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Scientists Develop Tool to Sequence Circular DNA; New Method Will Provide Insight into Genomes of Bacteria and Viruses, As Well As Extrachromosomal Circular DNA (eccDNA) in Humans; SMRT Long-Range Sequencing from Pacific Biosciences Employed

University of Alberta (Canada) biologists have invented a new way for sequencing circular DNA, according to a new study. The tool, called CIDER-Seq, will give other scientists rich, accurate data on circular DNA in any type of cell. The article describing the new method was published online on April 3, 2020 in Nature Protocols. The article is titled “Full-Length Sequencing of Circular DNA Viruses and Extrachromosomal Circular DNA Using CIDER-Seq.” While our own DNA is linear, circular DNA is common in the genomes of bacteria and viruses. Scientists have also discovered circular DNA within the nuclei of human and plant cells, called extrachromosomal circular DNA (eccDNA). Recently, research has begun to investigate the role of eccDNA in human cancer--but progress has been hampered due to the lack of effective methods for studying and sequencing eccDNA. "Our key advance is that, through our method, scientists can finally gain an unbiased, high-resolution understanding of circular DNA in any type of cell," explained Devang Mehta, PhD, postdoctoral fellow in the Department of Biological Sciences at the University of Alberta and lead author. "With our invention of CIDER-Seq, we can start to begin to understand the function of these mysterious circular DNAs in human and plant cells." CIDER-Seq uses DNA sequencing technology called single-molecule real-time (SMRT) long-read sequencing from Pacific Biociences to obtain full-length sequences without the need for PCR or restriction digestion. The method includes a web-lab protocol, as well as a new computational pipeline. It is optimized to examine both viral genomes and eccDNA and is made accessible to other scientists online. "We devised a new molecular biology method and a new bioinformatics algorithm to finally obtain full length sequences of eccDNA," explained Dr. Mehta. "Our method finally allows us to sequence these molecules completely and gives us and other researchers a tool to better understand what they actually do in the cell." The work was done in collaboration with Herve Vanderschuren, PhD, at the University of Liege in Belgium.

[Press release] [Nature Protocols abstract]