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Fueling protein–DNA interactions inside porous nanocontainers

Cisse, Ibrahim and Okumus, Burak and Joo, Chirlmin and Ha, Taekjip (2007) Fueling protein–DNA interactions inside porous nanocontainers. Proceedings of the National Academy of Sciences of the United States of America, 104 (31). pp. 12646-12650. ISSN 0027-8424. PMCID PMC1937520.

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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.

Item Type:Article
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URLURL TypeDescription CentralArticle Information
Cisse, Ibrahim0000-0002-8764-1809
Okumus, Burak0000-0001-9017-8467
Joo, Chirlmin0000-0003-2803-0335
Ha, Taekjip0000-0003-2195-6258
Additional Information:© 2007 by The National Academy of Sciences of the USA. Edited by Robert J. Silbey, Massachusetts Institute of Technology, Cambridge, MA, and approved April 25, 2007 (received for review December 5, 2006) We thank Tim Lohman (Washington University, St. Louis, MO) for the labeled ssDNA, Sua Myong for insightful discussion, and Salman Syed for timely provision of logistics that made this work possible. We also acknowledge the early participation of Stephanus Fengler in the aHL project. This work was funded by National Institutes of Health Grant GM074526 (to T.H.) and National Science Foundation Grant PHY0646550. T.H. is an Investigator with the Howard Hughes Medical Institute. Author contributions: I.C., B.O., C.J., and T.H. designed research; I.C., B.O., and C.J. performed research; I.C., B.O., and C.J. contributed new reagents/analytic tools; I.C., B.O., C.J., and T.H. analyzed data; and I.C., B.O., C.J., and T.H. wrote the paper. The authors declare no conflict of interest. This article is a PNAS Direct Submission. This article contains supporting information online at
Errata:Correction for Cisse et al., Single-Molecule Chemistry and Biology Special Feature: Fueling protein–DNA interactions inside porous nanocontainers Proceedings of the National Academy of Sciences Sep 2007, 104 (37) 14878; DOI: 10.1073/pnas.0707542104
Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:RecA; single molecule; vesicle encapsulation
Issue or Number:31
PubMed Central ID:PMC1937520
Record Number:CaltechAUTHORS:20201112-143946948
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Official Citation:Fueling protein–DNA interactions inside porous nanocontainers Ibrahim Cisse, Burak Okumus, Chirlmin Joo, Taekjip Ha Proceedings of the National Academy of Sciences Jul 2007, 104 (31) 12646-12650; DOI: 10.1073/pnas.0610673104
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106646
Deposited By: George Porter
Deposited On:16 Nov 2020 17:28
Last Modified:16 Nov 2020 17:28

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