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Visualizing the entire DNA from a chromosome in a single frame
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
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2015 (English)In: Biomicrofluidics, ISSN 1932-1058, Vol. 9, no 4, 044114Article in journal (Refereed) Published
Abstract [en]

The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds.

Place, publisher, year, edition, pages
2015. Vol. 9, no 4, 044114
National Category
Medical Image Processing
URN: urn:nbn:se:uu:diva-263040DOI: 10.1063/1.4923262ISI: 000360311900016OAI: oai:DiVA.org:uu-263040DiVA: diva2:857959
Swedish Research Council, 2007-584Swedish Research Council, 2007-4454EU, FP7, Seventh Framework Programme, 201418VINNOVA, P35735-1The Crafoord Foundation, 2008-0841The Crafoord Foundation, 2005-1123Swedish Research Council, 2009-2924Carl Tryggers foundation , 12:13
Available from: 2015-09-30 Created: 2015-09-24 Last updated: 2015-09-30Bibliographically approved

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