Study of the dynamics of DNA-RNA structures at the single molecule scale by optical tweezers

Envoyé par fabien.montel 
Laboratory name: Laboratoire de Physique, ENS de Lyon
CNRS identification code: UMR 5672
Supervisors: Fabien Montel, Vincent Vanoosthuyse
e-mail:, Phone number: +33 (0)4 26 23 38 23
Web page: []

Study of the dynamics of DNA-RNA structures at the single molecule scale by optical tweezers
Several activities that are essential for cell function also threaten the integrity of the somatic cell genome. Gene transcription, which produces messenger RNA from DNA, is one of these. By moving across the DNA to transcribe RNA, RNA polymerases can introduce distortions in the DNA double helix that can generate deleterious secondary structures. By interfering with primordial cellular functions such as transcription, DNA duplication or repair, these RNA-DNA secondary structures can compromise cell survival.

The 'R-loop' is one of the structures that locally distorts the double helix and has the ability to compromise the integrity of chromosomes. It is a three-stranded structure resulting from the abnormal hybridisation of nascent RNA to its DNA template. Recent data have shown that only a small proportion of R-loops are cytotoxic. The intrinsic properties of these cytotoxic R-loops remain poorly understood.

The objective of this project is to determine the stability and structure of R-loops at the single molecule level. First, we will construct a hybrid DNA-RNA structure coupled at its ends to microbeads that can be manipulated with optical tweezers. We will then perform destabilization/reformation cycles to obtain the distribution of forces necessary to force the opening of the R-loops. This information will allow us to establish a correspondence between the size and position of the R-loops and their ability to form 3D structures. Ultimately, this work will make it possible to determine precisely the link between the physical properties of R-loops and their toxicity and to better predict the genomic regions likely to form toxic R-loops.

References :
The extruded non-template strand determines the architecture of R-loops. Y. Carrasco-Salas, A. Malapert, S. Sulthana, B. Molcrette, L. Chazot-Franguiadakis, P. Bernard, F. Chédin, C. Faivre-Moskalenko, V. Vanoosthuyse. Nucleic Acids Research, Volume 47, Issue 13, 26 July 2019, Pages 6783–6795,

Zero-mode waveguide detection of flow-driven DNA translocation through nanopores. Auger T, Mathé J, Viasnoff V, Charron G, Di Meglio JM, Auvray L, Montel F. Phys Rev Lett. 2014 Jul 11;113(2):028302.

Zero-Mode Waveguide Detection of DNA Translocation Through FIB-organised Arrays of Engineered Nanopores. Auger T, Bourhis E, Donnez J, Durnez A, Di Meglio J-M, Auvray L, Montel F, Yates J, Gierak J. Microelectronic Engineering 187, 90-94 (2018)