Unusual nucleic acid structures

 

Dr. Jean-Louis Mergny

Directeur de recherche (DR1),
INSERM

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Tel: +33(0)540003022

 

Bio

Jean-Louis Mergny graduated from Ecole Normale SupĂ©rieure de la rue d’Ulm (Paris) and got his PhD in Pharmacology (University Paris VI) in 1991 under the supervision of T. Garestier & M. RougĂ©e (Triple-helices: spectroscopic studies). He went for a postdoctoral position in Basel, Switzerland with W. Gehring (Biozentrum). Afterwards he was hired by INSERM in 1993 in the MusĂ©um National d’Histoire Naturelle, where he worked mainly on nucleic acids structures from a biophysical point of view. He was promoted Research Director in 2002, and he joined the IECB at the end of 2009.

 

Keywords / Expertise / Techniques

unusual nucleic acid structures, G-quadruplexes, drug-DNA interactions, telomeres and telomerase, thermodynamics, UV-absorbance, fluorescence and circular dichroism spectroscopies.

 

Summary

Nucleic acids are prone to structural polymorphism: in addition to the well-known double helix, a number of alternative structures may be formed. However, most non-canonical conformations are stable only under non-physiological conditions and have been considered simple curiosities. Among these oddities, a family of nucleic acid secondary structures known as G-quadruplexes (G4) has emerged as more than a novelty. These structures can be formed by certain guanine-rich sequences and are stabilized by G-quartets. G-quadruplexes can be stable under physiological conditions and the evidence for quadruplex formation in vivo is compelling. Our goals are to conceive new biochemical, bioformatic, and physico-chemical tools to be used to demonstrate that G4 DNA or RNA is involved in particular biological functions.


Activity report

Our objectives are to answer the following questions:


Where and when ?

High-throughput sequencing methods and whole genome approaches are now being used to generate massive amounts of sequence data. Sometimes, statistical analyses point out the potential role of G-rich DNA or RNA motifs. However, the answer to the seemingly simple question “Is my sequence G4-prone?”, based on somewhat flawed or oversimplified search algorithms, is often inaccurate. For example, we previously demonstrated that stable quadruplexes may be formed by sequences that escape the consensus used for bioinformatics. Our first objective will be to experimentally obtain a better understanding of DNA and RNA G4 stability. The ultimate goal will be to build thermodynamic stability tables for quadruplexes as has been done by Santa Lucia and collaborators for duplex/hairpin DNA and to incorporate these data into MFOLD.

Figure 1. A G-rich single strand (top) may adopt different intramolecular G4 structures (bottom) depending on sequence and experimental conditions.


G-quadruplexes: Friends or foes?

Comparison of sequencing data with theoretical sequence distributions suggests that there is a selection against G-quadruplex prone sequences in the genome, probably as they pose real problems during replication or transcription and generate genomic instability (see below). Nevertheless, “G4-hot spots” have been found in certain regions of the genome: in telomeres, in repetitive sequences such as mini and microsatellite DNAs, in promoter regions, and in first exons of mRNAs. There might be a specific positive role for these sequences that compensates for the general selection against G4 forming sequences. Our goals are to understand the factors that modulate these effects. A number of proteins that interact with these unusual structures have been identified, including DNA binding proteins, helicases, and nucleases.

G4 regulation at the RNA level. The UTRs of a number of mRNA molecules harbor G-rich sequences that may form quadruplexes. This is true both in eukaryotes and prokaryotes. G4-prone sequences are not only present in mRNA but may also be found in short and long non-coding RNAs such as TERRA and hTR. These results prompted us to study in more detail the biological functions of these G4-prone RNAs. In collaboration with P. Hainaut (IARC, Lyon, France) and J. Hall (Curie, Orsay, France), we investigated the role of a potential G4 in P53 alternative splicing.


G-quadruplex ligands: Treats or tricks?

One may achieve structure-specific rather than sequence-specific recognition of DNA. Because of their particular geometric configuration and electrostatic potential, G-quadruplexes may indeed specifically accommodate small artificial ligands, such as planar molecules, and an impressive number of candidates have been evaluated. Together with chemists from the Institut Curie (M.P. Teulade-Fichou) we successfully identified a variety of G4 ligands and we wish to improve and functionalize these compounds, analyse their biological effects, and ultimately find new classes of anti-proliferative agents with anticancer properties.


Beyond Biology

Quadruplexes may well be biologically relevant, but they could also be used for various applications that are disconnected from cells. DNA is an attractive material for nanotechnologies because of its self-assembly properties. The ability of nucleic acids to self-assemble into a variety of nanostructures and nanomachines is being exploited by a growing number of researchers. Extremely sophisticated structures and nanodevices may be constructed with DNA. We believe that quadruplex structures offer interesting new possibilities and we have demonstrated that quadruplexes can be incorporated into nanodevices. An independent topic relates to the use of quadruplex DNAs as molecular beacons (MB). We previously demonstrated that a G4-based MB outperforms a regular MB thanks to its differential ionic sensitivity.

