Single molecule detection machine for nucleic acid analytics

Supersensitive detection systems are becoming an important element of today's Life Sciences. Their development aims to achieve utmost sensitivity and smallest possible sample consumption in detecting and determining the amount of bio molecules, in order to be able to diagnose diseases earlier, to find new active ingredients faster and more reliably, to prove the presence of environmental pollutants, or to control the quality of biological processes.

Fraunhofer FIT researchers now present a Single Molecule Detection Machine (SMDM) developed especially for these application fields. It uses a highly sensitive confocal microscope, also developed by Fraunhofer FIT, and fluorescence detection. Fluorescent markers are attached to bio molecules, e.g., DNA, RNA and proteins; 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 bio molecules.

"It took us several years of R&D to find our method of analysis, which is based on single molecule brightness levels, and to turn it into an algorithm. The resulting process now lets us generate the information we need about the molecule faster and with higher precision," says Prof. Harald Mathis, head of the BioMOS group at the Fraunhofer Institute for Applied Information Technology FIT, and also of the Fraunhofer SYMILA Application Center at Hamm-Lippstadt.

The smallest molecule concentration detectable by the SMDM is an unimaginably low 1 pg/µl (one trillionth of a gram per one millionth of a liter). By way of comparison: The system can detect that one cube of sugar was dissolved in three million liters 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, we are currently using the SMDM for quality control in nucleic acid analytics, specifically to determine the mass concentration of nucleic acids with high sensitivity. Actually, the sensitivity we achieve is several orders of magnitude higher than competing systems using UV absorption. In addition, our system performs its measurements on sample volumes of <1µl (less than one millionth of a liter), thus reducing costs by minimizing sample consumption. Currently, we can quantify DNA as well as RNA mixtures in concentrations ranging from 1 to 1,000 pg µl^-1.

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 precisely we developed an Open Micro-Electrophoresis Chip (OMEC) and integrated it with the SMDM. This chip allows us separate molecules for the analysis at the single molecule level.

Our second exhibit at BIOTECHNICA 2015 is our ZETA imaging software. We developed it specifically for the High Content Analysis of live cell imaging data, where cells are monitored and recorded over their full life cycle. Due to its open interfaces, ZETA can easily be integrated with complete High Content Analysis workflows and thus can support researchers in a wide range of applications in drug research.