Collective Conformations of DNA Polymers Assembled on Surface Density Gradients

Gabriel Shemer, Yahel Atsmon, Eyal Karzbrun, and Roy H. Bar-Ziv*

Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel

J. Am. Chem. Soc., Article ASAP

DOI: 10.1021/ja2106543

Publication Date (Web): February 15, 2012

Copyright © 2012 American Chemical Society

To study dense double-stranded DNA (dsDNA) polymer phases, we fabricated continuous density gradients of binding sites for assembly on a photochemical interface and measured both dsDNA occupancy and extension using evanescent fluorescence. Despite the abundance of available binding sites, the dsDNA density saturates after occupation of only a fraction of the available sites along the gradient. The spatial position at which the density saturates marks the onset of collective stretching of dsDNA, a direct manifestation of balancing entropic and excluded-volume interactions. The methodology presented here offers a new means to investigate dense dsDNA compartments.