Newly developed three-dimensional plasmon rulers capable of measuring nanometer-scale spatial changes in macromolecular systems could provide scientists with unprecedented details on critical dynamic events in biology. The spatial freedom afforded the 3-D plasmon ruler’s five nanorods enable it to measure the direction as well as the magnitude of structural changes in a macromolecule sample. (Images: Lawrence Berkeley National Laboratory) Developed by researchers at Lawrence Berkeley National Laboratory with colleagues at the University of Stuttgart in Germany, the measurement technique could provide new insights into the interaction of DNA strands with enzymes, protein folding, peptide motion and cell membrane vibrations. “We’ve demonstrated a 3-D 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 the lead researcher on the project. The 3-D plasmon ruler is constructed from five gold nanorods, in which one nanorod (red) is placed perpendicular between two pairs of parallel nanorods (yellow and green). The nanometer scale is where the biological and materials sciences converge. As 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 plasmons, electronic surface waves generated when light travels through the confined dimensions of nanoparticles or structures made of noble metals, 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 with other types of molecular rulers, which are based on chemical dyes and fluorescence resonance energy transfer (FRET), plasmon rulers neither blink nor photobleach, and they offer exceptional brightness. However, until now, plasmon rulers could be used only to measure distances along one dimension, a limitation that hampers any comprehensive understanding of all the biological and other soft-matter processes that take place in 3-D. Scanning electron micrograph of 3-D plasmon rules fabricated from gold nanorods by electron beam lithography. “Plasmonic coupling in multiple nanoparticles placed in proximity to each other leads to light-scattering spectra that are sensitive to a complete set of 3-D motions,” said Laura Na Liu, corresponding author of the group’s paper, which appears in Science. “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, who now is at Rice University, 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. She and her co-authors overcame this problem with a 3-D ruler constructed from five gold nanorods of individually controlled length and orientation, in which one nanorod is placed perpendicular between two pairs of parallel rod 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 3-D plasmonic structure will produce readily observable changes in the optical spectra.” Not only did conformational changes in their 3-D plasmon rulers alter light-scattering wavelengths, but the degrees of spatial freedom afforded its five nanorod structure also enabled Liu and her colleagues 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 3-D plasmon rulers in a dielectric medium on a glass substrate,” Liu said. The investigators envision a future in which 3-D plasmon rulers would, through biochemical linkers, be attached to a sample macromolecule; for example, to various points along a strand of DNA or RNA, or at different positions on a protein or peptide. The sample macromolecule then would be exposed to light, and the optical responses of the 3-D plasmon rulers would be measured via dark-field microspectroscopy. For more information, visit: www.cchem.berkeley.edu/pagrp