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PROSEQO SIGNED

PROtein SEQuencing using Optical single molecule real-time detection

Total Cost €

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EC-Contrib. €

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Partnership

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Project "PROSEQO" data sheet

The following table provides information about the project.

Coordinator
FONDAZIONE ISTITUTO ITALIANO DI TECNOLOGIA 

Organization address
address: VIA MOREGO 30
city: GENOVA
postcode: 16163
website: www.iit.it

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 Italy [IT]
 Project website http://www.singleproteinsequencing.eu
 Total cost 2˙906˙801 €
 EC max contribution 2˙906˙801 € (100%)
 Programme 1. H2020-EU.1.2.1. (FET Open)
 Code Call H2020-FETOPEN-2014-2015-RIA
 Funding Scheme RIA
 Starting year 2016
 Duration (year-month-day) from 2016-03-01   to  2019-02-28

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    FONDAZIONE ISTITUTO ITALIANO DI TECNOLOGIA IT (GENOVA) coordinator 811˙663.00
2    UNIVERSITE PARIS-SUD FR (ORSAY CEDEX) participant 709˙708.00
3    UNIVERSITAT DE BARCELONA ES (BARCELONA) participant 649˙643.00
4    ALACRIS THERANOSTICS GMBH DE (BERLIN) participant 374˙625.00
5    AB ANALITICA SRL IT (PADOVA) participant 361˙160.00

Map

 Project objective

The advent of analytical techniques with extremely low limits of detection has led to dramatic progresses mostly in the field of nucleic acids sequencing. Despite the advent of the next generation sequencing platforms, the current genome sequencing task remains formidable, and revolutionary advances in DNA sequencing technology are still demanded. Nevertheless, the primary actors in virtually all life processes are the proteins coded by DNA sequences known as genes. Proteins can yield far more compelling revelations than may be gleaned from DNA alone. Protein sequencing may radically transform patient treatment, enabling precise monitoring of disease response to therapeutics at the molecular level. Single-molecule sequencing of proteins is of enormous value, offering the potential to detect diminishingly small quantities of proteins that may have been altered by alternative splicing or post-translational modification. In this project, we build upon current state-of-the-art sequencing technologies to develop novel proof-of-principle technologies for high-throughput protein sequencing and single molecule DNA/RNA sequencing. The work proposed herein will provide: (i) a new sequencing technology development that utilizes plasmonic nanostructures in order to enhance the optical detection and to control the molecules movement by means of optical trapping; (ii) a novel approach of plasmonic based optical spectroscopy for sequencing of protein; (iii), a rigorous analytical model to reconstruct the exact sequence from the signals recorded; and (iv) a plasmonic device that can perform both nucleic acids and amino-acids sequencing in one functional unit. These research efforts provide a foundation for the novel use of systems for a wide range of applications, such as the framework to investigate next generation protein sequencing, as well as high-throughput DNA sequencing and genetic diagnostics.

 Deliverables

List of deliverables.
Demonstrator of SERS detection of single amino-acid Demonstrators, pilots, prototypes 2019-06-27 20:27:30
Demonstrator of integrated platform with micro/nanofluidics and nanotrapping elements Demonstrators, pilots, prototypes 2019-06-27 20:27:21
Demonstrator of FRET intensity and lifetime spectroscopic detection Demonstrators, pilots, prototypes 2019-06-27 20:27:23
Public report on sequencing tests n.3 Documents, reports 2019-06-27 20:27:21
Demonstrator of multiple plasmonic nanotrap platform Demonstrators, pilots, prototypes 2019-06-27 20:27:20
Public version of the Final Report Documents, reports 2019-06-27 20:27:28
Demonstrator of integrated optical system Demonstrators, pilots, prototypes 2019-06-27 20:27:19
Computational demonstration of final protocol of detection Demonstrators, pilots, prototypes 2019-05-20 14:08:21
Demonstrator of steerable optical trap Demonstrators, pilots, prototypes 2019-05-20 14:08:21
Report on nanofabrication process for multi-nanochannel integrated system Documents, reports 2019-05-20 14:08:21
Public report on sequencing tests n.1 Documents, reports 2019-05-20 14:08:20
Report on design of multi-nanochannel nanostructure integrated with plasmonic nanotrapping Documents, reports 2019-05-20 14:08:20
Public report on sequencing tests n.2 Documents, reports 2019-05-20 14:08:20
Data management plan Other 2019-05-30 13:14:12
Online publication of the PROSEQO website Documents, reports 2019-05-30 13:14:11
Report on project communication n.1 Documents, reports 2019-05-20 14:08:20

Take a look to the deliverables list in detail:  detailed list of PROSEQO deliverables.

