Affordable DNA Mapping using Solidstate-Nanopores

Project Information

DNA NANO MAP

Grant agreement ID: 751121

DOI

10.3030/751121

Project closed

EC signature date 8 March 2017

Start date 1 April 2017

End date 31 March 2019

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 175 419,60

EU contribution

€ 175 419,60

Coordinated by

ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Switzerland

Periodic Reporting for period 1 - DNA NANO MAP (Affordable DNA Mapping using Solidstate-Nanopores)

Reporting period: 2017-04-01 to 2019-03-31

Summary of the context and overall objectives of the project

The overall objective of this project is to enable affordable DNA analysis using solid state nanopores. Affordable DNA analysis will be one of the key features for microbiome analysis. Recent research has shown that there is a strong link between the content of the microbiome and the progression of a large number of diseases. Nanopore analysis could significantly reduce the cost of DNA analysis, making microbiome diagnostics affordable for all people.

Typical translocations of DNA through a nanopore decreases the ionic current through the pore temporarily due to partial blockage of the pore by the DNA molecule. However such a current signal provides no information on the sequence of the DNA as it translocates through the nanopore. To analyse DNA as it translocates through the pore it needs an additional modulation of the ionic current. We added sequence-specific labels on the DNA using a DNA methyltransferase that targets a specific sequence. The label that is attached to the DNA would induce an additional modification of the ionic current, only on the target sequences. Thus, the attenuation of the current signal over time results in a sequence specific signal. This sequence specific signal can then be used as a unique signature of the DNA sequence and can be used for microbiome analysis

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The first part of this work largely covered the analysis of different nanopore devices and their suitability for analysis of free DNA translocations. The second part of this work resulted in a large python package which can be used for the recording, saving, analysis and visualization of DNA translocations through the nanopore. The last part of this project resulted in an algorithm that could be used for the alignment of a DNA map to another map or a theoretical trace. All code is publicly available and can be found via the group website.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This work resulted largely in reproducible creation of nanopores in MoS2 material. A reproducible pipeline for the creation of nanopores is an essential element for the exploitation of this research.

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