A nanoprobe developed by biophysicists at NC State could allow researchers to trace the movements of different proteins along DNA \u2013 without the drawbacks of current methods.<\/p>\n
A host of proteins patrol your DNA helix like cops on a beat. These proteins have individual functions, including identifying damaged areas on the DNA strand and initiating repairs. To study these proteins, researchers commonly attach nanoprobes to them. The probes fluoresce under certain types of light, allowing their movements to be traced.<\/p>\n
The problem? According to biophysicist Shuang Lim, \u201cWe know that DNA is helical in shape \u2013 it\u2019s a spiral. When we observe these proteins moving along the strand, we should be able to tell if they\u2019re moving around the DNA as well as along it. Unfortunately, the technology we have now doesn\u2019t really allow us to do that.<\/p>\n
\u201cThe most common probes right now are quantum dots and gold nanorods,\u201d Lim continues. \u201cQuantum dots blink, which makes it difficult to determine where they are or what they may be doing at any given time. Imagine trying to watch a movie, but with random dark frames popping up as you watch. You can\u2019t get the complete picture. Gold nanorods, on the other hand, tend to wobble. The wobble also affects our ability to get an accurate idea of where these proteins are and how they may be interacting with the DNA strand.\u201d<\/p>\n
Lim, along with graduate student Kory Green and former postdoctoral scholar Janina Wirth, developed a nanoprobe that addresses these issues. Their probe \u2013 a nanoplasmonic upconverting nanoparticle \u2013 changes fluorescent intensity based upon its orientation.<\/p>\n
\u201cThese particles are disc shaped. When they\u2019re lying flat, they are bright, and when they\u2019re on edge, they\u2019re dark,\u201d Green says. \u201cThey don\u2019t blink and they don\u2019t wobble, so it\u2019s much easier to get accurate measurements from them.\u201d<\/p>\n
\u201cAnother advantage is that they are excited by \u2013 or show up when \u2013 exposed to infrared light,\u201d says Lim. \u201cMany of the quantum dot probes use material that is excited by blue, or ultraviolet (UV) light. UV exposure damages the samples that we want to study. But infrared light doesn\u2019t.\u201d<\/p>\n
Lim, Green and Wirth conducted a proof-of-concept study with their probe by observing it on a flat substrate and in a sucrose solution, to see if they could accurately detect how the nanoprobe was moving. The preliminary results were promising, so Lim and the team are moving toward their next steps, which include testing the probe on a DNA-patrolling protein.<\/p>\n
\u201cAll of these proteins do different things for our DNA, but we don\u2019t know exactly what they\u2019re doing,\u201d Lim says. \u201cWe\u2019re hoping to use this probe to build a library that characterizes all of these proteins, so that we can determine their function.\u201d<\/p>\n