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Collective Conformations of DNA Polymers Assembled on Surface Density Gradients

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journal contribution
posted on 07.03.2012, 00:00 by Gabriel Shemer, Yahel Atsmon, Eyal Karzbrun, Roy H. Bar-Ziv
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.