Researchers at the Lawrence Berkeley National Laboratory (Berkeley Lab) of the US Department of Energy (DOE) worked together with the researchers at the University of Stuttgart, Germany to develop 3D plasmon rulers to measure spatial variations in macromolecular systems at the nanometer level.
Scientists could use the 3D plasmon rulers to study the interaction of enzymes with DNA, the movement of peptides, the folding of proteins and cell membrane vibrations.
3-D plasmon ruler
Scientists require instruments to measure tiny structural changes and distances accurately as human machines and other equipments contract to the size of biomolecules. “Plasmons” are electronic surface waves, based on which researchers have developed linear rulers. When light transmits through the restricted spaces of noble metal nanoparticles or nanostructures such as silver or gold, plasmons are generated.
Plasmon rulers do not photobleach nor blink, and deliver outstanding brightness and photostability than other types of molecular rulers. Most plasmon rulers developed till date were not capable of measuring distances in 3D, due to which users were hindered from gaining a complete understanding of all soft-matter and biological processes occurring in 3D.
Laura Na Liu, corresponding author of a paper in the journal Science, which gives details of the research, stated that normal dipolar plasmon resonances cover a broad range due to radiative damping and the coupling between several particles results in unclear spectra that cannot be easily converted into distances. She along with her co-authors solved this challenge by constructing a 3D ruler from five gold nanorods of separately controlled lengths and orientation. One nanorod is positioned perpendicularly between two pairs of parallel nanorods to form an arrangement that resembles the letter H.
Liu and her co-workers could differentiate the magnitude and direction of structural changes with the degrees of spatial freedom offered by the 3D plasmon ruler’s five nanorod structure. Light scattering wavelengths were also altered by conformational changes in the 3D plasmon rulers.
In order to validate their invention, a series of samples were fabricated using high-accuracy electron beam lithography and stacking of layers, after which they were embedded with 3D plasmon rulers on a glass substrate in a dielectric medium. The results of the experiment were very close to the calculated spectra.
Scientists predict that 3D plasmon rulers would be connected to a sample macromolecule, through biochemical linkers at several points along a DNA or RNA strand, or at various positions on a peptide or protein. Light would be them focused on the sample macromolecule and the 3D plasmon ruler’s optical response could be measured using dark field microspectroscopy.