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3D plasmon ruler enables the 3D measure of macromolecules

By Damir Beciri
16 June 2011

3d-plasmon-ruler-graphic-1The world’s first three-dimensional plasmon rulers, capable of measuring nanometer-scale spatial changes in macromolecular systems, have been developed by researchers from the Lawrence Berkeley National Laboratory (Berkeley Lab), in collaboration with researchers at the University of Stuttgart. The 3D plasmon rulers could br uses to provide scientists with new details on dynamic events in biology

“We’ve demonstrated a 3D plasmon ruler, based on coupled plasmonic oligomers in combination with high-resolution plasmon spectroscopy, that enables us to retrieve the complete spatial configuration of complex macromolecular and biological processes, and to track the dynamic evolution of these processes”, said Paul Alivisatos, director of Berkeley Lab and leader of this research.

Compared to other types of molecular rulers, which are based on chemical dyes and fluorescence resonance energy transfer (FRET), plasmon rulers neither blink nor photobleach, while offering photostability and brightness. The downside of plasmon rulers until now was because they could only be used to measure distances along one dimension.

3d-plasmon-ruler-in-a-row

“Plasmonic coupling in multiple nanoparticles placed in proximity to each other leads to light scattering spectra that are sensitive to a complete set of 3D motions”, said Laura Na Liu. “The key to our success is that we were able to create sharp spectral features in the otherwise broad resonance profile of plasmon-coupled nanostructures by using interactions between quadrupolar and dipolar modes.”

Typical dipolar plasmon resonances are broad because of radiative damping, leading to indistinct spectra that are not readily converted into distances during the simple coupling between multiple particles. The researchers solved this problem with a 3D ruler constructed from five gold nanorods of individually controlled length and orientation, in which one nanorod is placed at a 90 degree angle between two pairs of parallel rod  nanorods to form a structure that resembles the letter H. This formation mages to suppresses radiative damping and allows for the excitation of two sharp quadrupolar resonances.

Not only did conformational changes in their 3D plasmon rulers alter light scattering wavelengths, but the spatial freedom afforded its five nanorods also enabled the researchers to distinguish the direction as well as the magnitude of structural changes.


“As a proof of concept, we fabricated a series of samples using high-precision electron beam lithography and layer-by-layer stacking nanotechniques, then embedded them with our 3D plasmon rulers in a dielectric medium on a glass substrate”, saod Liu. “Experimental results were in excellent agreement with the calculated spectra.”

The 3D plasmon rulers could be attached to a sample macromolecule, and be used for research at various points along a strand of DNA or RNA, or at different positions on a protein or peptide. The sample macromolecule would then be exposed to light and the optical responses of the 3D plasmon rulers would be measured via dark field microspectroscopy. The research could lead to new information about the interaction of DNA with enzymes, the folding of proteins, the motion of peptides or the vibrations of cell membranes.

“The realization of 3D plasmon rulers using nanoparticles and biochemical linkers is challenging, but 3D nanoparticle assemblies with desired symmetries and configurations have been already been demonstrated”, said Liu. “We believe these exciting experimental achievements along with the introduction of our new concept will pave the road toward the realization of 3D plasmon rulers in biological and other soft-matter systems.”

For more information, you can read the article published in the journal Science named: “Three-Dimensional Plasmon Rulers”.

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