This project will develop a strategy to detect levels of hydroxymethylation (hmC) in genomic DNA. We will first combine a method to selectively attach a biotin to hmC with our demonstrated technique of detecting single biotin modifications in DNA to demonstrate the efficacy of our approach and optimize experimental conditions. We will then apply the technique to clinical tissue samples. First, we will measure the global hmC content of normal breast tissue and of breast carcinoma and compare our findings with results from conventional approaches. Finally, we will utilize the capability of our approach to isolate modified DNA selectively and apply the system to identifying alterations in the hmC content of a fragment of the LZTS1 gene, an important tumor suppressor.
The research proposed here is focused on establishing solid-state nanopore technology as a diagnostic platform for cancer screening. We will develop the technology as a highly selective, highly sensitive approach to detect the epigenetic modification hydroxymethylation (hmC), variations of which are known bioindicators of cancer. Our technology will have direct impact on public health by enabling earlier diagnosis of cancer in patients and providing a new technique to study the fundmental role of epigenetics in tumor formation.
| Carlsen, Autumn T; Briggs, Kyle; Hall, Adam R et al. (2017) Solid-state nanopore localization by controlled breakdown of selectively thinned membranes. Nanotechnology 28:085304-85304 |
| Wang, Fanny; Zahid, Osama K; Swain, Brandi E et al. (2017) Solid-State Nanopore Analysis of Diverse DNA Base Modifications Using a Modular Enzymatic Labeling Process. Nano Lett 17:7110-7116 |
| Zahid, Osama K; Zhao, Boxuan Simen; He, Chuan et al. (2016) Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores. Sci Rep 6:29565 |
| Zahid, Osama K; Wang, Fanny; Ruzicka, Jan A et al. (2016) Sequence-Specific Recognition of MicroRNAs and Other Short Nucleic Acids with Solid-State Nanopores. Nano Lett 16:2033-9 |
