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High-resolution tweezers for DNA replication and sequence identification

Final Report Summary - MAGREPS (High-resolution tweezers for DNA replication and sequence identification)

We have developed new schemes to track the position of small beads used in our magnetic tweezers. Using an interferometric dark-field approach, we have enhanced the resolution by a factor 3 and the throughput by a factor 10. We have protected this scheme by a European patent that has been accepted and we shall now publish this result. We have also proposed a higher throughput method in a second patent.
We have measured the action of helicases and polymerases in single molecule assays revealing unexpected properties. We have found that the T4 gp43 polymerase working in strand displacement can extend a primer at high force and in exonuclease mode at low force (NAR 2012). This provided the ability to perform Sanger sequencing at the single molecule level, we have protected this feature by a patent. We have also characterized the interaction between enzymes like helicases and polymerases revealing their intrinsic coupling (NAR 2012). We have been able to reproduce mechanism of fork reversion involve in the restart of a blocked replication fork which was published (Science 2012). We have shown a similar mechanism for the RecG helicase (Nature Communication 2013). Extension of the work was done on different helicases; Dda (JMB 2012) and Upf1 (Nature Communication 2015).
We have studied the hybridization of an oligonucleotide on a DNA hairpin and found that this provided a second method for DNA sequencing leading to another patent and a publication (Nature Methods 2012). Revisiting sequencing by hybridization at the single molecule level, we have re-sequenced a mini-satellite DNA containing repeated sequences and highly GC rich (to be publish). We have discovered a very interesting feature of the method that we had not foreseen: the ability to determine epigenetic markers. This interesting finding has led to a new patent. All our patents have been licensed by the Depixus startup (former named PicoSeq). Thus this research work has led to a direct technology transfer which has benefited from the ERC proof of concept SIMDEQ. The Depixus startup has won several innovation prizes and has raised 3.7M€ in 2015 to further develop the technology that we had proposed. Depixus is hiring 15 personns on this task mostly ingeneer and biologists.
Owing to the embargo of patents, we have not published as expected but we will do it now that these embargos are being released. We have one paper submitted to NAR on the RecQ helicase, we have a second paper submitted to Nature Communication with our colleague in Barcelona on sequencing using intercalators. We have papers to write on Ded1 helicases, on Prp43, on Yeast-Upf1, Pif1, G4-Quadruplex and on oligonucleotide hybridization, on the sequencing by hybridization. We must also publish our result on the epigenetic marker detection.