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DNA NANO MAP SIGNED

Affordable DNA Mapping using Solidstate-Nanopores

Total Cost €

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EC-Contrib. €

0

Partnership

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 DNA NANO MAP project word cloud

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

basepairs    genomic    16s    biomolecular    amplification    molecule    sequencer    match    membrane    natural    heralded    clinical    small    pores    fluorescence    maps    dna    gut    suggest    sequence    expensive    nanopores    alternative    fraction    consist    subsequent    map    detect    tool    microscopy    pcr    methionine    provides    requirement    sequencing    cheap    extracted    trace    facilities    induce    pore    susceptible    identification    few    region    dyes    methyltransferases    machine    transfer    ph    too    mass    cleanroom    solid    idea    channel    amount    label    labels    fluorescent    gene    underlying    double    consuming    subsequently    stranded    basic    dominant    converted    rdna    limited    primer    easily    setting    technique    super    resolution    species    pattern    synthetic    mapping    molecules    analogues    bias    recognize    living    drop    microbial    time    adenosyl    composition    cofactor    translocates    attached    notoriously   

Project "DNA NANO MAP" data sheet

The following table provides information about the project.

Coordinator
ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE 

Organization address
address: BATIMENT CE 3316 STATION 1
city: LAUSANNE
postcode: 1015
website: www.epfl.ch

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 Switzerland [CH]
 Project website https://lben.epfl.ch/page-79460-en-html/
 Total cost 175˙419 €
 EC max contribution 175˙419 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2016
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2017
 Duration (year-month-day) from 2017-04-01   to  2019-03-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE CH (LAUSANNE) coordinator 175˙419.00

Map

 Project objective

DNA analysis will become an important clinical tool in identification the composition of microbial species living in the gut. The most dominant technique at the time is based on PCR amplification of the 16s rDNA gene and subsequent sequencing of the variable region in the gene. This method however is limited in the amount of detail it provides and is notoriously susceptible to primer bias. Furthermore, due to the requirement of a PCR machine and sequencer the technique is too expensive and time consuming for a clinical setting.

Over the past few years nanopores have been heralded as a cheap alternative for biomolecular analysis. Specifically solid-state nanopores, which consist of a small pore in a solid membrane, have the potential for cost-effective mass-production in cleanroom facilities. Furthermore, since these pores can detect double stranded DNA they can easily be used for analysis of DNA maps.

In this proposal I suggest to use DNA mapping with solid state nanopores. The basic idea is to sequence-specifically label DNA molecules using DNA Methyltransferases and synthetic analogues of the natural cofactor S-adenosyl-methionine. The pattern of labels attached to the DNA is unique for the underlying sequence.

In my Ph.D. I used this method to transfer fluorescent dyes to the DNA and subsequently extracted the DNA map using super resolution fluorescence microscopy. In this case, the attached label will induce a current-drop when the DNA molecule translocates through the channel. The extracted current-trace will then be converted to a DNA map in basepairs and can be used to match to a real sequence. This proposed method can be used to identify genomic elements and eventually be used to recognize species, for a fraction of the cost of 16s rDNA sequencing.

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The information about "DNA NANO MAP" are provided by the European Opendata Portal: CORDIS opendata.

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