Article

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

Departments of Physics and Chemistry, University of California, Berkeley, CA 94720, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 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.

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    • "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 cancer [2] [3] [4]. 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]. "
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    • "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 kon and koff values [Equation (1)]. "
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    • "The particles have a characteristic plasmon absorbance when the core diameter is larger than 2 nm and the plasmon absorbance is sensitive to the surrounding medium and expected to change when the particles are aggregated (Ingram et al. 1997; Templeton et al. 1998, 2000; Hostetler et al. 1999; Esumi et al. 1995; Link et al. 1999); The size of nanoparticles being similar to that of most biological molecules and structures, it can be of immense importance for both in vivo and in vitro biomedical research and applications. In this account, biophysical studies of the noble metals (Sönnichsen et al. 2005; Reinhard et al. 2007; Jain et al. 2006, 2008) as well as their applications in imaging (Sokolov et al. 2003; El-Sayed et al. 2005; Alivisatos 2004), biological sensing (Elghanian et al. 1997; Haes and Van Duyne 2002), medical diagnostics (Rosi and Mirkin 2005), and cancer medical treatment (Huang et al. 2006, 2007; El-Sayed et al. 2006; O'Neal et al. 2004; Jain et al. 2007a, b; Wang et al. 2010), have been reported. "
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