 

Selected publications

  • Lacroix, L., SĂ©osse, A. & Mergny, J.L. (2011). Fluorescence based duplex-quadruplex competition screen for telomerase RNA quadruplex ligands. Nucleic Acids Res. in press.
  • Marcel, V., Tran, P.L.T., Sagne, C., Martel-Planche, G., Vaslin, L., Teulade-Fichou, M.P., Hall, J., Mergny, J.L., Hainaut, P. & Van Dyck, E. (2011). G-quadruplex structures in TP53 intron 3: role in alternative splicing and in production of p53 mRNA isoforms. Carcinogenesis in press.
  • A.V. Struts*, G.F. Salgado*, Karina Martinez-Mayorga, Constantin Job, Katsunori Tanaka, Sonja Krane, Koji Nakanishi, and Michael F. Brown. Deuterium Spin-Lattice Relaxation Reveals Functional Dynamics of Retinal Chromophore of Rhodopsin. Nature Struct. & Mol. Biol., in press. *Equal contribution
  • GuĂ©din, A., Gros, J. & Mergny, J.L. (2010). How long is too long ? Effect of loop size on G-quadruplex stability. Nucleic Acids Res. Vol. 38, 7858-7868.
  • GuĂ©din, A., Lacroix, L. & Mergny, J.L. (2010), Thermal melting studies of ligand DNA interactions, Methods Mol. Biol. 613: 25-35.
  • Reinhold, W.C., Mergny, J.L., Liu, H., Ryan, M., Pfister, T.D., Kinders, R., Parchment, R., Doroshow, J., Weinstein, J.N., & Pommier, Y. (2010). Exon Array Analyses across the NCI-60 Reveal Potential Regulation of TOP1 by Transcription Pausing at Guanosine Quartets in the First Intron. Cancer Res. 70: 2191-2203.
  • Mergny, J.L. & Lacroix, L. (2009). UV melting of G-quadruplexes, Current Protocols in Nucleic Acids Chemistry. 17.1.1-17.1.15.
  • Stegle, O., Payet, L., Mergny, J.L, macKayy, D.J.C. & Huppert, J.L. (2009). Predicting and understanding the stability of G-quadruplexes. Bioinformatics, 25: pp374-382.
  • GuĂ©din, A., Alberti, P. & Mergny, J.L. (2009).Stability of intramolecular quadruplexes: sequence effects in the central loop. Nucleic Acids Res. 37: 5559-5567.
  • Mendez-Bermudez, A., Hills, M., Pickett, H., Mergny, J.L., Riou, J.F. & Royle, N. (2009).Human telomeres that contain (CTAGGG)n repeats show replication dependent instability in somatic cells and the male germline. Nucleic Acids Res. 37: 6225-6238.
  • Lim, K.W. Alberti, P., GuĂ©din, A., Lacroix, L., Riou, J.F., Royle, N., Mergny, J.L. & Phan, A.T. (2009). Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G•C•G•C tetrad. Nucleic Acids Res. 37: 6239-6248.

 

Research team

  • Dr. Jean-Louis MERGNY Team leader
  • Dr. Anne BOURDONCLE Teaching Assistant (MdC, UniversitĂ© de Poitiers)
  • Dr. Gilmar SALGADO Teaching Assistant (MdC, UniversitĂ© Bordeaux Segalen)
  • Dr. Liliya YATSUNYK Visiting Professor (sabbatical leave, Swathmore College)
  • Aurore GUÉDIN Technician Assistant (A.I., INSERM)
  • Lionel BEAUREPAIRE Technician Assistant (CDD-I.E., Aquitaine Regional Council)
  • GaĂ«lle LABRUNIE Technician Assistant (CDD-I.E., Aquitaine Regional Council)
  • Dr. NICOLE SMITH Post-doc (ANR-PNANO QuantADN)
  • Dr. DANIEL RENCIUK Post-doc (ANR-P3N G4ToolBox)
  • Dr. Rui MORIYAMA Post-doc (JSPS/ANR-F-DNA)
  • Dr. Jun ZHOU Post-doc (Aquitaine Regional Council)
  • Phong Lan THAO TRAN PhD student (Ministry of research)
  • Amandine RENAUD DE LA FAVERIE PhD student (Ministry of research)
  • Emilien DUBUC M2 student (UniversitĂ© Bordeaux Segalen)
  • Dursun Nizam KORKUT M1 student (UniversitĂ© Bordeaux Segalen)
  • Neha KOONJOO M1 student (UniversitĂ© Bordeaux Segalen)
  • Delphine ALBRECHT L3 student (UniversitĂ© Bordeaux 1)
  • Malcy TARIN BTS student (IUT La Rochelle)

This team is part of the Unit “RNA: Natural and Artificial Regulation”, INSERM/Université Bordeaux Segalen (Unit 869)

 
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