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Competence Machinery of Streptococcus pneumoniae as a Way for In Vivo De Novo DNA Sequencing

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Technical Report,01 Sep 2017,30 Nov 2018

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University of Lausanne Lausanne Switzerland

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The goal of this proposal is to design a system capable of DNA sequencing that utilizes in vivo cells. It is theorized that with TIRF microscopy it is possible to read a FRET signal as labeled DNA is imported into thebacterium Streptococcus pneumoniae using native transporter machinery that has been labeled with a corresponding fluorescent protein. The pneumococcal DNA uptake system always proceeds in a 3 to 5 fashionmaking downstream analysis and assembly easier. Along with this advantageous property, roughly 100 kb can be imported by a single pneumococcal DNA transporter in under 20 minutes. While the DNA is fragmented into a ssDNA molecule once entering the cell, the median intracellular fragment size still remains 6 kb. After an eclipseperiod of roughly 20 minutes, additional DNA can be imported by the same cell. Therefore, 1Mb can be imported by a single cell through one importer in under seven hours. Couple this with thousands of cells in unison, which areonly 1-2 microns in length, it would be possible to scale this system to any size desired to allow extremely high through-put sequencing. This method could revolutionize the method of genome sequencing, which is a technique that is used worldwide with increasing frequency. The ability to grow sequencing chips could reduce the overall cost of sequencing and combined with longer read lengths will make downstream analysis easier and increase sequencing availability. Sequencing of eukaryotic genomes would become much easier because of the potential scalability of the proposed system and the read lengths which help overcome assembly of repetitive regions ingenomes. This would make the field of personalized medicine much more feasible potentially aiding in general human health.

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  • Medicine and Medical Research

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