in both technological and biological fields. This has led to a series of measurements by fluorescence microscopy of single DNA molecules confined to nanofluidic slits. Despite the significant efforts expended on such experiments, and the corresponding theory and simulations of confined DNA, a clear and reproducible description of changes in the radius of gyration Rg of DNA under strong confinement has not yet emerged. Here, we perform molecular dynamic simulations of confined DNA to identify relevant variables that may account for the observed experimental variability. Our simulations indicate a significant amplification of repulsive excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality, and a strong dependence of the excluded volume size exponent on dimensionality. This previously neglected effect implies that any factor influencing the strength of the chain excluded volume on the effective DNA diameter, such as fluorescent label binding and intercalation, ionic strength, and counter–ion valence, can strongly influence the DNA dimensions under confinement. These factors, which are normally less important in bulk DNA solutions at moderate ionic strengths, must therefore be tightly controlled to achieve reproducible measurements of DNA under dimensional reduction conditions. By simulating DNA over a wide range of lengths, effective diameters, and confinement dimensions, and exploiting past theoretical treatments of the dimensional variation of excluded volume exponents and the amplitude prefactors for scale dependent polymer properties, we have developed a predictive relationship for the in-plane dimensions Rg of DNA under confinement.
Citation
Nanoscale

Keywords

DNA, Confinement, Nanofluidic

Citation

, L. , Douglas, J. , Stavis, S. , Strychalski, E. , Geist, J. and Nablo, B. (2015), Dimensional Reduction of Duplex DNA Under Nanofluidic Slit Confinement, Nanoscale, [online], https://doi.org/10.1039/c5sm01580d (Accessed September 22, 2021)
Created August 19, 2015, Updated November 10, 2018