posted on 2014-04-02, 00:00authored byDan Bracha, Roy H. Bar-Ziv
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.