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ProFF SIGNED

Programming in vitro evolution using molecular fitness functions

Total Cost €

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EC-Contrib. €

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Partnership

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 ProFF project word cloud

Explore the words cloud of the ProFF project. It provides you a very rough idea of what is the project "ProFF" about.

biopolymer    revolution    tunable    compartments    computational    combinatorial    modified    function    scouts    expression    silico    computer    chemistry    circle    tool    revamped    programs    programmable    functions    billions    fitness    green    efficiency    industrial    propagate    programming    perspectives    versatile    tools    unlimited    assisted    integrate    bottleneck    enzymes    molecular    libraries    close    compartmentalized    dynamics    hoc    breakthroughs    vitro    autonomously    pcr    tuning    candidate    emulsions    faster    droplet    generation    environments    allowed    genotype    itself    mechanisms    scoring    awesome    experiments    extensively    few    predefined    genetic    selectivity    biochemical    ad    possibly    limited    fast    precision    quantitative    signature    phenotypic    directed    intensive    perform    remove    introducing    virtuous    lacks    micrometric    evolution    model    computers    catalytic    individual    enzymatic    laboratory    sequencing    catalysts    labor    chemistries    experimental    dna    stages    co    natural    programmability    knobs    arduous    score    landscape   

Project "ProFF" data sheet

The following table provides information about the project.

Coordinator
CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS 

Organization address
address: RUE MICHEL ANGE 3
city: PARIS
postcode: 75794
website: www.cnrs.fr

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country France [FR]
 Total cost 2˙141˙379 €
 EC max contribution 2˙141˙379 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-CoG
 Funding Scheme ERC-COG
 Starting year 2015
 Duration (year-month-day) from 2015-09-01   to  2020-08-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS FR (PARIS) coordinator 2˙141˙379.00

Map

 Project objective

Natural enzymes are awesome catalysts, in terms of their catalytic efficiency, selectivity, control mechanisms, etc. Revamped as laboratory or industrial tools, they have allowed more than a few breakthroughs, such as PCR, next generation sequencing or green chemistry. The next revolution will be brought by a new generation of extensively modified “enzymatic” catalysts working in non-natural environments, possibly build from non-natural chemistries and targeting an unlimited range of non-natural functions. However, their design is still an arduous process; computational design lacks precision while the combinatorial approach, directed evolution, is limited by labor-intensive or ad hoc selection stages.

We will remove the selection bottleneck in directed evolution by introducing biochemical computers able to perform this step autonomously. Based on recent developments in DNA-based molecular programming, these molecular scouts will be co-compartmentalized with genetic libraries into billions of individual compartments in micrometric emulsions. At each generation and in each droplet, after expression of the genotype, these molecular programs will autonomously: i- evaluate the phenotypic signature of a candidate, ii- integrate this information into a predefined scoring function and iii- propagate the relevant genetic information according to this score.

The programmability of this approach will make directed evolution versatile, faster, and able to address more challenging problems. The evolution dynamics itself become tunable, offering new perspectives on the fitness landscape of biopolymer catalysts. A quantitative in silico model will be built and integrated in a computer-assisted tool for the fast set-up of in vitro experiments and tuning of the various experimental knobs. Overall, we will close a virtuous circle by evolving the molecular tools enabling the programmable selection of the next generation of catalytic tools.


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 Publications

year authors and title journal last update
List of publications.
2017 G. Gines, A. S. Zadorin, J.-C. Galas, T. Fujii, A. Estevez-Torres, Y. Rondelez
Microscopic agents programmed by DNA circuits
published pages: 351-359, ISSN: 1748-3387, DOI: 10.1038/nnano.2016.299
Nature Nanotechnology 12/4 2019-05-31
2017 Zadorin, Anton S.; Rondelez, Yannick
Natural selection in compartmentalized environment with reshuffling
published pages: , ISSN: , DOI:
1 2019-04-18
2018 Adèle Dramé-Maigné, Anton Zadorin, Iaroslava Golovkova, Yannick Rondelez
Quantifying the performance of high-throughput directed evolution protocols
published pages: , ISSN: , DOI:
2019-04-18
2017 Anton S. Zadorin, Yannick Rondelez
Selection strategies for randomly distributed replicators
published pages: , ISSN: , DOI:
2019-04-18
2016 Kevin Montagne, Guillaume Gines, Teruo Fujii, Yannick Rondelez
Boosting functionality of synthetic DNA circuits with tailored deactivation
published pages: 13474, ISSN: 2041-1723, DOI: 10.1038/ncomms13474
Nature Communications 7 2019-05-31

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