Dendritic and Nanowire Assemblies of Condensed DNA Polymer Brushes

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• 作者：Dan Bracha ; Roy H. Bar-Ziv
• 刊名：Journal of the American Chemical Society
• 出版年：2014
• 出版时间：April 2, 2014
• 年：2014
• 卷：136
• 期：13
• 页码：4945-4953
• 全文大小：690K
• 年卷期：v.136,no.13(April 2, 2014)
• ISSN：1520-5126

文摘

We investigated the collective conformational response of DNA polymer brushes to condensation induced by the trivalent cation spermidine. DNA brushes, a few kilobase-pairs long, undergo a striking transition into macroscopic domains of collapsed chains with fractal dendritic morphology. Condensation is initiated by focal nucleation of a towerlike bundle, which laterally expands in a chain-reaction cascade of structural chain-to-chain collapse onto the surface. The transition exhibits the hallmarks of a first-order phase transition with grain boundaries, hysteresis, and coexistence between condensed and uncondensed phases. We found that an extended DNA conformation is maintained throughout the transition and is a prerequisite for the formation of large-scale dendritic domains. We identified a critical DNA density above which the nucleation propensity and growth rate sharply increase. We hypothesize that the ability of DNA-scaffolding proteins to modify the local DNA density within a genome may act as a dynamic and sensitive mechanism for spatial regulation of DNA transactions in vivo by selective condensation of chromosomal territories. By assembling a DNA brush along a patterned line narrower than twice the DNA contour length and tuning the local surface densities, we were able to initiate nucleation at a predefined location and induced growth of a single condensed nanowire over a distance 2 orders of magnitude longer than the single-chain contour. Our results demonstrate spatial control of condensation as a new tool for constructing DNA-based synthetic systems with important implications for regulation of DNA transactions on surfaces.