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Photo of Tobias Ambjörnsson

Tobias Ambjörnsson

Senior lecturer

Photo of Tobias Ambjörnsson

Visualizing the entire DNA from a chromosome in a single frame

Author

  • C. Freitag
  • Charleston Noble
  • J. Fritzsche
  • F. Persson
  • Michaela Reiter-Schad
  • Adam Nilsson
  • A. Graneli
  • Tobias Ambjörnsson
  • K. U. Mir
  • Jonas Tegenfeldt

Summary, in English

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. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Department/s

  • Computational Biology and Biological Physics - Undergoing reorganization
  • Atomic Physics
  • BioCARE: Biomarkers in Cancer Medicine improving Health Care, Education and Innovation
  • Solid State Physics
  • NanoLund: Centre for Nanoscience

Publishing year

2015

Language

English

Publication/Series

Biomicrofluidics

Volume

9

Issue

4

Document type

Journal article

Publisher

American Institute of Physics (AIP)

Topic

  • Biochemistry and Molecular Biology
  • Biophysics
  • Other Physics Topics

Status

Published

ISBN/ISSN/Other

  • ISSN: 1932-1058