A nanoplasmonic molecular ruler for measuring nuclease activity and DNA footprinting

The interactions between proteins and nucleic acids play a critical role in some of life’s most crucial biochemical processes, including gene expression and protein production, and some promising anticancer agents exert their effects by interfering with these interactions.

Now, researchers have a new tool for studying those interactions – a nanoscale optical ruler than can detect small changes in the size of a given piece of DNA. This work is reported in the inaugural issue of the journal Nature Nanotechnology.

Fanqing Frank Chen, Ph.D., at the Lawrence Berkeley National Laboratory, led a team of investigators that developed a nanoplasmonic ruler designed to measure changes in DNA length quantitatively and in real time. The ruler uses gold nanoparticles and relies on the fact that gold nanoparticles emit light at well-defined wavelengths of light in a way that is strongly influenced by the exact physical and chemical environment surrounding the particle.

One way to influence that surrounding environment is to attach double-stranded DNA molecules to the surface of a gold nanoparticle. Using surface plasmon resonance spectroscopy, the investigators were able to measure the subtle changes that occur in light emissions as the length of an attached piece of DNA changed in response to interactions with proteins, including DNA-degrading enzymes known as nucleases.

To demonstrate the versatility of this ruler, the researchers created a 54-base-pair piece of DNA containing cleavage sites for a series of nucleases distributed along the length of the DNA. By measuring the change in plasmon light emissions from the gold nanoparticles, the investigators were able to quantify the speed at which each nuclease was able to cut DNA at its particular cleavage site.

The researchers note that the relationship between DNA length and emission wavelength agreed with calculated values based on well-established theoretical models, with the ruler displaying an average wavelength shift of 1.24 nanometers per base pair cleaved. The investigators also comment that because this method can detect changes in plasmon light emission from single gold nanoparticles, it should be useful in microfluidics-based high-throughput screening assays aimed at identifying proteins or drugs that alter DNA structure.

This work, which was supported in part by the National Cancer Institute, is detailed in a paper titled, “A nanoplasmonic molecular ruler for measuring nuclease activity and DNA footprinting.” Investigators from the University of California at Berkeley, the University of New Mexico Health Sciences Center, and the University of California at Riverside also participated in this study. An abstract of this paper is available at the journal’s website. View abstract.