Fueling protein-DNA interactions inside porous nanocontainers

Ibrahim Cisse, Burak Okumus, Chirlmin Joo, Taekjip Ha

Research output: Contribution to journalArticlepeer-review

129 Scopus citations


Vesicle encapsulation offers a biologically relevant environment for many soluble proteins and nucleic acids and an optimal immobilization medium for single-molecule fluorescence assays. Furthermore, the confinement of biomolecules within small volumes opens up new avenues to unique experimental configurations. Nevertheless, the vesicles' impermeability, even toward ions and other small molecules such as ATP, hinders more general applications. We therefore developed methods to induce pores into vesicles. Porous vesicles were then used to modulate the interaction between Escherichia coli RecA proteins and ssDNA by changing the extravesicular nucleotides. Repetitive binding and dissociation of the same RecA filament on the DNA was observed with a rebinding rate two orders of magnitude greater than in the absence of confinement, suggesting a previously unreported nucleation pathway for RecA filament. This method provides a biofriendly and simple alternative to surface tethering that is ideal for the study of transient and weakly interacting biological complexes.

Original languageEnglish
Pages (from-to)12646-12650
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number31
StatePublished - 31 Jul 2007


  • RecA
  • Single molecule
  • Vesicle encapsulation


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