title: Dendritic and nanowire assemblies of condensed DNA polymer brushes.
abstract: 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.
authors.affiliation: Department of Materials and Interfaces, The Weizmann Institute of Science , Rehovot 76100, Israel.
authors.forename: Dan
authors.initials: D
authors.lastname: Bracha
authors.forename: Roy H
authors.initials: RH
authors.lastname: Bar-Ziv
mesh_terms: D002412:Cations / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D053770:Nanowires / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011108:Polymers / Q000737:chemistry; D013095:Spermidine / Q000737:chemistry*
chemical_list: D002412:Cations; D011108:Polymers; D004247:DNA; D013095:Spermidine