DNA NANO MAP · Affordable DNA Mapping using Solidstate-Nanopores
„Хоризонт 2020“ — Действия „Мария Склодовска-Кюри“
- Период
- 2017-04-01 → 2019-03-31
- Финансиране от ЕС
- 175 420 €
- Участници
- 1
- Схема
- MSCA-IF-EF-ST
Линиите свързват координатора с партньорите.
Накратко на български
Метод за евтино картографиране на ДНК чрез твърдотелни нанопори и специални маркери, които разпознават конкретни последователности. Това помага за по-достъпна диагностика на микробиома, чийто състав е свързан с развитието на много заболявания.
Кратко обяснение, генерирано от езиков модел по текста на CORDIS. Оригиналът е по-долу.
Резултати накратко
Affordable DNA Mapping using Solidstate-Nanopores
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
Текст от CORDIS, на английски · Данни: CORDIS, © Европейски съюз
Цел на проекта
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.
Оригинален текст от CORDIS (на английски).
Участници
- ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE · LausanneКоординаторШвейцария
Връзки
Данни: CORDIS, © Европейски съюз