Tommaso P. Fraccia – SAM lab

UMR 8231 Chimie, Biologie, Innovation (CBI) ESPCI-CNRS

I’m Junior Research Chair (JRC) at the Institut Pierre-Gilles de Gennes pour la Microfluidique and at ESPCI Paris. As fresh PI I’m building a new research team, the Molecular Self-Assembly Lab (SAM Lab) which is hosted at the IPGG building in the heart of Paris.

My research themes are positioned at the interface between soft-matter physics and synthetic biology. My research activity is focused on the study of molecular self-assembly as fundamental driver of complexity in biological systems: from the formation and evolution of biopolymers in prebiotic conditions, to the modern cellular organization and functioning.

To achieve these objectives I exploit typical soft-matter concepts of self-assembly, phase transitions and phase separations in complex molecular mixtures. In particular, I have a strong background in the investigation of the spontaneous liquid crystal (LC) ordering of concentrated solutions of DNA/RNA nucleotides/oligomers.

I’m actually expanding such investigation to more complex mixtures including many different molecular species. To tackle this goal, I’m adopting microfluidics to achieve high-throughput multidimensional experimental investigations on soft matter systems under different physical-chemical conditions.

I have a strong background in several physical approaches for the characterization of soft phases of matter, such as microscopy (optical, polarized, fluorescence, confocal, electron), scattering of light (visible and X-rays), micro-rheology and differential dynamic microscopy.
At the same time I became experienced also in molecular biology and biochemistry techniques for nucleic acids manipulation, chemical modification and analysis.

I’m always looking for motivated students to join the lab for internships and PhD thesis. In case you’re interested don’t esitate to contact me at tommaso.fraccia@espci.fr.

Research

Liquid Crystal ordering of DNA and RNA oligomers and monomers

Liquid Crystal phases of nucleic acids. The inclination to form LC phases is a conserved feature of nucleic acids at each length of DNA and RNA molecules: from monomers to oligomers to polymers. These partially ordered phases are the result of different stages of hierarchical self-assembly driven by the stacking and pairing interactions of nucleobases.

Liquid Crystal templated polymerization of nucleic acids

Liquid crystals positive feedback polymerization loop. The LC matrix acts as an ordered but still fluid environment that can enhance the chemical polymerization of the constituent DNA or RNA molecules.

Microfluidics

Publications

Viscoelasticity of DNA Liquid Crystal
Lucchetti, L.; Fraccia, T.P.; Nava, G; Turiv, T.; Ciciulla, F.; Bethge, L.; Klussmann, S.; Lavrentovich, O. & Bellini, T. 
Phys. Rev. Lett. (submitted)

Liquid Crystal ordering of DNA Dickerson Dodecamer duplexes with different 5’- Phosphate terminations
Todisco, M.; Smith, G.P. & Fraccia, T. P.
Molecular Crystals and Liquid Crystals 683,1, 69-80 (2019)

Phase separations, liquid crystal ordering and molecular partitioning in mixtures of PEG and DNA oligomers
Di Leo, S.; Todisco, M.; Bellini, T. & Fraccia, T. P. 
Liquid Crystals 1-13 (2018)

Nonenzymatic Polymerization into Long Linear RNA Templated by Liquid Crystal Self-Assembly
Todisco, M; Fraccia, T. P.; Smith, G. P.; Corno, A.; Bethge, L.; Klussmann, S.; Paraboschi, E. M.; Asselta, R.; Colombo, D.; Zanchetta, G.; Clark, N. A & Bellini, T. 
ACS Nano 12, 10, 9750-9762 (2018)

Backbone-free Watson Crick duplex-stacked nucleic acids
Smith, G. P.*; Fraccia, T. P.*; Todisco, M.; Zanchetta, G.; Zhu, C.; Hayden, E.; Bellini, T. & Clark, N. A. 
Proc. Natl. Acad. Sci. USA 115, 33, E7658 (2018)
*equally contributing authors
Article awarded with Cozzarelli Prize 2018

Liquid Crystal Ordering of 4-Base-Long DNA Oligomers with Both G-C and A-T Pairing
Fraccia, T. P.; Smith, G. P.; Clark, N. A & Bellini, T.
Crystals 8, 5 (2018)

Giant optical nonlinearity in DNA lyotropic liquid crystals
Lucchetti L.; Fraccia, T. P.; Ciciulla F.; Simoni F. & Bellini, T.
Optics Express 25, 25951 (2017)

Non-linear Optical Measurement of the Twist Elastic Constant in Thermotropic and DNA Lyotropic Chiral Nematics
Lucchetti L.; Fraccia, T. P.; Ciciulla F. & Bellini, T.
Scientific Reports 7, 4959 (2017)