 Publications

year authors and title journal last update
List of publications.
2018 Chi Chen, Lijiao Ao, Yu-Tang Wu, Vjona Cifliku, Marcelina Cardoso Dos Santos, Emmanuel Bourrier, Martina Delbianco, David Parker, Jurriaan M. Zwier, Liang Huang, Niko Hildebrandt
Single-Nanoparticle Cell Barcoding by Tunable FRET from Lanthanides to Quantum Dots
published pages: 13686-13690, ISSN: 1433-7851, DOI: 10.1002/anie.201807585
Angewandte Chemie International Edition 57/41 2019-05-20
2018 Xue Qiu, Jingyue Xu, Jiajia Guo, Akram Yahia-Ammar, Nikiforos-Ioannis Kapetanakis, Isabelle Duroux-Richard, Julia J. Unterluggauer, Nicole Golob-Schwarzl, Christophe Regeard, Catherine Uzan, Sébastien Gouy, Michael DuBow, Johannes Haybaeck, Florence Apparailly, Pierre Busson, Niko Hildebrandt
Advanced microRNA-based cancer diagnostics using amplified time-gated FRET
published pages: 8046-8055, ISSN: 2041-6520, DOI: 10.1039/c8sc03121e
Chemical Science 9/42 2019-05-20
2019 Jiajia Guo, Carlos Mingoes, Xue Qiu, Niko Hildebrandt
Simple, Amplified, and Multiplexed Detection of MicroRNAs Using Time-Gated FRET and Hybridization Chain Reaction
published pages: 3101-3109, ISSN: 0003-2700, DOI: 10.1021/acs.analchem.8b05600
Analytical Chemistry 91/4 2019-05-20
2018 Jiajia Guo, Xue Qiu, Carlos Mingoes, Jeffrey R. Deschamps, Kimihiro Susumu, Igor L. Medintz, Niko Hildebrandt
Conformational Details of Quantum Dot-DNA Resolved by Förster Resonance Energy Transfer Lifetime Nanoruler
published pages: 505-514, ISSN: 1936-0851, DOI: 10.1021/acsnano.8b07137
ACS Nano 13/1 2019-05-20
2018 Alexandra Petreto, Marcelina Cardoso Dos Santos, Olivier Lefebvre, Gabriel Ribeiro Dos Santos, Paolo Ponzellini, Denis Garoli, Francesco De Angelis, Mehdi Ammar, Niko Hildebrandt
Optimizing FRET on Aluminum Surfaces via Controlled Attachment of Fluorescent Dyes
published pages: 18867-18876, ISSN: 2470-1343, DOI: 10.1021/acsomega.8b02774
ACS Omega 3/12 2019-05-20
2018 Xue Qiu, Jiajia Guo, Jingyue Xu, Niko Hildebrandt
Three-Dimensional FRET Multiplexing for DNA Quantification with Attomolar Detection Limits
published pages: 4379-4384, ISSN: 1948-7185, DOI: 10.1021/acs.jpclett.8b01944
The Journal of Physical Chemistry Letters 9/15 2019-05-28
2018 Chi Chen, Clyde Midelet, Shashi Bhuckory, Niko Hildebrandt, Martinus H. V. Werts
Nanosurface Energy Transfer from Long-Lifetime Terbium Donors to Gold Nanoparticles
published pages: 17566-17574, ISSN: 1932-7447, DOI: 10.1021/acs.jpcc.8b06539
The Journal of Physical Chemistry C 122/30 2019-05-28
2018 Paolo Ponzellini, Xavier Zambrana-Puyalto, Nicolò Maccaferri, Luca Lanzanò, Francesco De Angelis, Denis Garoli
Plasmonic zero mode waveguide for highly confined and enhanced fluorescence emission
published pages: 17362-17369, ISSN: 2040-3364, DOI: 10.1039/c8nr04103b
Nanoscale 10/36 2019-05-28
2018 M. Cardoso Dos Santos, J. Goetz, H. Bartenlian, K.-L. Wong, L. J. Charbonnière, N. Hildebrandt
Autofluorescence-Free Live-Cell Imaging Using Terbium Nanoparticles
published pages: 1327-1334, ISSN: 1043-1802, DOI: 10.1021/acs.bioconjchem.8b00069
Bioconjugate Chemistry 29/4 2019-05-28
2018 Denis Garoli, Dario Mosconi, Ermanno Miele, Nicolò Maccaferri, Matteo Ardini, Giorgia Giovannini, Michele Dipalo, Stefano Agnoli, Francesco De Angelis
Hybrid plasmonic nanostructures based on controlled integration of MoS 2 flakes on metallic nanoholes
published pages: 17105-17111, ISSN: 2040-3364, DOI: 10.1039/c8nr05026k
Nanoscale 10/36 2019-05-28
2017 P. Zilio, M. Dipalo, F. Tantussi, G. C. Messina, and F. De Angelis
Hot electrons in water : injection and ponderomotive acceleration by means of plasmonic nanoelectrodes
published pages: , ISSN: 2047-7538, DOI:
Light Science and applications 6 2019-05-20
2016 Denis Garoli, Pierfrancesco Zilio, Yuri Gorodetski, Francesco Tantussi, Francesco De Angelis
Beaming of Helical Light from Plasmonic Vortices via Adiabatically Tapered Nanotip
published pages: 6636-6643, ISSN: 1530-6984, DOI: 10.1021/acs.nanolett.6b03359
Nano Letters 16/10 2019-05-20

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