Physicists have developed a new method for counting molecules using DNA origami

Spatial resolution of light sources is the driving force behind ultrafast nanoscopy, a goal pursued by the RUN Regensburg Center for Ultrafast Nanoscopy. Researchers are reporting how to count the number of molecules in such a nanostar.

Thanks to the latest telescopes, we know that our galaxy is made up of over a trillion stars. In the nanocosm, clusters of individual light sources, such as molecules, also appear as dots.

The team placed individual dye molecules at well-defined distances from each other. This is accomplished using a new technique known as DNA origami. DNA as a storage medium in biology is used and programmed in such a way that molecules are arranged by folding DNA at will with dimensions of several nanometers.

At first, it is impossible to discern the fluorescent light of individual molecules on origami under a light microscope. Another trick is used to actually separate the molecules. Light from the origami structure passes through a semitransparent mirror and is recorded by photodetectors on both sides of the mirror.

It should be noted that an individual molecule can emit only one light particle at a time, which is recorded by only one or the other detector, but not both. Looking at the chronological order in which the light hits the individual detectors, one can infer the exact number of dye molecules in the origami structure.

In this way, the individual dye molecules can be counted. The number of dye molecules is determined by DNA programming. An origami structure with one dye emits exactly one quantum of light – one with five emits exactly five.

The individual dye molecules also interact with each other accordingly. When exposed to light, the dye absorbs energy. It can either emit it again as light, or pass it on to a nearby dye. However, if the neighboring dye is already in an excited state, two excitations will meet.

As with two cars trying to enter the same parking lot at the same time, the excitement disappears. Such annihilation is of great importance in molecular optoelectronics such as organic light-emitting diodes or solar cells, but also plays a role in ultra-high-resolution microscopy.

The research team was now able to show that the nanoscopic interactions of dye molecules with each other can be directly traced by determining the arrival times of light particles on two light detectors. This approach offers a new method for ultrafast nanoscopy of molecular complexes that will also find applications in the life sciences.

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Alexandr Ivanov earned his Licentiate Engineer in Systems and Computer Engineering from the Free International University of Moldova. Since 2013, Alexandr has been working as a freelance web programmer.
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Alexandr Ivanov

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