Liquid Crystal Ordering and Isotropic Gelation in Solutions of 4-base-long DNA Oligomers
Fraccia, T. P.; Smith, G. P.; Bethge, L.; Zanchetta, G.; Nava, G.; Klussman, S.; Clark, N. A. & Bellini, T.
ACS Nano 10, 8508-8516 (2016)

Evidence of Liquid Crystal–Assisted Abiotic Ligation of Nucleic Acids
Fraccia, T. P.; Zanchetta, G.; Rimoldi, V.; Clark, N. A. & Bellini, T. 
Orig. Life Evol. Biosph. 45, 51–68 (2015)

Abiotic Ligation of DNA Oligomers Templated by Their Liquid Crystal Ordering
Fraccia, T. P.; Smith, G. P.; Zanchetta, G.; Paraboschi, E.; Yi, Y.; Walba, D. M.; Dieci, G.; Clark, N. A & Bellini, T. 
Nature Communications 6, 6424 (2015)

Liquid crystal self-assembly of random-sequence DNA oligomers
Bellini, T.; Zanchetta, G.; Fraccia, T. P.; Cerbino, R.; Tsai, E.; Smith, G. P.; Moran, M. J.; Walba, D. M. & Clark, N. A.
Proc. Natl. Acad. Sci. USA 109, 1110–1115 (2012)

Curriculum Vitae

Education

02/2014 PhD in Physics, Astrophysics and Applied Physics from University of Milano (IT)

PhD thesis title:
Exploring the role of Liquid Crystal ordering of DNA oligomers in the prebiotic synthesis of nucleic acids
Supervisor: Prof. Tommaso Bellini

10/2010 M.S. in Physics from University of Milano (IT)

04/2008 B.S. in Physics from University of Milano (IT)

Positions

From 03/09/2018: Junior Research Chair at Institut Pierre-Gilles de Gennes (IPGG) – ESPCI Paris (F)

Since 01/11/2015 to 31/10/2018: Assistant Professor of Applied Physics (RTD/A – FIS/07), San Raffaele University, Rome, Italy and Research Collaborator at University of Milan (I).

From 01/01/2017 to 30/09/2017: Principal Investigator of an ELSI Origin Network (EON) Seed Grant funded project, coordinating three international research teams in Italy and USA

06/2017 (2 months): Visiting Scientist at the Soft Materials Research Center – University of Colorado at Boulder (CO, USA)

03/2017 (1 month): Visiting Research Associate at the Earth-Life Science Institute – Tokyo Institute of Technology (JP)

2014-2015: Postdoc fellow, part of Grant PRIN Program of the Italian MIUR Ministry, at University of Milano, Department of Medical Biotechnologies and Translational Medicine (IT).

Awards and Grants

Cozzarelli prize 2018 from the National Accademy of Science of the United States of America, awarding the paper “Backbone-free Watson Crick duplex-stacked nucleic acids”, published in 2018 on PNAS, for outstanding scientific quality and originality.

01/2018 Junior Research Chair from Institut Pierre-Gilles de Gennes pour la Microfluidique (IPGG), Paris (F): PI position and 3 years research funding for the project “Origin of Life on a Chip”.

08/2016 ELSI Origin Network Seed Grant from Earth Life Science Institute (ELSI) Tokyo, Japan, for the research project: Lipid Assisted Polymerization and Liquid-Crystal Autocatalysis of random RNA oligomers mixtures in simulated hydrothermal fields.

06/2016 “Daniela Pucci” prize from Italian Liquid Crystal Society (SICL) for the best PhD thesis on LC for the thesis:  Exploring the role of Liquid Crystal ordering of DNA oligomers in the prebiotic synthesis of nucleic acids.

07/2014 International Society for the Study of the Origin of Life (ISSOL) travel grant for 17th International Conference on the Origin of Life, ORIGINS 2014, Nara, Japan

Collaborations

  • Prof. Tommaso Bellini
    Biotechnology and Translational Medicine Dept. Università degli Studi di Milano (IT)
  • Prof. Noel A. Clark
    Soft Materials Research Center of University of Colorado at Boulder (USA)
  • Prof. Rosanna Asselta
    Humanitas University Milan (IT)
  • Prof. Liana Lucchetti
    SIMAU Dept. Università Politecnica delle Marche (IT)
  • Dr. Philippe Nghe
    ESPCI Paris (FR)
  • Dr. Tony Jia
    Earth Life Science Institute at Tokyo Institute of Technology (JP)
  • Dr. Nicolas Martin
    Centre de Recherche Paul Pascal, University of Bordeaux (FR)