Single molecule sequencing and biophysical properties of oxidized genomic dna using magnetic tweezers.
Next-generation DNA sequencing technologies are at the core of modern molecular biology and are rapidly entering the technological arsenal for personalized medicine. The recent explosion of sequencing technologies has provided researchers with various solutions to fit their sequencing needs, with a large spectrum of costs and limitations. However, most sequencing methods use enzymatic duplication of DNA to generate a strong enough sequencing signal. Therefore, chemical modifications potentially present on native bases are lost, and with them, an entire level of epigenetic information about. Although some workarounds are emerging, they are indirect, costly, and not yet amenable for the targeted sequencing of a given native genomic locus or biophysical analysis of the modified DNA. Given the need to understand the epigenetic layer of genetic information, I propose to develop a reliable and cheap method to map, at the single-molecule resolution, the epigenetic status of a genomic DNA locus of interest. This will be achieved through biochemical capture of this locus using CRISPR/Cas9 technology, and its epigenetic sequencing via single-molecule manipulation by magnetic tweezers. In addition to identifying the nature and the position of the modified bases at a given genomic DNA locus, I will use this magnetic tweezer technology to address fundamental questions about the effect of epigenetic modifications on the biophysical properties of DNA (formation of DNA structures and protein interactions). Specifically, I will focus on 8-oxoguanine, for which there is increasing interest since it is a hallmark of degenerative pathologies like cancer or Alzheimer’s Disease, and since it has recently entered the known epigenetic arsenal. This project has great potential applications in medical diagnosis. It will give me a first-hand experience in developing a cutting-edge technology, which will be of great benefit to my future independent research career.