Three-dimensional (3D) plasmon rulers, capable of measuring nanometer-scale spatial changes in macromolecular systems, have been developed by researchers at Lawrence Berkeley National Laboratory (Berkeley Lab) in collaboration with researchers at the University of Stuttgart, Germany. These 3D plasmon rulers could provide scientists with the opportunity to obtain unprecedented information on critical dynamic events in biology such as the interaction of DNA with enzymes, the folding of proteins, the motion of peptides, or the vibrations of cell membranes.

“We’ve demonstrated a 3D plasmon ruler, based on coupled plasmonic olig-omers 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.

Alivisatos, Laura Na Liu now at Rice University, and Mario Hentschel, Thomas Weiss, and Harald Giessen of the University of Stuttgart reported their findings in the June 17 issue of Science (DOI: 0.1126/science.1199958; p. 1407).

The nanometer scale is where the biological and materials sciences converge. As human machines and devices shrink to the size of biomolecules, scientists need tools by which to precisely measure minute structural changes and distances. To this end, researchers have been developing linear rulers based on the electronic surface waves known as “plasmons,” which are generated when light travels through the confined dimensions of noble metal nanoparticles or structures, such as gold or silver.

“Two noble metallic nanoparticles in close proximity will couple with each other through their plasmon resonances to generate a light-scattering spectrum that depends strongly on the distance between the two nanoparticles,” Alivisatos said. “This light-scattering effect has been used to create linear plasmon rulers that have been used to measure nanoscale distances in biological cells.”

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, and also offer exceptional photostability and brightness. However, until now, plasmon rulers could only be used to measure distances along one dimension, which is a limitation that hampers the development of any comprehensive understanding of biological or general soft-matter processes that take place in three dimensions.

“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 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.”

Liu said that typical dipolar plasmon resonances are broad because of radiative damping. As a result, the simple coupling between multiple particles produces indistinct spectra that are not readily converted into distances. The research team overcame this problem with a 3D ruler constructed from five gold nanorods of individually controlled length and orientation, where one nanorod is placed perpendicular between two pairs of parallel nanorods to form a structure that resembles the letter H.

“The strong coupling between the single nanorod and the two parallel nanorod pairs suppresses radiative damping and allows for the excitation of two sharp quadrupolar resonances that enable high-resolution plasmon spectroscopy,” Liu said. “Any conformational change in this 3D plasmonic structure will produce readily observable changes in the optical spectra.”

Not only did conformational changes in the 3D plasmon rulers alter light-scattering wavelengths, but the degrees of spatial freedom afforded by its five-nano-rod structure also enabled the research team to distinguish the direction as well as the magnitude of structural changes.

Scanning electron micrograph of a three-dimensional plasmon ruler fabricated from gold nanorods by electron beam lithography.

“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,” Liu said. “Experimental results were in excellent agreement with the calculated spectra.”

The researchers envision a future in which 3D plasmon rulers would, through biochemical linkers, be attached at different positions to a sample macromolecule, such as a strand of DNA or RNA, or 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 through dark-field microspectroscopy.

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