Article

Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes

Department of Physics, University of California, Berkeley, Berkeley, California, United States
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 03/2007; 104(8):2667-72. DOI: 10.1073/pnas.0607826104
Source: PubMed
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.

Full-text preview

Available from: pnas.org
  • Source
    • "These plasmonic properties enable metal NPs to be used in biodiagnostics, biophysical studies, and medical therapies when they are integrated into biological systems. The strong LSPR scattering displayed by Au NPs when conjugated with specific targeting molecules enables molecule-specific imaging and diagnosis of diseases such as cancer234. For instance, the cosputtering property of gold-silica nanocomposites opens up the possibility to use these nanocomposites as biosensors in the detection of human ovarian cancer cells [5]. "
    [Show abstract] [Hide abstract] ABSTRACT: Stable colloidal gold nanoparticles (Au NPs) are synthesized successfully using a seeding growth technique. The size of the nanoparticles is determined using transmission electron microscopy (TEM), and it is observed that the size of the nanoparticles ranges from 7 to 30 nm. The TEM images and optical absorption spectra of the Au NPs reveal that the suspension is well dispersed and consistent with the particle size. The feasibility of the seeding growth technique is investigated using Turbiscan Classic MA 2000 screening stability tester. Based on the peak thickness kinetics and mean value kinetics, the backscattered light profiles indicate that the suspension is highly stable without particle sedimentation as well as negligible agglomeration. In addition, the Au NPs are proven to remain stable over a period of 2 months. Particle sedimentation eventually occurs due to the weight of nanoparticles. It is concluded that the seeding growth technique is feasible in synthesizing stable Au NPs. Controlling the stability, size and shape of Au NPs are technologically important because of the strong correlation between these parameters and the optical, electrical, and catalytic properties of the nanoparticles.
    Full-text · Article · May 2015 · Journal of Nanomaterials
  • Source
    • "Alivisatos and coworkers demonstrated this concept with silver and gold PDs tethered with DNA and used it to follow the kinetics of hybridization [140]. Their so-called 'plasmon rulers' were later used to follow also the kinetics of individual restriction enzyme molecules [141], and to detect specific DNA sequences and proteins in complex media such as serum [142,143]. Finally, protein dimerization events on cellular membranes were followed through consequential formation of PDs out of gold particles attached to the investigated protein molecules [144]. "
    [Show abstract] [Hide abstract] ABSTRACT: This review discusses research on the plasmonic properties of small clusters of metal nanoparticles, with two and three particles. These are the simplest examples of ‘plasmonic molecules’. Coupling between two particles leads to new surface plasmon resonances and to the creation of a hot spot of a strong electric field in the gap between the particles. Such a hot spot can be used to enhance Raman scattering or fluorescence, making plasmonic dimers useful for applications in spectroscopy and sensing. Trimers offer a richer spectrum of options for coupling between particles, which can be analyzed using group theory to obtain the plasmonic modes, in analogy to vibrational modes. Symmetry plays an important role in our understanding of the physics of plasmonic dimers and trimers, and new physical phenomena may appear when the symmetry of a dimer or a trimer is broken, including directional emission, Fano resonances, plane chirality and more. The review introduces some of these concepts, the basic physics behind them and their possible applications. Focus Point sections describing selected outstanding recent developments accompany the review.
    Full-text · Article · Oct 2014 · Journal of Photochemistry and Photobiology C Photochemistry Reviews
  • Source
    • "Even then it is relatively hard to find concrete examples where it is obvious that single molecules must be resolved. One special case is the study of conformational changes during a molecular interaction, which may be interesting for biomacromolecules [38,39]. Another exception is the case when two molecules bind to each other in different ways, leading to different k on and k off values [Equation (1)]. "
    [Show abstract] [Hide abstract] ABSTRACT: There is no doubt that the recent advances in nanotechnology have made it possible to realize a great variety of new sensors with signal transduction mechanisms utilizing physical phenomena at the nanoscale. Some examples are conductivity measurements in nanowires, deflection of cantilevers and spectroscopy of plasmonic nanoparticles. The fact that these techniques are based on the special properties of nanostructural entities provides for extreme sensor miniaturization since a single structural unit often can be used as transducer. This review discusses the advantages and problems with such small sensors, with focus on biosensing applications and label-free real-time analysis of liquid samples. Many aspects of sensor design are considered, such as thermodynamic and diffusion aspects on binding kinetics as well as multiplexing and noise issues. Still, all issues discussed are generic in the sense that the conclusions apply to practically all types of surface sensitive techniques. As a counterweight to the current research trend, it is argued that in many real world applications, better performance is achieved if the active sensor is larger than that in typical nanosensors. Although there are certain specific sensing applications where nanoscale transducers are necessary, it is argued herein that this represents a relatively rare situation. Instead, it is suggested that sensing on the microscale often offers a good compromise between utilizing some possible advantages of miniaturization while avoiding the complications. This means that ensemble measurements on multiple nanoscale sensors are preferable instead of utilizing a single transducer entity.
    Full-text · Article · Dec 2012 · Sensors
Show more