title: Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes.
abstract: Pairs of Au nanoparticles have recently been proposed as "plasmon rulers" based on the dependence of their light scattering on the interparticle distance. Preliminary work has suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over the 1- to 100-nm length scale in biology. Here, we substantiate that plasmon rulers can be used to measure dynamical biophysical processes by applying the ruler to a system that has been investigated extensively by using ensemble kinetic measurements: the cleavage of DNA by the restriction enzyme EcoRV. Temporal resolutions of up to 240 Hz were obtained, and the end-to-end extension of up to 1,000 individual dsDNA enzyme substrates could be simultaneously monitored for hours. The kinetic parameters extracted from our single-molecule cleavage trajectories agree well with values obtained in bulk through other methods and confirm well known features of the cleavage process, such as DNA bending before cleavage. Previously unreported dynamical information is revealed as well, for instance, the degree of softening of the DNA just before cleavage. The unlimited lifetime, high temporal resolution, and high signal/noise ratio make the plasmon ruler a unique tool for studying macromolecular assemblies and conformational changes at the single-molecule level.
authors.affiliation: Departments of Physics and Chemistry, University of California, Berkeley, CA 94720, USA.
authors.forename: Björn M
authors.initials: BM
authors.lastname: Reinhard
authors.forename: Sassan
authors.initials: S
authors.lastname: Sheikholeslami
authors.forename: Alexander
authors.initials: A
authors.lastname: Mastroianni
authors.forename: A Paul
authors.initials: AP
authors.lastname: Alivisatos
authors.forename: Jan
authors.initials: J
authors.lastname: Liphardt
mesh_terms: D002384:Catalysis; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism*; D007700:Kinetics; D053758:Nanoparticles; D009690:Nucleic Acid Conformation; D012542:Scattering, Radiation; D013816:Thermodynamics
chemical_list: D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific; C027440:GATATC-specific type II deoxyribonucleases