Confocal microscopy, fluorescence allow single-molecule detection for nucleic acid analytics

Researchers at the Fraunhofer Institute for Applied Information Technology (FIT; Sankt Augustin, Germany) have developed a single-molecule detection device that analyzes ultra-small amounts of nucleic acid. The system, which employs confocal microscopy and fluorescence detection, can be used to identify biomarkers that are early indicators of a disease or allow forecasting the response to a therapy.

The new Single Molecule Detection Machine (SMDM) uses a Fraunhofer FIT-developed confocal microscope and fluorescence detection. Fluorescent markers are attached to biomolecules (for example, DNA, RNA, and proteins), and a laser is used to induce fluorescence. This detection mode is not only highly sensitive, but it can also produce a wide range of information about the type and behavior of the marked biomolecules.

The smallest molecule concentration detectable by the SMDM is 1 pg/µL (one trillionth of a gram per one millionth of a liter). The system can detect that one cube of sugar was dissolved in 3 million liters of water—roughly the amount of water contained in 1.2 Olympic swimming pools each 50 m long, 25 m wide, and 2 m deep. One cubic millimeter of this water would be enough to carry out the test.

In the Ribolution project, funded by Fraunhofer Zukunftsstiftung, the research team is currently using the SMDM for quality control in nucleic acid analytics, specifically to determine the mass concentration of nucleic acids with high sensitivity. Achieved sensitivity is several orders of magnitude higher than competing systems using UV absorption, the researchers claim. Better still, it helps reduce costs by minimizing sample consumption, they say.

The SMDM is also capable of measuring, with high sensitivity, the lengths of strands in nucleic acid mixtures. To determine distributions of lengths of strands, the research team developed an Open Micro-Electrophoresis Chip (OMEC) and integrated it with the SMDM. The chip allows them to separate molecules for the analysis at the single-molecule level.

The research team will showcase the SMDM at BIOTECHNICA 2015, to take place October 6-8 in Hannover, Germany. For more information, please visit

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